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Is P. gingivalis bacteria found in brain? | Yes | BACKGROUND: The results from cross sectional and longitudinal studies show that
periodontitis is closely associated with cognitive impairment (CI) and
Alzhemer's Disease (AD). Further, studies using animal model of periodontitis
and human post-mortem brain tissues from subjects with AD strongly suggest that
a gram-negative periodontal pathogen, Porphyromonas gingivalis (Pg) and/or its
product gingipain is/are translocated to the brain. However, neuropathology
resulting from Pg oral application is not known. In this work, we tested the
hypothesis that repeated exposure of wild type C57BL/6 mice to orally
administered Pg results in neuroinflammation, neurodegeneration, microgliosis,
astrogliosis and formation of intra- and extracellular amyloid plaque and
neurofibrillary tangles (NFTs) which are pathognomonic signs of AD.
METHODS: Experimental chronic periodontitis was induced in ten wild type 8-week
old C57BL/6 WT mice by repeated oral application (MWF/week) of Pg/gingipain for
22 weeks (experimental group). Another 10 wild type 8-week old C57BL/6 mice
received vehicle alone (control group) MWF per week for 22 weeks. Brain tissues
were collected and the presence of Pg/gingipain was determined by
immunofluorescence (IF) microscopy, confocal microscopy, and quantitative PCR
(qPCR). The hippocampi were examined for the signs of neuropathology related to
AD: TNFα, IL1β, and IL6 expression (neuroinflammation), NeuN and Fluoro Jade C
staining (neurodegeneration) and amyloid beta1-42 (Aβ42) production and
phosphorylation of tau protein at Ser396 were assessed by IF and confocal
microscopy. Further, gene expression of amyloid precursor protein (APP),
beta-site APP cleaving enzyme 1 (BACE1), a disintegrin and metalloproteinase
domain-containing protein10 (ADAM10) for α-secretase and presenilin1 (PSEN1) for
ɣ-secretase, and NeuN (rbFox3) were determined by RT-qPCR. Microgliosis and
astrogliosis were also determined by IF microscopy.
RESULTS: Pg/gingipain was detected in the hippocampi of mice in the experimental
group by immunohistochemistry, confocal microscopy, and qPCR confirming the
translocation of orally applied Pg to the brain. Pg/gingipain was localized
intra-nuclearly and peri-nuclearly in microglia (Iba1+), astrocytes (GFAP+),
neurons (NeuN+) and was evident extracellularly. Significantly greater levels of
expression of IL6, TNFα and IL1β were evident in experimental as compared to
control group (p<0.01, p<0.00001, p<0.00001 respectively). In addition,
microgliosis and astrogliosis were evident in the experimental but not in
control group (p <0.01, p<0.0001 respectively). Neurodegeneration was evident in
the experimental group based on a fewer number of intact neuronal cells assessed
by NeuN positivity and rbFOX3 gene expression, and there was a greater number of
degenerating neurons in the hippocampi of experimental mice assessed by Fluoro
Jade C positivity. APP and BACE1 gene expression were increased in experimental
group compared with control group (p<0.05, p<0.001 respectively). PSEN1 gene
expression was higher in experimental than control group but the difference was
not statistically significant (p = 0.07). ADAM10 gene expression was
significantly decreased in experimental group compared with control group
(p<0.01). Extracellular Aβ42 was detected in the parenchyma in the experimental
but not in the control group (p< 0.00001). Finally, phospho-Tau (Ser396) protein
was detected and NFTs were evident in experimental but not in the control group
(p<0.00001).
CONCLUSIONS: This study is the first to show neurodegeneration and the formation
of extracellular Aβ42 in young adult WT mice after repeated oral application of
Pg. The neuropathological features observed in this study strongly suggest that
low grade chronic periodontal pathogen infection can result in the development
of neuropathology that is consistent with that of AD. |
Is ibudilast effective for multiple sclerosis? | Yes, Ibudilast was shown to be effective for progressive multiple sclerosis. In a phase 2 trial involving patients with progressive multiple sclerosis, ibudilast was associated with slower progression of brain atrophy than placebo but was associated with higher rates of gastrointestinal side effects, headache, and depression. | We investigated the immunoregulatory effects of ibudilast, a nonselective
phosphodiesterase inhibitor, at a clinically applicable dose (60 mg/day p.o. for
four weeks) in multiple sclerosis (MS) patients. Sensitive real-time PCR for
quantifying cytokine mRNA in the blood CD4+ cells revealed that the ibudilast
monotherapy significantly reduced tumour necrosis factor-alpha and interferon
(IFN)-gamma mRNA and the IFN-gamma/interleukin-4 mRNA ratio, suggesting a shift
in the cytokine profile from Th1 toward Th2 domicy. In a flow cytometric
analysis, natural killer T cells, which have been reported to relate to Th2
responses in MS and its animal model (experimental autoimmune
encephalomyelitis), increased significantly after the therapy. None of the
significant immunological changes were seen in healthy subjects or untreated MS
patients. Ibudilast may be a promising therapy for MS and its clinical effects
warrant further study. Ibudilast is a relatively nonselective phosphodiesterase inhibitor which has
been marketed for almost 20 years in Japan for treating asthma. More recently it
has been found to have anti-inflammatory activity in both the peripheral immune
system and in the CNS via glial cell attenuation. This CNS-directed
anti-inflammatory activity is of potential use in the treatment of multiple
sclerosis, neuropathic pain, and in the improved efficacy and safety of opioids
by decreasing opioid tolerance, withdrawal and reinforcement. Its suitable
pharmacokinetics and generally good tolerability make it a promising potential
treatment for these conditions. BACKGROUND: Ibudilast is a phosphodiesterase inhibitor influencing inflammation
and neurodegeneration in multiple sclerosis (MS). This study evaluated the
safety, tolerability, and effects on MRI parameters of 2 different doses of
ibudilast in relapsing forms of MS.
METHODS: In this multicenter, double-blind, phase 2 trial, patients with
relapsing MS and gadolinium-enhancing lesions were randomly assigned 1:1:1 to
receive 30 or 60 mg ibudilast or placebo every day for 12 months. The primary
endpoint was the cumulative number of newly active lesions on bimonthly brain
MRI over 12 months. Secondary endpoints included relapse rate, change in
Expanded Disability Status Scale (EDSS) score, T2-hyperintense and
T1-hypointense lesion volumes, and percent brain volume change (PBVC).
RESULTS: A total of 297 patients were randomized in 19 centers. During the first
12 months, the mean number of active lesions and relapse rate did not differ
between treatment arms. A reduction in PBVC (p = 0.04) was found in the 60-mg
group (0.8%) compared with placebo (1.2%). Post hoc analysis showed a reduction
in the proportion active lesions that evolved into persistent black holes for
the 60-mg (0.14; p = 0.004) and 30-mg (0.17; p = 0.036) groups compared with the
placebo group (0.24). Over 2 years, there were fewer patients (p = 0.026) with
confirmed progression on the EDSS. Treatment with ibudilast was generally safe
and well tolerated.
CONCLUSION: Ibudilast showed no beneficial effect on the rate of newly active
lesions and relapses. However, preliminary evidence suggests that ibudilast
seems to act in a neuroprotective fashion as measured by 2 independent MRI
outcomes, with a possible beneficial clinical effect on disability progression.
CLASSIFICATION OF EVIDENCE: This interventional study provides Class III
evidence on the effect of ibudilast on disease activity. Ibudilast (IBD) is a non‑selective (3, 4, 10, 11) phosphodiesterase (PDE)
inhibitor, used mainly as a bronchodilator for the treatment of bronchial
asthma. PDE play a central role in cellular function (e.g. differentiation,
synaptic plasticity and inflammatory response) by metabolizing cyclic
nucleotides. The results from preclinical and clinical studies indicate that IBD
has a broader range of action through suppression of pro‑inflammatory cytokines
(IL‑6, IL‑1β, TNF‑α), toll‑like receptor 4 blockade (TLR‑4), inhibition of a
macrophage migration inhibitory factor (MIF), up‑regulation the
anti‑inflammatory cytokine (IL‑10), and promotion of neurotrophic factors (GDNF,
NGF, NT‑4). Recent data indicate that the efficacy of IBD appears to be
independent from PDE inhibition activity and rather linked to glial activity
attenuation. Additional advantages of IBD, such as crossing the blood-brain
barrier, good tolerance and activity by oral administration, makes it a
promising therapeutic candidate for treating neuroinflammatory conditions, where
the currently available treatment remains unsatisfying due to poor tolerability
and/or sub‑optimal efficacy. IBD has no direct receptor affinity with exemption
of some undefined effect on adenosine receptors that makes the drug devoid of
its receptors‑mediated adverse effects. Current article provides an overview of
the pharmacology of IBD with a focus on preclinical and clinical data supporting
its potential neuroprotective benefits for neurological conditions, including
multiple sclerosis, neuropathic pain, medication overuse headache, stroke,
opioid, alcohol and methamphetamine abuse. PURPOSE OF REVIEW: Multiple sclerosis (MS) is an immune-mediated disorder that
affects the central nervous system (CNS), often first affecting people in early
adulthood. Although most MS patients have a relapsing-remitting course (RRMS) at
disease onset, a substantial proportion later develop chronic progression,
termed secondary progressive MS (SPMS). Approximately 10% of MS patients
experience chronic progression from disease onset, termed primary progressive
multiple sclerosis (PPMS). Although several disease-modifying treatment (DMT)
options exist for relapsing forms of this disease, DMT options are few for
progressive MS (PPMS and SPMS). Herein, we strive to define progressive MS,
review major clinical trials aimed at progressive MS, and delineate potential
strategies in the management of progressive MS.
RECENT FINDINGS: In 2017, the first DMT for PPMS, the B lymphocyte-depleting
monoclonal antibody, ocrelizumab, came to market. Ocrelizumab reduced 12-week
confirmed disability progression (CDP) by 24% versus placebo. Siponimod, a
selective sphingosine-1-phosphate receptor modulator, reduced 3-month CDP by 21%
versus placebo in SPMS. Ibudilast slowed brain atrophy in PPMS and SPMS patients
in a multicenter phase 2b study. Smaller early phase studies of alpha-lipoic
acid and simvastatin each found slowing of rate of whole brain atrophy in SPMS
patients. Reasons now exist for optimism in the search for DMTs for progressive
MS. It remains a challenge to identify outcome measures that accurately reflect
the underlying pathology in progressive MS, which is less inflammatory and more
degenerative than RRMS. Management of progressive multiple sclerosis (MS) is one of the main challenges
of the new century. Based on our knowledge of pathophysiology, three therapeutic
strategies are proposed: anti-inflammatory (ocrelizumab, siponimod…);
remyelinating (opicinumab); and neuroprotective (high-dose biotin, ibudilast,
simvastatin…). Nevertheless, despite recent promising positive clinical trials,
new methodological approaches for therapeutic protocols with adaptable outcomes
to assess progression are still needed. Author information:
(1)From the Mellen Center for Multiple Sclerosis, Neurological Institute
(R.J.F., S. Natarajan, R.A.B., D.O.), the Imaging Institute (X.H., M.J.L.,
K.E.S., X.Z.), and the Department of Biomedical Engineering (P.J., K.N., B.
Thoomukuntla), Cleveland Clinic, Cleveland, Ohio State University, Columbus
(M.R.), and University of Cincinnati, Cincinnati (A.Z.) - all in Ohio; the Data
Coordinating Center, Network for Excellence in Neuroscience Clinical Trials
(NeuroNEXT), University of Iowa, Iowa City (C.S.C., J.B., D.E., E.K., M.K.,
J.D.L., J.Y.); the National Institute of Neurological Disorders and Stroke,
Bethesda, MD (R.C.); the Clinical Coordinating Center, NeuroNEXT, Massachusetts
General Hospital, Neurological Clinical Research Institute, Harvard Partners
(M.E.C., M.M., A.A., B. Thornell), the Department of Neurology, Massachusetts
General Hospital, Harvard Medical School (E.C.K.), and Brigham and Women's
Hospital (C.S.), Boston; patient advocate (T.G.) and Swedish Medical Center at
Seattle (P.R.), Seattle; University of Rochester Medical Center, Rochester
(A.G.), Corinne Goldsmith Dickinson Center for Multiple Sclerosis, Mount Sinai
Medical Center (S.K.), Weill Cornell Medical College (J.S.P.), Columbia
University Medical Center (C.S.R.), and Montefiore Medical Center, Albert
Einstein College of Medicine (S.S.), New York, State University of New York
(SUNY) at Stony Brook, Stony Brook (P.K.C.), SUNY Upstate Medical University,
Syracuse (B.J.), and SUNY at Buffalo, Buffalo (B.W.-G.) - all in New York;
MediciNova, La Jolla (K.M.), University of California at Davis, Sacramento
(M.A.), and University of California at Los Angeles, Los Angeles (B.S.G.) - all
in California; Washington University School of Medicine, St. Louis (R.T.N.);
Barrow Neurological Institute, St. Joseph's Hospital and Medical Center,
Phoenix, AZ (J.P.D.); NeuroRx Research, Montreal (S. Naraya); the School of
Health Sciences, College of Health and Human Sciences, Purdue University, West
Lafayette, IN (X.Z.); University of Colorado Denver, Aurora (E.A.); University
of Alabama at Birmingham, Birmingham (K.B.); Feinberg School of Medicine,
Northwestern University, Chicago (B.A.C.); University of Miami Miller School of
Medicine, Miami (S.D.); University of Utah, Salt Lake City (L.D.D.); University
of Texas Southwestern Medical Center, Dallas (A.F.); University of Virginia at
Charlottesville, Charlottesville (M.D.G.); Emory University, Atlanta (N.L.);
University of Kansas Medical Center, Kansas City (S.G.L.); Vanderbilt
University, Nashville (H.M.); University of Pittsburgh Medical Center,
Pittsburgh (V.S.); and Oregon Health and Science University, Portland (V.Y.). |
Does gepotidacin activate bacterial topoisomerase? | No, gepotidacin is a bacterial topoisomerase inhibitor. | |
What is the 3D genome browser? | The 3D Genome Browser, http://3dgenome.org, allows users to conveniently explore both their own and over 300 publicly available chromatin interaction data of different types. The browser provides multiple methods linking distal cis-regulatory elements with their potential target genes. Users can seamlessly integrate thousands of other omics data to gain a comprehensive view of both regulatory landscape and 3D genome structure. | Recent releases of genome three-dimensional (3D) structures have the potential
to transform our understanding of genomes. Nonetheless, the storage technology
and visualization tools need to evolve to offer to the scientific community fast
and convenient access to these data. We introduce simultaneously a database
system to store and query 3D genomic data (3DBG), and a 3D genome browser to
visualize and explore 3D genome structures (3DGB). We benchmark 3DBG against
state-of-the-art systems and demonstrate that it is faster than previous
solutions, and importantly gracefully scales with the size of data. We also
illustrate the usefulness of our 3D genome Web browser to explore human genome
structures. The 3D genome browser is available at http://3dgb.cs.mcgill.ca/. Author information:
(1)Bioinformatics and Genomics Program, The Pennsylvania State University,
University Park, State College, PA, 16802, USA.
(2)Department of Biochemistry and Molecular Biology, College of Medicine, The
Pennsylvania State Hershey, Hershey, PA, 17033, USA.
(3)Department of Computer and Information Science, University of Pennsylvania,
Philadelphia, PA, 19104, USA.
(4)Department of Genetics, The Edison Family Center for Genome Sciences and
Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108,
USA.
(5)Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599,
USA.
(6)Department of Biostatistics, University of North Carolina, Chapel Hill, NC,
27599, USA.
(7)Department of Computer Science, University of North Carolina, Chapel Hill,
NC, 27599, USA.
(8)Department of Quantitative Health Sciences, Lerner Research Institute,
Cleveland Clinic Foundation, Cleveland, OH, 44195, USA.
(9)Center for Computational Biology and Bioinformatics, Huck Institutes of the
Life Sciences, The Pennsylvania State University, University Park, State
College, PA, 16802, USA.
(10)Department of Genetics, The Edison Family Center for Genome Sciences and
Systems Biology, Washington University School of Medicine, St. Louis, MO, 63108,
USA. [email protected].
(11)Bioinformatics and Genomics Program, The Pennsylvania State University,
University Park, State College, PA, 16802, USA. [email protected].
(12)Department of Biochemistry and Molecular Biology, College of Medicine, The
Pennsylvania State Hershey, Hershey, PA, 17033, USA. [email protected]. |
Are gut proteobacteria associated with inflammatory disease? | The onset of inflammatory bowel disease is associated with enteric proteobacterial infection, yet the mechanistic basis for this association is unclear. | SCOPE: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon.
α-Mangostin (α-MG), the most abundant xanthone in mangosteen fruit, exerts
anti-inflammatory and antibacterial activities in vitro. We evaluated the impact
of dietary α-MG on murine experimental colitis and on the gut microbiota of
healthy mice.
METHODS AND RESULTS: Colitis was induced in C57BL/6J mice by administration of
dextran sulfate sodium (DSS). Mice were fed control diet or diet with α-MG
(0.1%). α-MG exacerbated the pathology of DSS-induced colitis. Mice fed diet
with α-MG had greater colonic inflammation and injury, as well as greater
infiltration of CD3(+) and F4/80(+) cells, and colonic myeloperoxidase, than
controls. Serum levels of granulocyte colony-stimulating factor, IL-6, and serum
amyloid A were also greater in α-MG-fed animals than in controls. The colonic
and cecal microbiota of healthy mice fed α-MG but no DSS shifted to an increased
abundance of Proteobacteria and decreased abundance of Firmicutes and
Bacteroidetes, a profile similar to that found in human UC.
CONCLUSION: α-MG exacerbated colonic pathology during DSS-induced colitis. These
effects may be associated with an induction of intestinal dysbiosis by α-MG. Our
results suggest that the use of α-MG-containing supplements by patients with UC
may have unintentional risk. OBJECTIVE: To compare colonic microbial composition in systemic sclerosis (SSc)
patients and healthy controls and to determine whether certain microbial genera
are associated with gastrointestinal (GI) tract symptoms in patients with SSc.
METHODS: Healthy controls were age- and sex-matched (1:1) with adult SSc
patients. Cecum and sigmoid mucosal lavage samples were obtained during
colonoscopy. The microbiota in these samples were determined by Illumina HiSeq
2000 16S sequencing, and operational taxonomic units were selected. Linear
discrimit analysis effect size was used to identify the genera that showed
differential expression in SSc patients versus controls. Differential expression
analysis for sequence count data was used to identify specific genera associated
with GI tract symptoms.
RESULTS: Among 17 patients with SSc (88% female; median age 52.1 years), the
mean ± SD total GI Tract 2.0 score was 0.7 ± 0.6. Principal coordinate analysis
illustrated significant differences in microbial communities in the cecum and
sigmoid regions in SSc patients versus healthy controls (both P = 0.001).
Similar to the findings in inflammatory disease states, SSc patients had
decreased levels of commensal bacteria, such as Faecalibacterium and
Clostridium, and increased levels of pathobiont bacteria, such as Fusobacterium
and γ-Proteobacteria, compared with healthy controls. Bifidobacterium and
Lactobacillus, which are typically reduced under conditions of inflammation,
were also increased in abundance in patients with SSc. In SSc patients with
moderate/severe GI tract symptoms, the abundance of Bacteroides fragilis was
decreased, and that of Fusobacterium was increased, compared with patients who
had no or mild symptoms.
CONCLUSION: This study demonstrates a distinct colonic microbial signature in
SSc patients compared with healthy controls. This unique ecologic change may
perpetuate immunologic aberrations and contribute to clinical manifestations of
SSc. Author information:
(1)Department of Molecular Microbiology and Immunology, University of Southern
California, Los Angeles, CA 90089, USA.
(2)Department of Medicine, Section of Gastroenterology, University of Chicago,
Chicago, IL 60637, USA.
(3)College of Food Science and Nutritional Engineering, China Agricultural
University, Beijing 100083, China; Department of Food Science and Technology,
University of California, Davis, Davis, CA 95616, USA.
(4)Argonne National Laboratory, Argonne, IL 60439, USA.
(5)Department of Medicine, Section of Gastroenterology, University of Chicago,
Chicago, IL 60637, USA; Department of Pediatrics Section of Pediatric
Gastroenterology, Hepatology, & Nutrition, University of Chicago, Chicago, IL
60637, USA.
(6)Department of Medicine, Section of Gastroenterology, University of Chicago,
Chicago, IL 60637, USA; Argonne National Laboratory, Argonne, IL 60439, USA.
(7)Department of Food Science and Technology, University of California, Davis,
Davis, CA 95616, USA.
(8)Department of Molecular Microbiology and Immunology, University of Southern
California, Los Angeles, CA 90089, USA. Electronic address:
[email protected]. Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the
gastrointestinal tract of uncertain origin, which includes ulcerative colitis
(UC) and Crohn's disease (CD). The composition of gut microbiota may change in
IBD affected individuals, but whether dysbiosis is the cause or the consequence
of inflammatory processes in the intestinal tissue is still unclear. Here, the
composition of the microbiota and the metabolites in stool of 183 subjects (82
UC, 50 CD, and 51 healthy controls) were determined. The metabolites content and
the microbiological profiles were significantly different between IBD and
healthy subjects. In the IBD group, Firmicutes, Proteobacteria, Verrucomicrobia,
and Fusobacteria were significantly increased, whereas Bacteroidetes and
Cyanobacteria were decreased. At genus level Escherichia, Faecalibacterium,
Streptococcus, Sutterella and Veillonella were increased, whereas Bacteroides,
Flavobacterium, and Oscillospira decreased. Various metabolites including
biogenic amines, amino acids, lipids, were significantly increased in IBD, while
others, such as two B group vitamins, were decreased in IBD compared to healthy
subjects. This study underlines the potential role of an inter-omics approach in
understanding the metabolic pathways involved in IBD. The combined evaluation of
metabolites and fecal microbiome can be useful to discriminate between healthy
subjects and patients with IBD. |
What brain procedure can be done using the NeuroBlate system? | NeuroBlate System is used for Laser interstitial thermal therapy. | Surgical extent-of-resection has been shown to have an impact on high-grade
glioma (HGG) outcomes; however, complete resection is rarely achievable in
difficult-to-access (DTA) tumors. Controlled thermal damage to the tumor may
have the same impact in DTA-HGGs. We report our multicenter results of laser
interstitial thermal therapy (LITT) in DTA-HGGs. We retrospectively reviewed 34
consecutive DTA-HGG patients (24 glioblastoma, 10 anaplastic) who underwent LITT
at Cleveland Clinic, Washington University, and Wake Forest University (May
2011-December 2012) using the NeuroBlate(®) System. The extent of thermal damage
was determined using thermal damage threshold (TDT) lines: yellow TDT line (43
°C for 2 min) and blue TDT line (43°C for 10 min). Volumetric analysis was
performed to determine the extent-of-coverage of tumor volume by TDT lines.
Patient outcomes were evaluated statistically. LITT was delivered as upfront in
19 and delivered as salvage in 16 cases. After 7.2 months of follow-up, 71% of
cases demonstrated progression and 34% died. The median overall survival (OS)
for the cohort was not reached; however, the 1-year estimate of OS was 68 ± 9%.
Median progression-free survival (PFS) was 5.1 months. Thirteen cases who met
the following two criteria-(1) <0.05 cm(3) tumor volume not covered by the
yellow TDT line and (2) <1.5 cm(3) additional tumor volume not covered by the
blue TDT line-had better PFS than the other 21 cases (9.7 vs. 4.6 months; P =
0.02). LITT can be used effectively for treatment of DTA-HGGs. More complete
coverage of tumor by TDT lines improves PFS which can be translated as the
extent of resection concept for surgery. Magnetic resoce-guided laser interstitial thermal therapy (MRgLITT) is a
novel minimally invasive modality that uses heat from laser probes to destroy
tissue. Advances in probe design, cooling mechanisms, and real-time MR
thermography have increased laser utilization in neurosurgery. The authors
perform a systematic analysis of two commercially available MRgLITT systems used
in neurosurgery: the Visualase® thermal therapy and NeuroBlate® Systems. Data
extraction was performed in a blinded fashion. Twenty-two articles were included
in the quantitative synthesis. A total of 223 patients were identified with the
majority having undergone treatment with Visualase (n=154, 69%). Epilepsy was
the most common indication for Visualase therapy (n=8 studies, 47%). Brain mass
was the most common indication for NeuroBlate therapy (n=3 studies, 60%). There
were no significant differences, except in age, wherein the NeuroBlate group was
nearly twice as old as the Visualase group (p<0.001). Frame, total
complications, and length-of-stay (LOS) were non-significant when adjusted for
age and number of patients. Laser neurosurgery has evolved over recent decades.
Clinical indications are currently being defined and will continue to emerge as
laser technologies become more sophisticated. Head-to-head comparison of these
systems was difficult given the variance in indications (and therefore patient
population) and disparate literature. In common with other stereotactic procedures, stereotactic laser
thermocoagulation (SLT) promises gentle destruction of pathological tissue,
which might become especially relevant for epilepsy surgery in the future.
Compared to standard resection, no large craniotomy is necessary, cortical
damage during access to deep-seated lesions can be avoided and interventions
close to eloquent brain areas become possible. We describe the history and
rationale of laser neurosurgery as well as the two available SLT systems
(Visualase® and NeuroBlate®; CE marks pending). Both systems are coupled with
magnetic resoce imaging (MRI) and MR thermometry, thereby increasing patient
safety. We report the published clinical experiences with SLT in epilepsy
surgery (altogether approximately 200 cases) with respect to complications,
brain structural alterations, seizure outcome, neuropsychological findings and
treatment costs. The rate of seizure-free patients seems to be slightly lower
than for resection surgery. Due to the inadequate quality of studies, the
neuropsychological superiority of SLT has not yet been unambiguously
demonstrated. INTRODUCTION: We describe the feasibility of using minimally invasive robotic
laser interstitial thermotherapy (LITT) for achieving an anterior two-thirds as
well as a complete corpus callosotomy.
METHODS: Ten probe trajectories were plotted on normal magentic resoce
imaging (MRI) scans using the Brainlab Stereotactic Planning Software (Brainlab,
Munich, Germany). The NeuroBlate® System (Monteris Medical, MN, USA) was used to
conform the thermal burn to the corpus callosum along the trajectory of the
probe. The distance of the ideal entry site from either the coronal suture and
the torcula or nasion and the midline was calculated. The distance of the probe
tip from the dorsal and ventral limits of the callosotomy in the sagittal plane
were also calculated.
RESULTS: Anterior two-thirds callosotomy was possible in all patients using a
posterior parieto-occipital paramedian trajectory through the non-domit
lobe. The average entry point was 3.64 cm from the midline, 10.6 cm behind the
coronal suture, and 9.2 cm above the torcula. The probe tip was an average of
1.4 cm from the anterior commissure. For a total callosotomy, an additional
contralaterally placed frontal probe was used to target the posterior
one-third of the corpus callosum. The average entry site was 3.3 cm from the
midline and 9.1 cm above the nasion. The average distance of the probe tip from
the base of the splenium was 0.94 cm.
CONCLUSION: The directional thermoablation capability of the NeuroBlate®
system allows for targeted lesioning of the corpus callosum, to achieve a
two-thirds or complete corpus callosotomy. A laser distance of < 2 cm is
sufficient to reach the entire corpus callosum through one trajectory for an
anterior two-thirds callosotomy and two trajectories for a complete callosotomy. |
Describe genomiser | Genomiser is an analysis framework that is able not only to score the relevance of variation in the non-coding genome, but also to associate regulatory variants to specific Mendelian diseases. Genomiser scores variants through either existing methods such as CADD or a bespoke machine learning method and combines these with allele frequency, regulatory sequences, chromosomal topological domains, and phenotypic relevance to discover variants associated to specific Mendelian disorders. Genomiser is able to identify causal regulatory variants as the top candidate in 77% of simulated whole genomes, allowing effective detection and discovery of regulatory variants in Mendelian disease. | Author information:
(1)Queen Mary University of London, London E1 4NS, UK; Genomics England Ltd.,
London EC1M 6BQ, UK.
(2)Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany.
(3)Skarnes Faculty Group, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK.
(4)Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioorganic
Chemistry, Polish Academy of Sciences, 61-704 Poz, Poland.
(5)Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for
Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany.
(6)Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany; Berlin-Brandenburg Center for
Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany.
(7)Department of Biomedical Informatics and Intelligent Systems Program,
University of Pittsburgh, Pittsburgh, PA 15206, USA.
(8)Division of Environmental Genomics and Systems Biology, Lawrence Berkeley
National Laboratory, Berkeley, CA 94720, USA.
(9)Department of Medical Informatics and Clinical Epidemiology, Oregon Health &
Science University, Portland, OR 97239, USA.
(10)Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research,
Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of
Medicine University of New South Wales, Darlinghurst, NSW 2010, Australia.
(11)Anacleto Lab Department of Computer Science, University of Milan, Via
Comelico, 20135 Milan, Italy.
(12)Institute for Medical and Human Genetics, Charité-Universitätsmedizin
Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for
Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany; Berlin-Brandenburg
Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin,
Augustenburger Platz 1, 13353 Berlin, Germany; Institute for Bioinformatics,
Department of Mathematics and Computer Science, Freie Universität Berlin,
Takustrasse, 14195 Berlin, Germany. Electronic address: [email protected]. |
Which ultraconserved element is associated with Embryonic Stem Cells (ESC) self-renewal? | Ultraconserved elements (UCEs) show the peculiar feature to retain extended perfect sequence identity among human, mouse, and rat genomes. Most of them are transcribed and represent a new family of long non-coding RNAs (lncRNAs), the transcribed UCEs (T-UCEs). Despite their involvement in human cancer, the physiological role of T-UCEs is still unknown. A lncRNA containing the uc.170+, named T-UCstem1, was identified with in vitro and in vivo evidence that it plays essential roles in embryonic stem cells (ESCs) by modulating cytoplasmic miRNA levels and preserving transcriptional dynamics. | |
What is TPMCalculator? | The quantification of RNA sequencing (RNA-seq) abundance using a normalization method that calculates transcripts per million (TPM) is a key step to compare multiple samples from different experiments. TPMCalculator is a one-step software to process RNA-seq alignments in BAM format and reports TPM values, raw read counts and feature lengths for genes, transcripts, exons and introns. The program describes the genomic features through a model generated from the gene transfer format (GTF) file used during alignments reporting of the TPM values and the raw read counts for each feature. | |
Describe clinical presentation of Escobar syndrome. | The Escobar variant of multiple pterygium syndrome (MPS) is a rare, autosomal recessive disorder which is characterized by pterygia, arthrogryposis (joint contractures), facial dysmorphism along with other anomalies. | Escobar syndrome is a rare condition with autosomal-recessive inheritance,
characterised by multiple pterygia, kyphoscoliosis, multiple joint contractures
and craniofacial dysmorphisms. A number of other abnormalities are also
attributed to the syndrome. Here, we present a case of isolated extrinsic
extensor-tendon hypoplasia of the right index finger in a 7-year-old patient
with Escobar syndrome. To our knowledge, this has not been previously described
in connection with this syndrome. Escobar syndrome is a form of arthrogryposis multiplex congenita and features
joint contractures, pterygia, and respiratory distress. Similar findings occur
in newborns exposed to nicotinergic acetylcholine receptor (AChR) antibodies
from myasthenic mothers. We performed linkage studies in families with Escobar
syndrome and identified eight mutations within the gamma -subunit gene (CHRNG)
of the AChR. Our functional studies show that gamma -subunit mutations prevent
the correct localization of the fetal AChR in human embryonic kidney-cell
membranes and that the expression pattern in prenatal mice corresponds to the
human clinical phenotype. AChRs have five subunits. Two alpha, one beta, and one
delta subunit are always present. By switching gamma to epsilon subunits in late
fetal development, fetal AChRs are gradually replaced by adult AChRs. Fetal and
adult AChRs are essential for neuromuscular signal transduction. In addition,
the fetal AChRs seem to be the guide for the primary encounter of axon and
muscle. Because of this important function in organogenesis, human mutations in
the gamma subunit were thought to be lethal, as they are in gamma -knockout
mice. In contrast, many mutations in other subunits have been found to be viable
but cause postnatally persisting or beginning myasthenic syndromes. We conclude
that Escobar syndrome is an inherited fetal myasthenic disease that also affects
neuromuscular organogenesis. Because gamma expression is restricted to early
development, patients have no myasthenic symptoms later in life. This is the
major difference from mutations in the other AChR subunits and the striking
parallel to the symptoms found in neonates with arthrogryposis when maternal
AChR auto-antibodies crossed the placenta and caused the transient inactivation
of the AChR pathway. BACKGROUND: Escobar syndrome or multiple pterygium syndrome is characterized by
a web across every flexion crease in the extremities, most notably the popliteal
space. In addition, this syndrome is associated with two other structural
anomalies: a vertical talus and congenital lordoscoliosis. We present a case
report of a patient with Escobar syndrome who was initially managed
conservatively and subsequently had severe and debilitating progression and
respiratory decompensation ultimately requiring surgical intervention.
STUDY DESIGN: Case report.
METHODS: After preoperative evaluation by a pediatrician, pulmonologist, and
otolaryngologist, the patient underwent one-stage anterior and posterior spinal
fusion with instrumentation as well as multiple osteotomies, rib resections, and
vertebrectomies.
RESULTS: The patient's postoperative course was complicated by wound necrosis
requiring irrigation and debridement, a urinary tract infection, and a
tracheostomy for persistent atelectasis. The patient eventually recovered from
all complications. There were never any focal neurologic deficits. The patient
had a 3-year follow-up with radiographically confirmed maintece of
correction. Fusion was obtained in the anterior and posterior segments.
Clinically, the patient is able to stand upright, can participate in functional
activities, and has not required any pain medication. The patient's functional
vital capacity improved from 23% predicted preoperatively to 60% predicted
postoperatively.
CONCLUSIONS: Patients with severe spinal deformity secondary to Escobar syndrome
can be successfully treated surgically. We propose early surgical intervention
in this group to prevent curve progression, restrictive lung disease, and the
need for complex salvage procedures. Escobar syndrome is characterized with multiple pterygia or webs of the skin and
multiple congenital anomalies. We present a 15-year-old patient with Escobar
syndrome who complained of persistent blunt abdominal pain for 1 year.
Preoperative evaluation confirmed the diagnosis of imperforate hymen, and the
patient underwent hymenectomy under intravenous sedation. The patient's
postoperative course was uneventful and her complaints resolved completely.
After a 3-month follow-up, she reported having normal menstrual bleeding
intervals each month without any complications. Patients with Escobar syndrome
may suffer from abdominal pain due to imperforate hymen. Careful evaluation of
these patients must include a complete gynaecological assessment and, if
indicated, surgical treatment must be performed without delay. The Escobar variant of multiple pterygium syndrome (MPS) is a rare, autosomal
recessive disorder which may lead to many serious or even lethal fetal
abnormalities. MPS is characterized by pterygia, arthrogryposis (joint
contractures), and intrauterine growth restriction (IUGR). In the case described
below, increased fetal nuchal translucency was the first abnormality diagnosed
already in the first trimester of pregcy. Other symptoms of the disease were
found during the second trimester of pregcy using ultrasonography
examination. Also, genetic amniocentesis revealed no genetic disorders and the
Escobar syndrome was diagnosed post mortem. Parental and maternal genetic
examinations were performed and allowed for early prenatal diagnostics in the
next pregcy resulting in the birth of a healthy newborn. Escobar syndrome (ES) or multiple pterygia syndrome (MIM#265000) is an
infrequent condition characterized by facial dysmorphism, multiple webbing
(pterygia), congenital contractures (arthrogryposis) and other internal
anomalies. We describe an 8-days-old male newborn from consanguineous parents
with ES who also presented heterotaxia syndrome and esophageal atresia,
anomalies that not have been previously reported as associated to ES. Multiple pterygium syndrome (MPS) is a syndrome that is characterized abnormal
face, short length and skin pterygiums on some body legions (servical,
antecubital, popliteal, interdigital and on neck). It is also called as
Pterygium Colli syndrome, Escobar syndrome or Pterygium syndrome. Escobar
(multyple pterygium) syndrome is a rare syndrome. Intrauterin growth
reterdation, abnormal face, wide-spead pterygiums that resulted in joint
contractures, ptosis, chryptoorchidism, patellar dysplasia and foot deformities
are seen on this syndrome. Primarly autosomal resesive crossing are observed;
also autosomal domit and X-linked crossing. This case were presented as it
has components of Escobar syndrome and Isolated Patellar Aplasia syndrome in
same time. Background: Escobar syndrome, a nonlethal variant of multiple pterygium
syndromes (MPS), is a rare autosomal recessive disorder characterized by
pterygia and multiple joint contractures along with other anomalies. Variants in
cholinergic receptor nicotinic gamma subunit (CHRNG) have been previously
reported in patients with Escobar syndrome. Objective: We studied a
consanguineous Pakistani family affected with Escobar syndrome to identify the
underlying genetic defect through short tandem repeat (STR) genotyping and
direct DNA sequencing. Results: Genotyping with microsatellite markers (D2S427,
D2S2344, and D2S206) revealed linkage of the disease phenotype in the family to
the CHRNG locus. Using Sanger sequencing, we identified a homozygous nonsense
CHRNG variant c.136C>T (p.R46*), predicted to produce a truncated protein that
leads to acetylcholine receptor deficiency, causing MPS. The unaffected parents
and siblings in the family were heterozygous carriers of this disease-causing
variant. Conclusion: We report the identification of a nonsense CHRNG variant in
a consanguineous Pakistani family affected with Escobar syndrome. |
What is small-activating RNA? | small activating RNAs are double stranded RNAs (dsRNAs) that target gene promoters and trigger gene activation. | PURPOSE: RNA activation (RNAa) is a mechanism of gene activation triggered by
promoter-targeted small double stranded RNAs (dsRNAs), also known as small
activating RNAs (saRNAs). Myogenic regulatory factor MyoD is regarded as the
master activator of myogenic differentiation cascade by binding to enhancer of
muscle specific genes. Stress urinary incontinence (SUI) is a condition
primarily resulted from urethral sphincter deficiency. It is thus expected that
by promoting differentiation of adipose-derived stem cells (ADSCs) into
myoblasts by activating MyoD gene through RNAa may offer benefits to SUI.
MATERIALS AND METHODS: Rats ADSCs were isolated, proliferated in vitro, and
identified by flow cytometry. Purified ADSCs were then transfected with a MyoD
saRNA or control transfected. Real-time polymerase chain reaction (RT-PCR) and
western blotting were used to detect MyoD mRNA and protein expression,
respectively. Immunocytochemical staining was applied to determine the
expression of desmin protein in transfected cells. Cell viability was measured
by using CellTiter 96R AQueous One Solution Cell Proliferation Assay kit.
RESULTS: Transfection of a MyoD saRNA (dsMyoD) into ADSCs significantly induced
the expression of MyoD at both the mRNA and protein levels, and inhibited cell
proliferation. Desmin protein expression was detected in dsMyoD treated ADSCs 2
weeks later.
CONCLUSION: Our findings show that RNAa mediated overexpression of MyoD can
promote transdifferentiation of ADSCs into myoblasts and may help treat stress
urinary incontinence (SUI)-a condition primarily resulted from urethral
sphincter deficiency. |
What is the mechanism of action of Ivosidenib? | Ivosidenib is an inhibitor of the IDH1 mutant enzyme that exhibits profound 2-HG lowering in tumor models. It is effective for IDH1-mutant relapsed/refractory acute myeloid leukemia. | PURPOSE OF REVIEW: Hypomethylating agents (HMAs) are the standard of care for
patients with myelodysplastic syndromes (MDS). Although these agents induce
responses in up to 40% of patients, most patients ultimately experience loss of
response. The purpose of this review is to provide an overview of the different
therapies under development for MDS after HMA therapy.
RECENT FINDINGS: Recent advances in the understanding of MDS pathogenesis have
led to the development of new potential therapies after HMA failure. Newer HMAs,
less susceptible to in-vivo deamination, such as guadecitabine or ASTX727 have
shown activity. Alterations of immune checkpoints in MDS have led to multiple
clinical trials evaluating the activity of monoclonal antibodies targeting these
proteins (pembrolizumab, nivolumab, ipilimumab). Different combinations and new
formulations of cytotoxic agents, such as clofarabine or CPX-351, are newer
options for specific subsets of patients. Finally, targeted agents inhibiting
multiple kinases (rigosertib), BCL2 (venetoclax) or mutant IDH1 (ivosidenib),
IDH2 (enasidenib), FLT3 (sorafenib, midostaurin) or spliceosome components
(H3B-8800) are other novel options.
SUMMARY: Despite the poor prognosis associated with HMA failure, clinical
trials, new cytotoxic agents and allogeneic stem-cell transplantation, can offer
therapeutic opportunities for these patients for whom there is no standard of
care. Somatic point mutations at a key arginine residue (R132) within the active site
of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1) confer a novel gain of
function in cancer cells, resulting in the production of d-2-hydroxyglutarate
(2-HG), an oncometabolite. Elevated 2-HG levels are implicated in epigenetic
alterations and impaired cellular differentiation. IDH1 mutations have been
described in an array of hematologic maligcies and solid tumors. Here, we
report the discovery of AG-120 (ivosidenib), an inhibitor of the IDH1 mutant
enzyme that exhibits profound 2-HG lowering in tumor models and the ability to
effect differentiation of primary patient AML samples ex vivo. Preliminary data
from phase 1 clinical trials enrolling patients with cancers harboring an IDH1
mutation indicate that AG-120 has an acceptable safety profile and clinical
activity. A phase I study suggests that ivosidenib can induce remission in patients with
relapsed or refractory acute myeloid leukemia characterized by IDH1 mutations.
The drug spurred complete remission or complete remission with partial
hematologic recovery in 30.4% of patients. The most common side effects of at
least grade 3 were prolonged QT interval and IDH differentiation syndrome. Author information:
(1)Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer
Center, New York, NY, USA.
(2)Center for Hematologic Maligcies, Memorial Sloan Kettering Cancer Center,
New York, NY, USA.
(3)Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
(4)Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY,
USA.
(5)Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
(6)Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center,
New York, NY, USA.
(7)Computational & Systems Biology Program, Memorial Sloan Kettering Cancer
Center, New York, NY, USA.
(8)Gerstner Sloan Kettering Graduate School, Memorial Sloan Kettering Cancer
Center, New York, NY, USA.
(9)The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial
Sloan Kettering Cancer Center, New York, NY, USA.
(10)Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer
Center, New York, NY, USA.
(11)Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New
York, NY, USA.
(12)Department of Pathology, Memorial Sloan Kettering Cancer Center, New York,
NY, USA.
(13)Feil Family Brain and Mind Research Institute, Weill Cornell Medical
College, New York, New York, USA.
(14)Agios Pharmaceuticals, Inc, Cambridge, MA, USA.
(15)Cancer Biology & Genetics Program, Memorial Sloan Kettering Cancer Center,
New York, NY, USA. [email protected].
(16)Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer
Center, New York, NY, USA. [email protected].
(17)Center for Hematologic Maligcies, Memorial Sloan Kettering Cancer Center,
New York, NY, USA. [email protected].
(18)Department of Medicine, Memorial Sloan Kettering Cancer Center, New York,
NY, USA. [email protected].
(19)Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
[email protected].
(20)Department of Medicine, Memorial Sloan Kettering Cancer Center, New York,
NY, USA. [email protected].
(21)Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
[email protected]. The FDA approved ivosidenib for patients with IDH1-mutant relapsed/refractory
acute myeloid leukemia. The approval was based on results of a phase I trial in
which 32.8% of patients treated with the drug had a complete remission or a
complete remission with a partial hematologic recovery. Ivosidenib (Tibsovo®) is a small molecule, orally available inhibitor of mutated
cytosolic isocitrate dehydrogenase 1 (IDH1) that is being developed by Agios
Pharmaceuticals for the treatment of cancer in patients with IDH1 mutations. The
mutated form of the IDH1 enzyme produces a metabolite, 2-hydroxyglutarate
(2-HG), which is thought to play a role in the formation and progression of
acute myeloid leukaemia (AML), gliomas and other cancers. Elevated 2-HG levels
interfere with cellular metabolism and epigenetic regulation, thereby
contributing to oncogenesis. Ivosidenib targets the IDH1 metabolic pathway to
prevent a build-up of the oncometabolite 2-HG. This article summarizes the
milestones in the development of ivosidenib leading to this first approval in
the USA for the treatment of patients with relapsed or refractory AML with a
susceptible IDH1 mutation. Clinical development for AML, cholangiocarcinoma,
glioma, myelodysplastic syndromes and solid tumours is ongoing worldwide. The FLT3 inhibitor midostaurin, the antibody-drug conjugate gemtuzumab
ozogamicin, CPX-351 (liposomal daunorubicin and cytarabine), and the IDH2
inhibitor enasidenib are among the novel agents approved for use in the clinic
this past year. This year, 2018, already has seen the regulatory approval of the
BCL2 inhibitor venetoclax in the form of breakthrough designation and the IDH1
inhibitor ivosidenib received full FDA approval. Much remains to be learned
about how best to use these drugs to improve patient outcomes and how best to
employ and interpret next-generation sequencing to determine measurable residual
disease (MRD) levels that can more accurately predict risk of relapse. |
Which is the basis of the ATAC-Seq protocol? | This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription-factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase-seq for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying nucleosome positions in accessible regions of the genome. | This unit describes Assay for Transposase-Accessible Chromatin with
high-throughput sequencing (ATAC-seq), a method for mapping chromatin
accessibility genome-wide. This method probes DNA accessibility with hyperactive
Tn5 transposase, which inserts sequencing adapters into accessible regions of
chromatin. Sequencing reads can then be used to infer regions of increased
accessibility, as well as to map regions of transcription-factor binding and
nucleosome position. The method is a fast and sensitive alternative to DNase-seq
for assaying chromatin accessibility genome-wide, or to MNase-seq for assaying
nucleosome positions in accessible regions of the genome. Author information:
(1)Center for Personal Dynamic Regulomes, Stanford University School of
Medicine, Stanford, California, USA.
(2)Department of Dermatology, Stanford University School of Medicine, Stanford,
California, USA.
(3)Department of Genetics, Stanford University School of Medicine, Stanford,
California, USA.
(4)Department of Bioengineering, Stanford University School of Medicine and
School of Engineering, Stanford, California, USA.
(5)Program in Cancer Biology, Stanford University School of Medicine, Stanford,
California, USA.
(6)Program in Biomedical Informatics, Stanford University School of Medicine,
Stanford, California, USA.
(7)Department of Pathology, Stanford University School of Medicine, Stanford,
California, USA.
(8)Department of Otolaryngology Head and Neck Surgery, Stanford University
School of Medicine, Stanford, California, USA.
(9)Department of Computer Science, Stanford University, Stanford, California,
USA.
(10)Chan Zuckerberg Biohub, San Francisco, California, USA. Identifying and characterizing highly accessible chromatin regions assists in
determining the location of genomic regulatory elements and understanding
transcriptional regulation. In this chapter, we describe an approach to map
accessible chromatin features in plants using the Assay for
Transposase-Accessible Chromatin, combined with high-throughput sequencing
(ATAC-seq), which was originally developed for cultured animal cells. This
technique utilizes a hyperactive Tn5 transposase to cause DNA cleavage and
simultaneous insertion of sequencing adapters into open chromatin regions of the
input nuclei. The application of ATAC-seq to plant tissue has been challenging
due to the difficulty of isolating nuclei sufficiently free of interfering
organellar DNA. Here we present two different approaches to purify plant nuclei
for ATAC-seq: the INTACT method (Isolation of Nuclei TAgged in specific Cell
Types) to isolate nuclei from individual cell types of the plant, and tissue
lysis followed by sucrose sedimentation to isolate sufficiently pure total
nuclei. We provide detailed instructions for transposase treatment of nuclei
isolated using either approach, as well as subsequent preparation of ATAC-seq
libraries. Sequencing-ready ATAC-seq libraries can be prepared from plant tissue
in as little as one day. The procedures described here are optimized for
Arabidopsis thaliana but can also be applied to other plant species. Assay for Transposase-Accessible Chromatin with high-throughput sequencing
(ATAC-seq) is a method used for the identification of open (accessible) regions
of chromatin. These regions represent regulatory DNA elements (e.g., promoters,
enhancers, locus control regions, insulators) to which transcription factors
bind. Mapping the accessible chromatin landscape is a powerful approach for
uncovering active regulatory elements across the genome. This information serves
as an unbiased approach for discovering the network of relevant transcription
factors and mechanisms of chromatin structure that govern gene expression
programs. ATAC-seq is a robust and sensitive alternative to DNase I
hypersensitivity analysis coupled with next-generation sequencing (DNase-seq)
and formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) for
genome-wide analysis of chromatin accessibility and to the sequencing of
micrococcal nuclease-sensitive sites (MNase-seq) to determine nucleosome
positioning. We present a detailed ATAC-seq protocol optimized for human primary
immune cells i.e. CD4+ lymphocytes (T helper 1 (Th1) and Th2 cells). This
comprehensive protocol begins with cell harvest, then describes the molecular
procedure of chromatin tagmentation, sample preparation for next-generation
sequencing, and also includes methods and considerations for the computational
analyses used to interpret the results. Moreover, to save time and money, we
introduced quality control measures to assess the ATAC-seq library prior to
sequencing. Importantly, the principles presented in this protocol allow its
adaptation to other human immune and non-immune primary cells and cell lines.
These guidelines will also be useful for laboratories which are not proficient
with next-generation sequencing methods. This chapter describes sequencing-based methods for profiling dynamic changes in
DNA accessibility and gene expression in Saccharomyces cerevisiae. Assay for
transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) is a
powerful technique for identifying nucleosome-free regions of the genome.
Combining ATAC-Seq with RNA Sequencing (RNA-Seq) is a rapid approach for
studying the relationship between genome structure and changes in global
patterns of gene expression from a single experiment. A laboratory protocol is
presented for these methods as well as examples of typical results and
visualizations. |
What is vcfanno? | Vcfanno flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. Substantial performance gains are reported by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license. | |
What is the association of Disease-Associated STRs (daSTRs) with domain boundaries? | Nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains. For instance, Fragile X syndrome patients exhibit severe boundary disruption in a manner that correlates with local loss of CTCF occupancy and the degree of FMR1 silencing. | Author information:
(1)Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
19104, USA; Epigenetics Institute, Perelman School of Medicine, University of
Pennsylvania, Philadelphia, PA 19104, USA.
(2)Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
19104, USA; Genomics and Computational Biology Program, Perelman School of
Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics
Institute, Perelman School of Medicine, University of Pennsylvania,
Philadelphia, PA 19104, USA.
(3)Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
19104, USA.
(4)The Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The
Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of
Pathology and Laboratory Medicine, The University of Pennsylvania, Philadelphia,
PA 19104, USA.
(5)Biochemistry and Molecular Medicine, University of California-Davis,
Sacramento, CA 95616, USA; MIND Institute, UC Davis, Sacramento, CA 95616, USA.
(6)Department of Bioengineering, University of Pennsylvania, Philadelphia, PA
19104, USA; Epigenetics Institute, Perelman School of Medicine, University of
Pennsylvania, Philadelphia, PA 19104, USA; Department of Genetics, University of
Pennsylvania, Philadelphia, PA 19104, USA. Electronic address:
[email protected]. |
What is the link between ultraconserved elements and three-dimensional mammalian genome organization? | Ultraconserved elements (UCEs) occupy specific arenas of three-dimensional mammalian genome organization. UCEs are enriched within contact domains and, further, that the subset of UCEs within domains shared across diverse cell types are linked to kidney-related and neuronal processes. In boundaries, UCEs are generally depleted, with those that do overlap boundaries being overrepresented in exonic UCEs. Regarding loop anchors, UCEs are neither overrepresented nor underrepresented, but those present in loop anchors are enriched for splice sites. As the relationships between UCEs and human Hi-C features are conserved in mouse, UCEs contribute to interspecies conservation of genome organization and, thus, genome stability. | |
What are the "Ohnologs"? | Whole genome duplications (WGD) have now been firmly established in all major eukaryotic kingdoms. In particular, all vertebrates descend from two rounds of WGDs, that occurred in their jawless ancestor some 500 MY ago. Paralogs retained from WGD, also coined 'ohnologs' after Susumu Ohno, have been shown to be typically associated with development, signaling and gene regulation. | Some zebrafish genes appear to lack an ortholog in the human genome and
researchers often call them "novel" genes. The origin of many so-called "novel"
genes becomes apparent when considered in the context of genome duplication
events that occurred during evolution of the phylum Chordata, including two
rounds at about the origin of the subphylum Vertebrata (R1 and R2) and one round
before the teleost radiation (R3). Ohnologs are paralogs stemming from such
genome duplication events, and some zebrafish genes said to be "novel" are more
appropriately interpreted as "ohnologs gone missing", cases in which ohnologs
are preserved differentially in different evolutionary lineages. Here we
consider ohnologs present in the zebrafish genome but absent from the human
genome. Reasonable hypotheses are that lineage-specific loss of ohnologs can
play a role in establishing lineage divergence and in the origin of
developmental innovations. How does the evolution of ohnologs differ from the
evolution of gene duplicates arising from other mechanisms, such as tandem
duplication or retrotransposition? To what extent do different major vertebrate
lineages or different teleost lineages differ in ohnolog content? What roles do
differences in ohnolog content play in the origin of developmental mechanisms
that differ among lineages? This review explores these questions. Most copy number variations are neutral, but some are deleterious and associated
with various human diseases. Copy number variations are distributed non-randomly
in vertebrate genomes, and it was recently reported that ohnologs, which are
duplicated genes derived from whole genome duplication, are refractory to copy
number variations. However, it is unclear what genomic factors affect the
deleterious effects of copy number variations and the biological significance of
the biased genomic distribution of copy number variations remains poorly
understood. Here we show that non-ohnologs neighbouring ohnologs are unlikely to
have copy number variations, resulting in ohnolog-rich regions in vertebrate
genomes being copy number variation deserts. Our results suggest that the
genomic location of ohnologs is a determining factor in the retention of copy
number variations and that the dosage-balanced ohnologs are likely to cause the
deleterious effects of copy number variations in these regions. We propose that
investigating copy number variation of genes in regions that are typically copy
number variation deserts is an efficient means to find disease-related copy
number variations. Ohnologs -paralogous gene pairs generated by whole genome duplication- are
enriched for dosage sensitive genes, that is, genes that have a phenotype due to
copy number changes. Dosage sensitive genes frequently occur in the same
metabolic pathway and in physically interacting proteins. Accumulating evidence
reveals that functionally related genes tend to co-localize in the
three-dimensional (3D) arrangement of chromosomes. We query whether the spatial
distribution of ohnologs has implications for their dosage balance. We analyzed
the colocalization frequency of ohnologs based on chromatin interaction datasets
of seven human cell lines and found that ohnolog pairs exhibit higher spatial
proximity in 3D nuclear organization than other paralog pairs and than randomly
chosen ohnologs in the genome. We also found that colocalized ohnologs are more
resistant to copy number variations and more likely to be disease-associated
genes, which indicates a stronger dosage balance in ohnologs with high spatial
proximity. This phenomenon is further supported by the stronger similarity of
gene co-expression and of gene ontology terms of colocalized ohnologs. In
addition, for a large fraction of ohnologs, the spatial colocalization is
conserved in mouse cells, suggestive of functional constraint on their 3D
positioning in the nucleus. Identifying the molecular changes that lead to ecological specialization during
speciation is one of the major goals of molecular evolution. One question that
remains to be thoroughly investigated is whether ecological specialization
derives strictly from adaptive changes and their associated trade-offs, or from
conditionally neutral mutations that accumulate under relaxed selection. We used
whole-genome sequencing, genome annotation and computational analyses to
identify genes that have rapidly diverged between two incipient species of
Saccharomyces paradoxus that occupy different climatic regions along a
south-west to north-east gradient. As candidate loci for ecological
specialization, we identified genes that show signatures of adaptation and
accelerated rates of amino acid substitutions, causing asymmetric evolution
between lineages. This set of genes includes a glycyl-tRNA-synthetase, GRS2,
which is known to be transcriptionally induced under heat stress in the model
and sister species S. cerevisiae. Molecular modelling, expression analysis and
fitness assays suggest that the accelerated evolution of this gene in the
Northern lineage may be caused by relaxed selection. GRS2 arose during the
whole-genome duplication (WGD) that occurred 100 million years ago in the yeast
lineage. While its ohnolog GRS1 has been preserved in all post-WGD species, GRS2
has frequently been lost and is evolving rapidly, suggesting that the fate of
this ohnolog is still to be resolved. Our results suggest that the asymmetric
evolution of GRS2 between the two incipient S. paradoxus species contributes to
their restricted climatic distributions and thus that ecological specialization
derives at least partly from relaxed selection rather than a molecular trade-off
resulting from adaptive evolution. Comparative functional genomic studies require the proper identification of gene
orthologs to properly exploit animal biomedical research models. To identify
gene orthologs, comprehensive, conserved gene synteny analyses are necessary to
unwind gene histories that are convoluted by two rounds of early vertebrate
genome duplication, and in the case of the teleosts, a third round, the teleost
genome duplication (TGD). Recently, the genome of the spotted gar, a holostean
outgroup to the teleosts that did not undergo this third genome duplication, was
sequenced and applied as an orthology bridge to facilitate the identification of
teleost orthologs to human genes and to enhance the power of teleosts as
biomedical models. In this study, we apply the spotted gar orthology bridge to
help describe the gene history of the vertebrate TNFAIP8 family. Members of the
TNFAIP8 gene family have been linked to regulation of immune function and
homeostasis and the development of multiple cancer types. Through a conserved
gene synteny analysis, we identified zebrafish orthologs to human TNFAIP8L1 and
TNFAIP8L3 genes and two co-orthologs to human TNFAIP8L2, but failed to identify
an ortholog to human TNFAIP8. Through the application of the orthology bridge,
we determined that teleost orthologs to human TNFAIP8 genes were likely lost in
a genome inversion event after their divergence from their common ancestor with
spotted gar. These findings demonstrate the value of this enhanced approach to
gene history analysis and support the development of teleost models to study
complex questions related to an array of biomedical issues, including immunity
and cancer. |
What is TissueEnrich? | TissueEnrich is a tool that calculates tissue-specific gene enrichment in an input gene set. TissueEnrich can assign tissue identities to single cell clusters and differentiated embryonic stem cells. | SUMMARY: RNA-Seq data analysis results in lists of genes that may have a similar
function, based on differential gene expression analysis or co-expression
network analysis. While tools have been developed to identify biological
processes that are enriched in the genes sets, there remains a need for tools
that identify enrichment of tissue-specific genes. Therefore, we developed
TissueEnrich, a tool that calculates tissue-specific gene enrichment in an input
gene set. We demonstrated that TissueEnrich can assign tissue identities to
single cell clusters and differentiated embryonic stem cells.
AVAILABILITY AND IMPLEMENTATION: The TissueEnrich web application is freely
available at http://tissueenrich.gdcb.iastate.edu/. The R package is available
through Bioconductor at https://bioconductor.org/packages/TissueEnrich. Both the
web application and R package are for non-profit academic use under the MIT
license.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics
online. |
Describe OligoSTORM | OligoSTORM and OligoDNA-PAINT meld the Oligopaint technology for fluorescent in situ hybridization (FISH) with, respectively, Stochastic Optical Reconstruction Microscopy (STORM) and DNA-based Point Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) to enable in situ single-molecule super-resolution imaging of nucleic acids. Both strategies enable ≤20 nm resolution and are appropriate for imaging nanoscale features of the genomes of a wide range of species, including human, mouse, and fruit fly (Drosophila). | Author information:
(1)Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur,
Boston, MA, 02115, USA.
(2)Wyss Institute for Biologically Inspired Engineering, Harvard University,
Boston, MA, 02115, USA.
(3)Department of Systems Biology, Harvard Medical School, Boston, MA, 02115,
USA.
(4)Howard Hughes Medical Institute, Cambridge, MA, 02138, USA.
(5)Department of Chemistry and Chemical Biology, Harvard University, Cambridge,
MA, 02138, USA.
(6)Department of Developmental Biology, Stanford University, Stanford, CA,
94305, USA.
(7)Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
(8)Wyss Institute for Biologically Inspired Engineering, Harvard University,
Boston, MA, 02115, USA. [email protected].
(9)Department of Systems Biology, Harvard Medical School, Boston, MA, 02115,
USA. [email protected].
(10)Howard Hughes Medical Institute, Cambridge, MA, 02138, USA.
[email protected].
(11)Department of Chemistry and Chemical Biology, Harvard University, Cambridge,
MA, 02138, USA. [email protected].
(12)Department of Physics, Harvard University, Cambridge, MA, 02138, USA.
[email protected].
(13)Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur,
Boston, MA, 02115, USA. [email protected]. |
Which metabolic pathways have been associated with Systemic Lupus Erythematosus? | Genetic polymorphisms of the xenobiotic metabolic pathway involved in estrogen metabolism might contribute towards pathophysiology of systemic lupus erythematosus (SLE). According to the analysis on metabolic pathway, SLE could cause significant changes in unsaturated fatty acid and amino acid metabolism pathway. Results suggest reducing FLI1 in lupus decreases the pathogenicity of T cells by decreasing TCR-specific activation and IL-4 production in part through the modulation of glycosphingolipid metabolism | While the knowledge concerning the role of the immune system in many internal
disorders has grown rapidly in recent years, there are few methods to assess
immune system activation in clinical practice. Measurement of urine neopterin,
product of a metabolic pathway controlled by interferon-gamma, has been found
useful in many clinical conditions. The present study concerns neopterin
excretion in 157 patients with different internal disorders. As expected, we
found an increase in urine neopterin in patients with maligt tumors,
autoimmune disorders like systemic lupus erythematosus or inflammatory bowel
disease, and infections. Elevated neopterin levels were also observed in acute
pancreatitis and in acute myocardial infarction. In addition, significant
correlations between urine neopterin and zinc and neopterin and copper excretion
were found suggesting a physiological role of neopterin as urine antioxidant. Evaluation of: Chung CP, Avalos I, Oeser A et al. High prevalence of the
metabolic syndrome in patients with systemic lupus erythematosus: association
with disease characteristic and cardiovascular risk factors. Ann. Rheum. Dis.
66(2), 208-214 (2007). Systemic lupus erythematosus is associated with higher
rates of cardiovascular morbidity and mortality, related to accelerated
atherosclerosis. This additional clinical complication can be attributed to
traditional risk factors for atherosclerosis, use of corticosteroids and might
also be the result of inflammatory mechanisms, all of which are aggravated in
lupus patients. In this regard, inflammation is not only associated with
systemic lupus patients but is also present in patients with metabolic syndrome
and insulin resistance. The paper under evaluation examined the hypothesis that
patients with lupus have a higher prevalence of the metabolic syndrome and that
there is an association of the metabolic syndrome with other cardiovascular risk
factors and inflammation. Systemic Lupus erythematosus (SLE) is an autoimmune disease caused, in part, by
abnormalities in cells of the immune system including B and T cells. Genetically
reducing globally the expression of the ETS transcription factor FLI1 by 50% in
two lupus mouse models significantly improves disease measures and survival
through an unknown mechanism. In this study we analyze the effects of reducing
FLI1 in the MRL/lpr lupus prone model on T cell function. We demonstrate that
adoptive transfer of MRL/lpr Fli1(+/+) or Fli1(+/-) T cells and B cells into
Rag1-deficient mice results in significantly decreased serum immunoglobulin
levels in animals receiving Fli1(+/-) lupus T cells compared to animals
receiving Fli1(+/+) lupus T cells regardless of the genotype of co-transferred
lupus B cells. Ex vivo analyses of MRL/lpr T cells demonstrated that Fli1(+/-) T
cells produce significantly less IL-4 during early and late disease and
exhibited significantly decreased TCR-specific activation during early disease
compared to Fli1(+/+) T cells. Moreover, the Fli1(+/-) T cells expressed
significantly less neuraminidase 1 (Neu1) message and decreased NEU activity
during early disease and significantly decreased levels of glycosphingolipids
during late disease compared to Fli1(+/+) T cells. FLI1 dose-dependently
activated the Neu1 promoter in mouse and human T cell lines. Together, our
results suggest reducing FLI1 in lupus decreases the pathogenicity of T cells by
decreasing TCR-specific activation and IL-4 production in part through the
modulation of glycosphingolipid metabolism. Reducing the expression of FLI1 or
targeting the glycosphingolipid metabolic pathway in lupus may serve as a
therapeutic approach to treating lupus. The current study was conducted to elucidate the effect of genetic variations in
one-carbon metabolism on the epigenetic regulation of major histocompatibility
complex II transactivator (MHC2TA), reduced folate carrier 1 (RFC1/SLC19A1) and
human leukocyte antigen (HLA)-DR in systemic lupus erythematosus (SLE).
PCR-RFLP/AFLP, bisulfite-sequencing and real-time PCR approaches were used for
genetic, epigenetic and expression analysis respectively. SLE cases exhibited
elevated plasma homocysteine levels compared to healthy controls (24.93 ± 1.3
vs. 11.67 ± 0.48 μmol/l), while plasma folate levels showed no association (7.10
± 2.49 vs. 7.64 ± 2.09 ng/ml). The RFC1 80G>A polymorphism showed 1.32-fold risk
(95% CI: 1.02-1.72) for SLE, while glutamate carboxypeptidase II (GCPII) 1561C>T
showed reduced risk (OR: 0.47, 95% CI: 0.24-0.90). The expression of RFC1 (0.37
± 0.09 vs. 0.60 ± 0.17) and HLA-DR (0.68 ± 0.17 vs. 0.98 ± 0.02) was down
regulated in the SLE cases. The hypermethylation of RFC1 as observed in the
current study may contribute for its down regulation. Plasma folate and
thymidylate synthase (TYMS) 5'-UTR 28 bp tandem repeat showed an inverse
association with methylation of RFC1 and MHC2TA. SLE cases with
hypocomplementemia showed hypermethylation of RFC1, hypomethylation/up
regulation of MHC2TA and down regulation of HLA-DR. The hypermethylation of
MHC2TA and down regulation of RFC1, MHC2TA and HLA-DR were observed in
anti-cardiolipin antibody positive SLE cases. The up regulation of RFC1 and
HLA-DR was observed in anti-dsDNA antibody positive SLE cases. The
hypomethylation/upregulation of RFC1 and MHC2TA was observed in anti-RNP
antibody positive cases. To conclude, one-carbon genetic variants influence
epigenetic of MHC2TA and RFC1, thus contributing to phenotypic heterogeneity of
SLE. In view of documented evidence that catechol estrogen-DNA adducts serve as
epitopes for binding of anti-nuclear antibodies, genetic polymorphisms of the
xenobiotic metabolic pathway involved in estrogen metabolism might contribute
towards pathophysiology of systemic lupus erythematosus (SLE). To test this
hypothesis, a case-control study was conducted. Cytochrome P 450 1A1 (CYP1A1) m4
(OR: 4.93, 95% CI: 1.31-18.49), catecholamine-o-methyl transferase (COMT) H108L
(OR: 1.39, 95% CI: 1.03-1.88) and glutathione-S-transferase (GST) T1 null (OR:
1.83, 95% CI: 1.11- 3.01) variants showed association with SLE risk. SHEsis
web-based platform analysis showed mild to moderate linkage disequilibrium
between the CYP1A1 ml, m2 and m4 variants (D': 0.19-0.37). Among the different
haplotypes of CYP1A1, CAC-haplotype harboring CYP1A1 ml variant showed
association with SLE risk (OR: 1.46, 95% CI: 1.11-1.92). Multifactor
dimensionality reduction analysis (MDR) showed potential gene-gene interactions
between the phase II variants i.e. COMT H108L x GSTT1 null x GSTM1 null (p <
0.0001) and also between the phase II and I variants i.e. COMT H108L x GSTTI
null x CYP1A1 ml x CYP1A1 m2 in inflating the risk of SLE by 3.33-folds (95% CI:
2.30-4.82) and 4.00-folds (95% CI: 2.77-5.78), respectively. To conclude,
hyperinducibility of CYP1A1 due to ml and m4 variants and defective phase-II
detoxification due to COMT H108L and GSTT1 null variants increase the
susceptibility to SLE. Putatively functional polymorphisms of one-carbon and xenobiotic metabolic
pathways influence susceptibility for wide spectrum of diseases. The current
study was aimed to explore gene-gene interactions among these two metabolic
pathways in four diseases i.e. breast cancer, systemic lupus erythematosus
(SLE), coronary artery disease (CAD) and Parkinson's disease (PD). Multifactor
dimensionality reduction analysis was carried out on four case-control datasets.
Cross-talk was observed between one-carbon and xenobiotic pathways in breast
cancer (RFC 80 G>A, COMT H108L and TYMS 5'-UTR 28 bp tandem repeat) and SLE
(CYP1A1 m1, MTRR 66 A>G and GSTT1). Gene-gene interactions within one-carbon
metabolic pathway were observed in CAD (GCPII 1561 C>T, SHMT 1420 C>T and MTHFR
677 C>T) and PD (cSHMT 1420 C>T, MTRR 66 A>G and RFC1 80 G>A). These interaction
models showed good predictability of risk for PD (The area under the receiver
operating characteristic curve (C) = 0.83) and SLE (C = 0.73); and moderate
predictability of risk for breast cancer (C = 0.64) and CAD (C = 0.63).
Cross-talk between one-carbon and xenobiotic pathways was observed in diseases
with female preponderance. Gene-gene interactions within one-carbon metabolic
pathway were observed in diseases with male preponderance. |
What are the 3 main bacteria found in human milk? | Human milk is rich in diverse bacteria, particularly Staphylococcus, Streptococcus and Pseudomonas genera. | Contrary to long-held dogma, human milk is not sterile. Instead, it provides
infants a rich source of diverse bacteria, particularly microbes belonging to
the Staphylococcus, Streptococcus, and Pseudomonas genera. Very little is known
about factors that influence variation in the milk microbiome among women and
populations, although time postpartum, delivery mode, and maternal factors such
as diet and antibiotic use might be important. The origins of the bacteria in
milk are thought to include the maternal gastrointestinal tract (via an
entero-mammary pathway) and through bacterial exposure of the breast during
nursing. Currently, almost nothing is known about whether variation in microbe
consumption by the infant via human milk and that of the mammary gland, itself,
impacts short-term and/or long-term infant and maternal health although several
studies suggest this is likely. We urge the clinical and public health
communities to be patient, however, in order to allow human milk and lactation
researchers to first understand what constitutes 'normal' in terms of the milk
microbiome (as well as factors that impact microbial community structure) prior
to jumping the gun to investigate if and how this important source of microbes
impacts maternal and infant health. |
Which algorithm has been developed for trio-based benchmarking of variant calls? | Geck is a tool for trio-based comparative benchmarking tool of variant calls. It is a statistical mixture model for comparing two variant calling pipelines from genotype data they produce after running on individual members of a trio. | |
Which molecule is targeted by Caplacizumab? | Caplacizumab is anti-von Willebrand factor (VWF) antibody that blocks the interaction between VWF and platelets. It is used for treatment of acquired thrombotic thrombocytopenic purpura (aTTP). | Daily therapeutic plasma exchange (TPE) transformed the historically fatal
prognosis of acquired, anti-ADAMTS13 antibody-mediated thrombotic
thrombocytopenic purpura (TTP), leading to the current overall survival rates of
>80%. However, relapses occur in up to 40% of patients and refractory disease
with fatal outcomes still occurs. In this context, the introduction of rituximab
has probably been the second major breakthrough in TTP management. Rituximab is
now routinely recommended during the acute phase, typically in patients with a
suboptimal response to treatment, or even as frontline therapy, with high
response rates. In more severe patients, salvage strategies may include twice
daily TPE, pulses of cyclophosphamide, vincristine, as well as splenectomy in
the more desperate cases. In this life-threatening disease, relapses can be
efficiently prevented in patients with a severe acquired ADAMTS13 deficiency and
otherwise in remission with the use of rituximab. In the coming years, the TTP
therapeutic landscape should be enriched by original strategies stemming from
clinical experience and new agents that are currently being evaluated in large,
ideally international, clinical trials. Promising agents under evaluation
include N-acetylcysteine, bortezomib, recombit ADAMTS13 and caplacizumab, an
inhibitor of the glycoprotein-Ib/IX-von Willebrand factor axis. The thrombotic-thrombocytopenic purpura (TTP) is an acute, life-threatening
disease, characterised by enhanced platelet aggregation, disturbed
microcirculation and organ dysfunction. With the currently available treatment
(plasma exchange, infusions, corticosteroids) mortality ist still as high as
10-15 %. Recent, pathophysiology-based developments may improve the outcome. The
most promising candidates for future treatment of TTP are: rituximab for
termination of the autoimmune process, caplacizumab for prevention of
platelet-VWF-interaction, and recombit ADAMTS13 for replacement of the
inhibited or missing enzyme. Essentials Acquired thrombotic thrombocytopenic purpura (aTTP) is linked with
significant morbidity/mortality. Caplacizumab's effect on major thromboembolic
(TE) events, exacerbations and death was studied. Fewer caplacizumab-treated
patients had a major TE event, an exacerbation, or died versus placebo.
Caplacizumab has the potential to reduce the acute morbidity and mortality
associated with aTTP.
SUMMARY: Background Acquired thrombotic thrombocytopenic purpura (aTTP) is a
life-threatening autoimmune thrombotic microangiopathy. In spite of treatment
with plasma exchange and immunosuppression, patients remain at risk for
thrombotic complications, exacerbations, and death. In the phase II TITAN study,
treatment with caplacizumab, an anti-von Willebrand factor Nanobody® was shown
to reduce the time to confirmed platelet count normalization and exacerbations
during treatment. Objective The clinical benefit of caplacizumab was further
investigated in a post hoc analysis of the incidence of major thromboembolic
events and exacerbations during the study drug treatment period and thrombotic
thrombocytopenic purpura-related death during the study. Methods The
Standardized Medical Dictionary for Regulatory Activities (MedDRA) Query (SMQ)
for 'embolic and thrombotic events' was run to investigate the occurrence of
major thromboembolic events and exacerbations in the safety population of the
TITAN study, which consisted of 72 patients, of whom 35 received caplacizumab
and 37 received placebo. Results Four events (one pulmonary embolism and three
aTTP exacerbations) were reported in four patients in the caplacizumab group,
and 20 such events were reported in 14 patients in the placebo group (two acute
myocardial infarctions, one ischemic stroke, one hemorrhagic stroke, one
pulmonary embolism, one deep vein thrombosis, one venous thrombosis, and 13 aTTP
exacerbations). Two of the placebo-treated patients died from aTTP during the
study. Conclusion In total, 11.4% of caplacizumab-treated patients and 43.2% of
placebo-treated patients experienced one or more major thromboembolic events,
experienced an exacerbation, or died. This analysis shows the potential for
caplacizumab to reduce the risk of major thromboembolic morbidities and
mortality associated with aTTP. Daily therapeutic plasma exchange (TPE) transformed the historically fatal
prognosis of acquired, anti-ADAMTS13 antibody-mediated thrombotic
thrombocytopenic purpura (TTP), leading to the current overall survival rates of
>80%. However, relapses occur in up to 40% of patients and refractory disease
with fatal outcomes still occurs, typically within the first days of management.
In this context, the introduction of rituximab has been the second major
breakthrough in TTP management. Rituximab is now routinely recommended during
the acute phase, typically in patients with a suboptimal response to treatment,
and increasingly as frontline therapy, with high response rates in the following
weeks. In more severe patients, salvage strategies typically include twice daily
TPE, pulses of cyclophosphamide, as well as splenectomy in the more desperate
cases. In this life-threatening and debilitating disease, relapses can be
efficiently prevented in patients with a severe acquired ADAMTS13 deficiency and
otherwise in remission with the use of rituximab. In the coming years, the TTP
therapeutic landscape should be enriched by original strategies stemming from
clinical experience and new agents that are currently being evaluated in large,
international, clinical trials. Promising agents under evaluation include
caplacizumab (an inhibitor of the glycoprotein-Ib/IX-Von-Willebrand factor
axis), N-acetylcysteine, recombit ADAMTS13, and anti-plasmocyte compounds. Publisher: PATHOPHYSIOLOGISCHE DIFFERENZIERUNG: Das Krankheitsbild der
thrombotischen Mikroangiopathie (TMA) wird pathophysiologisch in verschiedene
Gruppen differenziert: TTP, HUS, aHUS, medikamentös induzierte,
Systemerkrankungs-assoziierte und posttherapeutische TMA. Diese Unterscheidung
ist auch im klinischen Alltag essenziell zur Auswahl der optimalen
Therapiestrategie.
KLINISCHE MANIFESTATION UND DIAGNOSESTELLUNG: Das kombinierte Auftreten einer
Thrombopenie und einer hämolytischen Anämie in Verbindung mit neurologischen
oder renalen Organschädigungen sollte an das Vorliegen einer TMA denken lassen.
Laborchemisch essenziell zu bestimmen sind ADAMTS-13 bei TTP, bakterieller bzw.
Shiga-Toxin-Nachweis beim STEC-HUS sowie spezifische Komplement-Untersuchungen
beim aHUS.
THERAPIE: Bis vor wenigen Jahren waren Plasmapheresen und ggf. immunsuppressive
Behandlungen die einzigen wirksamen Behandlungsansätze. Inzwischen gibt es
weitere Therapiemöglichkeiten: So steht der Antikörper Caplacizumab kurz vor der
Zulassung zur supportiven Therapie der TTP. Der Komplement-blockierende
Antikörper Eculizumab ist bereits zugelassen und besitzt einen festen
Stellenwert in der Behandlung des aHUS. Zudem hat Defibrotide 2016 von der
amerikanischen Food and Drug Administration (FDA) eine Zulassung zur Behandlung
des SOS/TMA-Syndroms erhalten. Thrombotic thrombocytopenic purpura (TTP) is characterized by microangiopathic
hemolytic anemia and a consumptive thrombocytopenia, as a result of severe
deficiency of ADAMTS13. The standard of care of the acute episode is treatment
with plasma exchange and immunosuppression. After the acute episode is resolved,
patients face a significant risk of relapse and long-term complications
associated with significant morbidity and even mortality. Novel treatments have
been under development and will be discussed in this review. Caplacizumab, a
obody that blocks the interaction between VWF and platelets, has shown
promising results in decreasing the time to recover from the acute events that
will hopefully translate into long-term clinical benefit for patients. In
addition, identifying biomarkers to allow us to better predict the risk for
relapse and the development of these long-term complications in patients with
TTP are a few of the challenges that require our attention moving forward. Ablynx, a Sanofi Company, has developed the anti-von Willebrand factor Nanobody®
caplacizumab (Cablivi™) for the treatment of acquired thrombotic
thrombocytopenic purpura (aTTP). Based on positive results in phase II and III
trials in patients with aTTP, caplacizumab was recently approved in the EU for
the treatment of adults experiencing an episode of aTTP, in conjunction with
plasma exchange and immunosuppression. This article summarizes the milestones in
the development of caplacizumab leading to this first approval. |
In which tissues is the lincRNA Xist expressed? | Relative expression of X-linked genes was examined in liver, kidney and brain tissue by real-time PCR in adult XX(Y)* and XY* males and XX females. X-chromosome inactive specific transcript (Xist) was expressed only in female adipose tissue. X-chromosome inactive specific transcript (Xist) was expressed only in female adipose tissue. It was also expressed in duodenum and testis. | Mammalian X-chromosome inactivation is thought to be controlled by the X
inactivation centre (XIC, X-controlling element -Xce-in mice). A human gene,
XIST and its mouse counterpart, Xist, which map to the XIC/Xce, are expressed
exclusively from inactive X chromosomes, suggesting their involvement in the
process of X-inactivation. We now report the presence of Xist/XIST transcripts
in newborn and adult mouse testes, and in human testicular tissue with normal
spermatogenesis, but not in the testes of patients who lack germ cells. Our
results indicate that while the X chromosome in males is active in somatic
cells, it undergoes inactivation during spermatogenesis. Expression of the X inactive-specific transcript (Xist) is thought to be
essential for the initiation of X chromosome inactivation and dosage
compensation during female embryo development. In the present study, we analyzed
the patterns of Xist transcription and the onset of X chromosome inactivation in
bovine preattachment embryos. Reverse transcription-polymerase chain reaction
(RT-PCR) revealed the presence of Xist transcripts in all adult female somatic
tissues evaluated. In contrast, among the male tissues examined, Xist expression
was detected only in testis. No evidence for Xist transcription was observed
after a single round of RT-PCR from pools of in vitro-derived embryos at the 2-
to 4-cell stage. Xist transcripts were detected as a faint amplicon at the
8-cell stage initially, and consistently thereafter in all stages examined up to
and including the expanded blastocyst stage. Xist transcripts, however, were
subsequently detected from the 2-cell stage onward after nested RT-PCR.
Preferential [3H]thymidine labeling indicative of late replication of one of the
X chromosomes was noted in female embryos of different developmental ages as
follows: 2 of 7 (28.5%) early blastocysts, 6 of 13 (46.1%) blastocysts, 8 of 11
(72.1%) expanded blastocysts, and 14 of 17 (77.7%) hatched blastocysts. These
results suggest that Xist expression precedes the onset of late replication in
the bovine embryo, in a pattern compatible with a possible role of bovine Xist
in the initiation of X chromosome inactivation. Sex hormones are likely to be involved in sex differences in adipose tissue
distribution. To test whether estrogen regulates genes expressed in the adipose
tissue in a site-specific manner, we studied the effect of exogenous estradiol
on the gene expression in visceral and subcutaneous adipose tissues of male
ob/ob mice. We screened genes expressed in a site- and sex-specific manner, and
genes that were affected by exogenous estradiol by DNA chip analysis. They were
verified by real-time PCR. Myosin heavy chain 2B (Myh4) and phosphoglycerate
mutase muscle-specific subunit (Pgam) were expressed specifically in the
subcutaneous adipose tissue, and uroplakin IIIb (UP3) was expressed specifically
in the visceral adipose tissue. DEAD-box Y RNA helicase (DBY) and eukaryotic
initiation factor 2 gamma Y (eIF2gamma Y) were expressed only in male adipose
tissue. X-chromosome inactive specific transcript (Xist) was expressed only in
female adipose tissue. When estradiol was subcutaneously administrated to male
mice, the expression of monocyte-chemoattractant protein-1 (MCP-1) and androgen
receptor (AR) genes was regulated in a site-specific manner. The difference in
the amount of estrogen receptor did not account for the site-specific effect of
estrogen. Our findings show that estrogen affects the expression of some
adipocyte genes in a site-specific manner. AIM: We hypothesized that patients with Klinefelter's syndrome (KS) not only
undergo X inactivation, but also that genes escape from inactivation. Their
transcripts would constitute a significant difference, as male metabolism is not
adapted to a 'female-like' gene dosage. We evaluated the expression of selected
X-linked genes in our 41, XX(Y)* male mice to determine whether these genes
escape inactivation and whether tissue-specific differences occur.
METHODS: Correct X inactivation was identified by Xist expression. Relative
expression of X-linked genes was examined in liver, kidney and brain tissue by
real-time PCR in adult XX(Y)* and XY* males and XX females.
RESULTS: Expression of genes known to escape X inactivation was analysed.
Relative mRNA levels of Pgk1 (control, X inactivated), and the genes Eif2s3x,
Kdm5c, Ddx3x and Kdm6a escaping from X inactivation were quantified from liver,
kidney and brain. Pgk1 mRNA expression showed no difference, confirming correct
X inactivation. In kidney and liver, XX(Y)* males resembled the female
expression pattern in all four candidate genes and were distinguishable from XY*
males. Contrastingly, in brain tissue XX(Y)* males expressed all four genes
higher than male and female controls.
CONCLUSION: Altered expression of genes escaping X inactivation probably
contributes directly to the XX(Y)* phenotype. An adjustment of sex ratio of offspring to the conditions present at conception
is seen in many mammals including horses. This depends on preferential survival
of male embryos under conditions of high energy intake. In several species,
growth factors including insulin like growth factor (IGF)-1 have been shown to
promote embryonic development by decreasing apoptosis and increasing cell
proliferation. We hypothesized that sex-related differences in IGF-1 expression
in equine embryos during the phase of maternal recognition of pregcy might
exist and thus contribute to preferential survival of embryos from either of
both sexes under specific environmental conditions. Insulin like growth factor-1
mRNA expression of in vivo-produced equine embryos on different days of
pregcy (Day 8, N = 6; Day 10, N = 8; Day 12, N = 14) was analyzed. Insulin
like growth factor-1 mRNA expression was evaluated by reverse transcription
quantitative polymerase chain reaction. The sex of the embryo was determined by
detection of X-inactivation specific transcript (Xist) RNA and equine sex
determining region of the Y chromosome DNA. Embryos positive for Xist expression
were classified as female, and Xist negative and equine sex determining region
of the Y chromosome positive embryos were classified as male. From 28 embryos
tested, 15 (54%) showed positive Xist expression and were thus classified as
female. Insulin like growth factor-1 mRNA expression was influenced by sex (P =
0.01) but not by day of pregcy (relative expression of IGF-1 in relation to
β-actin, Day 8: male 5.1 ± 2.1, female 11.4; Day 10: male 5.2 ± 1.6, female 17.4
± 6.7; Day 12: male 2.6 ± 0.3, female 11.6 ± 2.4). Results demonstrate an
increased expression of IGF-1 in female equine embryos. Sex-related influences
on expression of the IGF system are probably related to a gradual X chromosome
inactivation. |
Which is the main component of the Lewy body? | Lewy bodies comprise of aggregated intracellular vesicles and proteins and α-synuclein is reported to be a major protein component. | Neuronal loss in specific brain regions and neurons with intracellular
inclusions termed Lewy bodies are the pathologic hallmark in both Parkinson's
disease (PD) and dementia with Lewy bodies (DLB). Lewy bodies comprise of
aggregated intracellular vesicles and proteins and α-synuclein is reported to be
a major protein component. Using human brain tissue from control, PD and DLB and
light and confocal immunohistochemistry with antibodies to superoxide dismutase
2 as a marker for mitochondria, α-synuclein for Lewy bodies and βIII Tubulin for
microtubules we have examined the relationship between Lewy bodies and
mitochondrial loss. We have shown microtubule regression and mitochondrial and
nuclear degradation in neurons with developing Lewy bodies. In PD, multiple Lewy
bodies were often observed with α-synuclein interacting with DNA to cause marked
nuclear degradation. In DLB, the mitochondria are drawn into the Lewy body and
the mitochondrial integrity is lost. This work suggests that Lewy bodies are
cytotoxic. In DLB, we suggest that microtubule regression and mitochondrial loss
results in decreased cellular energy and axonal transport that leads to cell
death. In PD, α-synuclein aggregations are associated with intact mitochondria
but interacts with and causes nuclear degradation which may be the major cause
of cell death. The pesticide rotenone has been shown to cause systemic inhibition of
mitochondrial complex I activity, with consequent degeneration of dopamine
neurons along the nigrostriatal pathway, as observed in Parkinson's disease
(PD). Recently, intracranial infusion of rotenone was found to increase the
protein levels of the Lewy body constituents, α-synuclein and small
ubiquitin-related modifier-1(SUMO-1), in the lesioned hemisphere of the mouse
brain. These findings are supportive of a mouse model of PD, but information
about the dopamine-synthesizing enzyme, tyrosine hydroxylase (TH), an essential
marker of dopaminergic status, was not reported. Clarification of this issue is
important because an intracranial rotenone mouse model of Parkinson's disease
has not been established. Towards this end, the present study examined the
effects of intracranial rotenone treatment on TH and α-synuclein
immunohistochemistry in addition to forelimb motor function. Mice were
unilaterally infused with either vehicle or rotenone (2μg/site) in both the
medial forebrain bundle and the substantia nigra. The forelimb asymmetry
(cylinder) test indicated a significant decrease in use of the contralateral
forelimb in lesioned animals as compared to the sham group. Densitometric
analysis revealed a significant depletion of TH immunofluorescence within the
ipsilateral striatum and substantia nigra of lesioned animals. Moreover, a
significant bilateral increase in α-synuclein immunofluorescence was found in
the substantia nigra of lesioned mice, as compared to control animals. These
findings indicate that this intracranial rotenone mouse model will be useful for
studies of neurodegenerative disorders such as PD. INTRODUCTION: Parkinson's disease (PD) is characterized by bradykinesia,
rigidity, postural instability and tremor. Several pathologic processes can
produce this syndrome, but neurodegeneration accompanied by neuronal inclusions
composed of α-synuclein (Lewy bodies) is considered the typical pathologic
correlate of PD.
METHODS: The neuropathologic features of PD are reviewed based upon personal
experience and review of the literature. Molecular pathology of PD is summarized
from cell biological and animal studies.
RESULTS: The pathologic feature that correlates with signs and symptoms of PD is
neuronal loss in the substantia nigra with dopaminergic denervation of the
striatum. Neuronal degeneration in the substantia nigra preferentially affects
the ventrolateral cell group that projects to posterolateral putamen and is
accompanied by formation of Lewy bodies composed of aggregated α-synuclein. Some
patients with PD are found at autopsy to have other pathologic processes, such
as multiple system atrophy, progressive supranuclear palsy and cerebrovascular
disease (vascular Parkinsonism). The peripheral autonomic nervous system is also
affected. The triggering event in PD is unknown, but recent studies suggest a
role for loss of nuclear membrane integrity. Once α-synuclein aggregates forms,
evidence supports cell-to-cell propagation.
CONCLUSION: PD is a multisystem synucleinopathy caused by poorly characterized
genetic and environmental factors that produces degeneration in selectively
vulnerable neuronal populations. It took almost 100 years before a meaningful advance occurred in any basic
science understanding of Parkinson disease (PD) following James Parkinson's
description in 1817. The Lewy body was described in 1912, and the substantia
nigra was found to be depigmented with neuronal loss and gliosis in 1919. The
link between dopamine and PD began in 1957, 140 years after Parkinson's Essay.
Arvid Carlsson and Oleh Hornykiewicz were the major pioneers. The revolutionary
therapeutic breakthrough was the introduction of high dosage levodopa therapy by
George Cotzias in 1967. Following 40 years of the dopa/dopamine era, we have
entered the era of alpha-synuclein, the protein present in Lewy bodies. Heiko
Braak found that alpha-synuclein accumulates initially in the olfactory system
and lower brainstem and then travels in an anatomic pattern to involve other
regions of the brain and thereby cause progressive symptoms. Alpha-synuclein was
somehow converted to a rogue protein. Where this originates and how it is
propagated are under intense investigation. At the same time that the
alpha-synuclein era was developing, clinical advances took place by recognizing
PD as hosting a wide variety of nonmotor features with eventual cognitive
impairment in many. Therapeutics has also evolved. Although the most effective
therapy for the motor features remains levodopa, surgical approaches and drugs
for nonmotor problems continue to expand our ability to treat people with PD. We
can expect therapeutic advances in neuroprotection as the basic science
discoveries uncovered in the alpha-synuclein era are translated into effective
treatments. |
What forms part of the senescence associated secretory phenotype, or SASP? | The diverse arrays of proteins secreted by senescent cells have been described to influence aging and to have both pro-tumorigenic and anti-tumorigenic influences on the surrounding microenvironment. Further characterization of these proteins, known as the senescence-associated secretory phenotype (SASP), and their regulators is required to understand and further manipulate such activities. The senescence-associated secretory phenotype (SASP) is characterized by IL1B, CXCL8, CCL2, TNF, CCL27 and other pro-inflammatory factors including a novel SASP component CLEC11A. | Here we show that pemetrexed-treated mesothelioma cells undergo accelerated
senescence. This is characterized by the secretion of proinflammatory and
mitogenic cytokines, reminiscent of an SASP (senescence-associated secretory
phenotype). Conditioned media from senescent MPM (maligt pleural
mesothelioma) cells trigger the emergence of EMT
(epithelial-to-mesenchymal)-like, clonogenic and chemoresistant cell
subpopulations, expressing high levels of ALDH (aldehyde dehydrogenase) activity
(ALDH(bright) cells). We show by fluorescence-activated cell sorting of purified
ALDH(bright) and ALDH(low) cells, that both cell-autonomous and
cell-non-autonomous mechanisms converge to maintain the SASP-induced, EMT-like
cell subpopulations. Chemoresistant ALDH(bright) cells exist within primary MPM
specimens and enrichment for ALDH(bright) cells correlates with an earlier tumor
onset into NOD/SCID mice. We show that RAS(v12) expression induces SASP-like
changes in untransformed human mesothelial cells, and that p53 ablation
increases the effect of RAS(v12) expression. We identify STAT3 activation as a
crucial event downstream to SASP signaling. In fact, small hairpin RNA-mediated
ablation of STAT3 deeply attenuates the induction of EMT genes and the increase
of ALDH(bright) cells induced by SASP-cytokines. This strongly affects the
chemoresistance of MPM cells in vitro and leads to anticancer effects in vivo. Endothelial cell senescence is characterized by acquisition of
senescence-associated secretory phenotype (SASP), able to promote inflammaging
and cancer progression. Emerging evidence suggest that preventing SASP
development could help to slow the rate of aging and the progression of
age-related diseases, including cancer. Aim of this study was to evaluate
whether and how adalimumab, a monoclonal antibody directed against tumor
necrosis factor-α (TNF-α), a major SASP component, can prevent the SASP. A
three-pronged approach has been adopted to assess the if adalimumab is able to:
i) modulate a panel of classic and novel senescence- and SASP-associated markers
(interleukin [IL]-6, senescence associated-β-galactosidase, p16/Ink4a,
plasminogen activator inhibitor 1, endothelial nitric oxide synthase,
miR-146a-5p/Irak1 and miR-126-3p/Spred1) in human umbilical vein endothelial
cells (HUVECs); ii) reduce the paracrine effects of senescent HUVECs' secretome
on MCF-7 breast cancer cells, through wound healing and mammosphere assay; and
iii) exert significant decrease of miR-146a-5p and increase of miR-126-3p in
circulating angiogenic cells (CACs) from psoriasis patients receiving adalimumab
in monotherapy.TNF-α blockade associated with adalimumab induced significant
reduction in released IL-6 and significant increase in eNOS and miR-126-3p
expression levels in long-term HUVEC cultures.A significant reduction in
miR-146a-5p expression levels both in long-term HUVEC cultures and in CACs
isolated from psoriasis patients was also evident. Interestingly, conditioned
medium from senescent HUVECs treated with adalimumab was less consistent than
medium from untreated cells in inducing migration- and mammosphere- promoting
effects on MCF-7 cells.Our findings suggest that adalimumab can induce
epigenetic modifications in cells undergoing senescence, thus contributing to
the attenuation of SASP tumor-promoting effects. Age-related accumulation of ploidy changes is associated with decreased
expression of genes controlling chromosome segregation and cohesin functions. To
determine the consequences of whole chromosome instability (W-CIN) we
down-regulated the spindle assembly checkpoint component BUB1 and the mitotic
cohesin SMC1A, and used four-color-interphase-FISH coupled with BrdU
incorporation and analyses of senescence features to reveal the fate of W-CIN
cells. We observed significant correlations between levels of not-diploid cells
and senescence-associated features (SAFs). W-CIN induced DNA double strand
breaks and elevated oxidative stress, but caused low apoptosis. SAFs of W-CIN
cells were remarkably similar to those induced by replicative senescence but
occurred in only 13 days versus 4 months. Cultures enriched with not-diploid
cells acquired a senescence-associated secretory phenotype (SASP) characterized
by IL1B, CXCL8, CCL2, TNF, CCL27 and other pro-inflammatory factors including a
novel SASP component CLEC11A. These findings suggest that W-CIN triggers
premature senescence, presumably to prevent the propagation of cells with an
abnormal DNA content. Cells deviating from diploidy have the ability to
communicate with their microenvironment by secretion of an array of signaling
factors. Our results suggest that aneuploid cells that accumulate during aging
in some mammalian tissues potentially contribute to age-related pathologies and
inflammation through SASP secretion. The diverse arrays of proteins secreted by senescent cells have been described
to influence aging and to have both pro-tumorigenic and anti-tumorigenic
influences on the surrounding microenvironment. Further characterization of
these proteins, known as the senescence-associated secretory phenotype (SASP),
and their regulators is required to understand and further manipulate such
activities. The use of high-throughput technology allows us to obtain visual and
quantitative data on a large number of samples quickly and easily. Not only is
this an invaluable tool for conducting large-scale RNAi or compound screenings,
but also allows rapid validation of candidates of interest. Here, we describe
how we use the Widefield High-Content Analysis Systems to characterize the
phenotypes of cells following modulation by potential regulators of
Oncogene-Induced Senescence (OIS) by measuring numerous markers of senescence,
including the SASP. This approach can be also used to screen for siRNA able to
perturb the expression of SASP components during OIS. Anti-senescence therapies, such as drugs that specifically kill senescent cells,
to stave off ageing are currently under investigation. While these interventions
show promise, their potential pitfalls are discussed herein. We have shown that
the mitochondria are essential for development of senescence and many of the
associated phenotypes, including the often detrimental senescence-associated
secretory phenotype (SASP). Here, we disentangle many ways in which the
mitochondria may influence senescence and development of the SASP and focus on
possible pathways that could be exploited for future generation of
anti-senescence therapies with a clear aim; to specifically eliminate the
problematic features of senescent cells, while maintaining their beneficial
characteristics. Cellular senescence is a permanent growth arrest in cells with damage or stress
that could lead to transformation. Some tumor cells also undergo senescence in
response to chemotherapy. Senescent cells secrete cytokines and other factors of
the senescence-associated secretory phenotype (SASP) that contribute to tumor
suppression by enforcing arrest and recruiting immune cells that remove these
damaged or oncogene-expressing cells from organisms. However, some cells can
develop a SASP comprising factors that are immunosuppressive and protumorigenic
by paracrine mechanisms. Likewise, the SASP in treated cancers can either
contribute to durable responses or drive relapse. Here, we discuss the studies
that have demonstrated a complex and often conflicting role for the SASP in
tumorigenesis and treatment response. |
How many pseudogenes are contained in the C. elegans genome? | Evidence suggests that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. At least 4% of the annotated C. elegans genes can be recognized as pseudogenes simply from closer inspection of the sequence data. Thus out of 18000 transcripts, around 3500 are expected to be pseudogenes. | Only a minority of the genes, identified in the Caenorhabditis elegans genome
sequence data by computer analysis, have been characterized experimentally. We
attempted to determine the expression patterns for a random sample of the
annotated genes using reporter gene fusions. A low success rate was obtained for
evolutionarily recently duplicated genes. Analysis of the data suggests that
this is not due to conditional or low-level expression. The remaining
explanation is that most of the annotated genes in the recently duplicated
category are pseudogenes, a proportion corresponding to 20% of all of the
annotated C. elegans genes. Further support for this surprisingly high figure
was sought by comparing sequences for families of recently duplicated C. elegans
genes. Although only a preliminary analysis, clear evidence for a gene having
been recently inactivated by genetic drift was found for many genes in the
recently duplicated category. At least 4% of the annotated C. elegans genes can
be recognized as pseudogenes simply from closer inspection of the sequence data.
Lessons learned in identifying pseudogenes in C. elegans could be of value in
the annotation of the genomes of other species where, although there may be
fewer pseudogenes, they may be harder to detect. Messenger RNAs (mRNAs) that contain premature translation termination codons
(PTCs) are targeted for rapid degradation in all eukaryotes tested. The
mechanisms of nonsense-mediated mRNA decay (NMD) have been described in
considerable detail, but the biological roles of NMD in wild-type organisms are
poorly understood. mRNAs of wild-type organisms known to be degraded by NMD
("natural targets" of NMD) include by-products of regulated alternative
splicing, out-of-frame mRNAs derived from unproductive gene rearrangements,
cytoplasmic pre-mRNAs, endogenous retroviral and transposon RNAs, and mRNAs
having upstream open reading frames or other unusual sequence features. NMD may
function to eliminate aberrant PTC-containing mRNAs in order to protect cells
from expression of potentially deleterious truncated proteins. Pseudogenes are
nonfunctional genes or gene fragments that accumulate mutations through genetic
drift. Such mutations will often introduce shifts of reading frame and/or PTCs,
and mRNAs of expressed pseudogenes may thus be substrates of NMD. We demonstrate
that mRNAs expressed from C. elegans pseudogenes are degraded by NMD and discuss
possible implications for both mRNA surveillance and protein evolution. We
describe an expressed pseudogene that encodes a small nucleolar RNA (snoRNA)
within an intron and suggest this represents an evolutionary intermediate
between snoRNA-encoding host genes that do or do not encode proteins. Author information:
(1)Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen
Institute for Molecular Sciences, Department of Neurobiology, University of
Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address:
[email protected].
(2)Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen
Institute for Molecular Sciences, Department of Neurobiology, University of
Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address:
[email protected].
(3)Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen
Institute for Molecular Sciences, Department of Neurobiology, University of
Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address:
[email protected].
(4)Laboratory of Molecular Brain Research, A. I. Virtanen Institute for
Molecular Sciences, Department of Neurobiology, University of Eastern Finland,
Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address:
[email protected].
(5)Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen
Institute for Molecular Sciences, Department of Neurobiology, University of
Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address:
[email protected].
(6)Laboratory of Functional Genomics and Bioinformatics, A. I. Virtanen
Institute for Molecular Sciences, Department of Neurobiology, University of
Eastern Finland, Yliopistonranta 1, 70211 Kuopio, Finland. Electronic address:
[email protected]. |
What is a Aquaporin channel? | Aquaporins are membrane channels expressed in almost every organism and involved in the bidirectional transfer of water and small solutes across cell membranes. Aquaporins have important biological roles and have been implicated in several pathophysiological conditions suggesting a great translational potential in aquaporin-based diagnostics and therapeutics. | Water is the major component of cells and tissues throughout all forms of life.
Fluxes of water and solutes through cell membranes and epithelia are essential
for osmoregulation and energy homeostasis. Aquaporins are membrane channels
expressed in almost every organism and involved in the bidirectional transfer of
water and small solutes across cell membranes. Aquaporins have important
biological roles and have been implicated in several pathophysiological
conditions suggesting a great translational potential in aquaporin-based
diagnostics and therapeutics. Detecting aquaporin function is critical for
assessing regulation and screening for new activity modulators that can prompt
the development of efficient medicines. Appropriate methods for functional
analysis comprising suitable cell models and techniques to accurately evaluate
water and solute membrane permeability are essential to validate aquaporin
function and assess short-term regulation. The present review describes
established assays commonly used to assess aquaporin function in cells and
tissues, as well as the experimental biophysical strategies required to reveal
functional regulation and identify modulators, the first step for aquaporin drug
discovery. |
What is cluster of differentiation? | Cluster of Differentiation (CD) are cellular antigens used to identify cell populations, such as T-lymphocyte populations and macrophages. | Objective To evaluate the role of macrophage infiltration in the differentiation
process of ureteral polyps and cancers. Methods This retrospective
immunohistochemical study analysed archival samples of pathologically-confirmed
specimens of low- and high-grade ureteral cancer, ureteral papilloma and
ureteral polyps. The samples were immunohistochemically stained for cluster of
differentiation (CD)4, CD8, CD16, CD25, CD56 and CD68 using immunofluorescence
in order to identify different T-lymphocyte populations and macrophages. Results
A total of 70 specimens were included in the analysis: 21 specimens of ureteral
cancer, 17 specimens of ureteral papilloma, and 32 specimens of ureteral polyps.
The largest proportion of CD4+CD25+ regulatory T cells was observed in the
low-grade ureteral cancer group and almost none were observed in ureteral
papillomas. The largest proportion of CD8+ cytotoxic T-lymphocytes was observed
in the ureteral polyps. The largest proportion of CD56+ natural killer cells was
detected in the ureteral polyps, with very low levels observed in the other
three groups. The largest proportion of CD16+CD68+ macrophages was observed in
the high-grade ureteral cancer group, which was significantly higher than that
observed in the ureteral papillomas. Conclusions This study revealed that
CD16+CD68+ macrophages appear to participate in ureteral neoplastic
transformation. |
List two medication included in the Juluca pill. | Juluca® pill includes dolutegravir and rilpivirine. It is the first two-drug single-tablet regimen (STR) to be approved for the treatment of HIV-1 infection in adults. | |
Which tool has been developed for tagging biomedical concepts via interactive learning? | ezTag is a web-based annotation tool that supports annotating a wide variety of biological concepts with or without pre-existing training data. It allows curators to perform annotation and provide training data with humans in the loop. ezTag supports both abstracts in PubMed and full-text articles in PubMed Central. It also provides lexicon-based concept tagging as well as the state-of-the-art pre-trained taggers such as TaggerOne, GNormPlus and tmVar. ezTag is freely available at http://eztag.bioqrator.org. | Recently, advanced text-mining techniques have been shown to speed up manual
data curation by providing human annotators with automated pre-annotations
generated by rules or machine learning models. Due to the limited training data
available, however, current annotation systems primarily focus only on common
concept types such as genes or diseases. To support annotating a wide variety of
biological concepts with or without pre-existing training data, we developed
ezTag, a web-based annotation tool that allows curators to perform annotation
and provide training data with humans in the loop. ezTag supports both abstracts
in PubMed and full-text articles in PubMed Central. It also provides
lexicon-based concept tagging as well as the state-of-the-art pre-trained
taggers such as TaggerOne, GNormPlus and tmVar. ezTag is freely available at
http://eztag.bioqrator.org. |
Which cells produce Interleukin 17A? | Interleukin (IL)-17A is secreted from T helper type 17 (TH17) cells. | Millions of children are affected by different neurodevelopmental disorders, out
of which autism spectrum disorder (ASD) poses a major hurdle to normal life
style due to associated behavioral abnormalities. Several studies have shown an
increased expression/release of Th17 related cytokine, IL-17A in ASD. IL-17A may
enhance neuroinflammation via its IL-17A receptor, i.e. IL-17RA expressed in
immune cells (such as monocytes) of autistic children. Increased oxidative
stress has been implicated in a number of neuropsychiatric disorders including
ASD. However, whether IL-17A/IL-17RA signaling contributes to oxidative
inflammation in monocytes of autistic children has not been explored previously.
With this background, we performed this study in peripheral monocytes of ASD
patients and age-matched typically developing children. Our study shows that ASD
individuals have increased IL-17RA expression in monocytes which is associated
with increased nuclear factor kappa-light-chain-enhancer of activated B cells
(NFκB) pathway and inducible nitric oxide synthase (iNOS)/nitrotyrosine
expression as compared to typically developing children. Moreover, in vitro
activation of IL-17 receptor by IL-17A in monocytes isolated from ASD
individuals leads to enhanced iNOS expression via NFκB pathway. IL-17RA antibody
treatment in vitro reversed IL-17A-induced increase in NFκB and
iNOS/nitrotyrosine expression in monocytes isolated from ASD subjects. These
data connect increased IL-17A/IL-17RA signaling in ASD patients with enhanced
oxidative inflammation in monocytes. Therefore, IL-17 receptor signaling in
monocytes may potentiate the effects of IL-17A released by other immune cells
and may aggravate neuroinflammation in ASD. Our study further suggests that
blockade of IL-17A/IL-17 receptor signaling may be beneficial in the children
with ASD. |
Is durvalumab used for lung cancer treatment? | Yes, Durvalumab is an anti-PDL-1 antibody that is used for treatment of non-small-cell lung cancer. | A new approach to the management of non-small-cell lung cancer (NSCLC) has
recently emerged that works by manipulating the immune checkpoint controlled by
programmed death receptor 1 (PD-1) and its ligand programmed death ligand 1
(PD-L1). Several drugs targeting PD-1 (pembrolizumab and nivolumab) or PD-L1
(atezolizumab, durvalumab, and avelumab) have been approved or are in the late
stages of development. Inevitably, the introduction of these drugs will put
pressure on healthcare systems, and there is a need to stratify patients to
identify those who are most likely to benefit from such treatment. There is
evidence that responsiveness to PD-1 inhibitors may be predicted by expression
of PD-L1 on neoplastic cells. Hence, there is considerable interest in using
PD-L1 immunohistochemical staining to guide the use of PD-1-targeted treatments
in patients with NSCLC. This article reviews the current knowledge about PD-L1
testing, and identifies current research requirements. Key factors to consider
include the source and timing of sample collection, pre-analytical steps (sample
tracking, fixation, tissue processing, sectioning, and tissue prioritization),
analytical decisions (choice of biomarker assay/kit and automated staining
platform, with verification of standardized assays or validation of
laboratory-devised techniques, internal and external quality assurance, and
audit), and reporting and interpretation of the results. This review addresses
the need for integration of PD-L1 immunohistochemistry with other tests as part
of locally agreed pathways and protocols. There remain areas of uncertainty, and
guidance should be updated regularly as new information becomes available. Recently developed anti-tumour therapies targeting immune checkpoints include
tremelimumab and durvalumab. These agents have incompletely characterised side
effect profiles. The authors report a 68-year-old man treated for non-small cell
lung cancer (NSCLC) with a combination of tremelimumab and durvalumab. After
treatment he developed diplopia, ptosis, fatigue, weakness, and an inflammatory
myopathy affecting the extraocular muscles requiring hospitalisation.
Electromyography (EMG) testing and muscle biopsy suggested inflammatory myopathy
without sign of myasthenia. Within 1 month of withdrawal of cancer therapies and
initiation of oral steroid therapy, ocular and systemic symptoms had resolved.
This notable adverse effect has not been previously described for these drugs
administered singly or in combination, and ophthalmologists should be aware of
this presentation in patients treated with these agents. Publisher: Az immunellenõrzõpont-gátló kezelés forradalmian új, hatékony terápia
tüdõrákban is, egyéb rosszindulatú megbetegedésekhez hasonlóan. A dohányzással
összefüggõ tüdõrák a megbetegedések döntõ többségét képviseli; magas szomatikus
mutációs rátája és fokozott immunogenitása összefügg az immunterápia
hatékonyságával. A PD-1-gátló vegyületek közül a nivolumab és pembrolizumab, a
PD-L1-gátlók közül az atezolizumab már törzskönyvezett indikáció tüdõrákban. Az
avelumab és a durvalumab szintén ígéretes kezelési lehetõség. Másod-, illetõleg
többedvonalban a nivolumab és az atezolizumab PD-L1-expresszió ismerete nélkül
is alkalmazható, míg a pembrolizumab PD-L1-pozitivitás esetén. Mérföldkõ a nem
kissejtes tüdõrák (NSCLC) kezelésében a ≥50%-os PD-L1-expresszió esetén a
pembrolizumab elsõ vonalbeli alkalmazásának lehetõsége a KEYNOTE 024-es
vizsgálat eredménye alapján. Ebben a szelektált betegcsoportban a pembrolizumab
adásával csaknem megkétszerezõdött progressziómentes túlélés a standard kezelési
karhoz képest, és a teljes túlélés is jelentõsen javult, lényegesen jobb
toxicitási profil mellett. Ennek megfelelõen új terápiás standardról
beszélhetünk az elõrehaladott NSCLC elsõ vonalbeli kezelésében. Az
immunellenõrzõpont-gátlókkal számos egyéb klinikai vizsgálat is folyik
tüdõrákban citotoxikus kemoterápiával kombinálva, illetõleg adjuváns
indikációban, célzott terápiával kombinálva. Assessment of programmed cell death ligand 1 (PD-L1) immunohistochemical
staining is used for decision on treatment with programmed cell death 1 and
PD-L1 checkpoint inhibitors in lung adenocarcinomas and squamous cell
carcinomas. This study aimed to compare the staining properties of tumor cells
between the antibody clones 28-8, 22C3, SP142, and SP263 and investigate
interrater variation between pathologists to see if these stainings can be
safely evaluated in the clinical setting. Using consecutive sections from a
tissue microarray with tumor tissue from 55 resected lung cancer cases, staining
with five PD-L1 assays (28-8 from two different vendors, 22C3, SP142, and SP263)
was performed. Seven pathologists individually evaluated the percentage of
positive tumor cells, scoring each sample applying cutoff levels used in
clinical studies: <1% positive tumor cells (score 0), 1-4% (score 1), 5-9%
(score 2), 10-24% (score 3), 25-49% (score 4), and >50% positive tumor cells
(score 5). Pairwise analysis of antibody clones showed weighted kappa values in
the range of 0.45-0.91 with the highest values for comparisons with 22C3 and
28-8 and the lowest involving SP142. Excluding SP142 resulted in kappa
0.75-0.91. Weighted kappa for interobserver variation between pathologists was
0.71-0.96. Up to 20% of the cases were differently classified as positive or
negative by any pathologist compared with consensus score using ≥1% positive
tumor cells as cutoff. A significantly better agreement between pathologists was
seen using ≥50% as cutoff (0-5% of cases). In conclusion, the concordance
between the PD-L1 antibodies 22C3, 28-8 and SP263 is relatively good when
evaluating lung cancers and suggests that any one of these assays may be
sufficient as basis for decision on treatment with nivolumab, pembrolizumab, and
durvalumab. The scoring of the pathologist presents an intrinsic source of error
that should be considered especially at low PD-L1 scores. Immune checkpoint inhibitors (ICI) are now a therapeutic option for advanced
non-small cell lung cancer (NSCLC) patients. ICI, such as the PD-1 inhibitors
nivolumab and pembrolizumab and the PD-L1 inhibitor atezolizumab, have already
been marketed for the treatment of pretreated patients with advanced NSCLC.
Other notable PD-L1 inhibitors under development include avelumab and
durvalumab. Areas covered: This article reviews literature on durvalumab
development, from the preclinical data to the results of phase III clinical
trials, whether published or presented at international scientific conferences.
Ongoing clinical trials were also reviewed. Expert opinion: Early phase trials
of durvalumab monotherapy (and in combination) have demonstrated activity in
advanced NSCLC patients and it has demonstrated a good safety profile. The
authors believe that durvalumab will likely play an important role in future
treatment strategies for NSCLC. The PACIFIC trial assessing durvalumab after
standard chemoradiotherapy for locally advanced NSCLC has already met its
primary endpoint and the potential of durvalumab will be reinforced if phase III
randomized studies of first-line (MYSTIC trial) and second or subsequent (ARCTIC
trial) lines of therapy demonstrate superiority over the current standard of
care. BACKGROUND: Most patients with locally advanced, unresectable, non-small-cell
lung cancer (NSCLC) have disease progression despite definitive
chemoradiotherapy (chemotherapy plus concurrent radiation therapy). This phase 3
study compared the anti-programmed death ligand 1 antibody durvalumab as
consolidation therapy with placebo in patients with stage III NSCLC who did not
have disease progression after two or more cycles of platinum-based
chemoradiotherapy.
METHODS: We randomly assigned patients, in a 2:1 ratio, to receive durvalumab
(at a dose of 10 mg per kilogram of body weight intravenously) or placebo every
2 weeks for up to 12 months. The study drug was administered 1 to 42 days after
the patients had received chemoradiotherapy. The coprimary end points were
progression-free survival (as assessed by means of blinded independent central
review) and overall survival (unplanned for the interim analysis). Secondary end
points included 12-month and 18-month progression-free survival rates, the
objective response rate, the duration of response, the time to death or distant
metastasis, and safety.
RESULTS: Of 713 patients who underwent randomization, 709 received consolidation
therapy (473 received durvalumab and 236 received placebo). The median
progression-free survival from randomization was 16.8 months (95% confidence
interval [CI], 13.0 to 18.1) with durvalumab versus 5.6 months (95% CI, 4.6 to
7.8) with placebo (stratified hazard ratio for disease progression or death,
0.52; 95% CI, 0.42 to 0.65; P<0.001); the 12-month progression-free survival
rate was 55.9% versus 35.3%, and the 18-month progression-free survival rate was
44.2% versus 27.0%. The response rate was higher with durvalumab than with
placebo (28.4% vs. 16.0%; P<0.001), and the median duration of response was
longer (72.8% vs. 46.8% of the patients had an ongoing response at 18 months).
The median time to death or distant metastasis was longer with durvalumab than
with placebo (23.2 months vs. 14.6 months; P<0.001). Grade 3 or 4 adverse events
occurred in 29.9% of the patients who received durvalumab and 26.1% of those who
received placebo; the most common adverse event of grade 3 or 4 was pneumonia
(4.4% and 3.8%, respectively). A total of 15.4% of patients in the durvalumab
group and 9.8% of those in the placebo group discontinued the study drug because
of adverse events.
CONCLUSIONS: Progression-free survival was significantly longer with durvalumab
than with placebo. The secondary end points also favored durvalumab, and safety
was similar between the groups. (Funded by AstraZeneca; PACIFIC
ClinicalTrials.gov number, NCT02125461 .). Immune checkpoint inhibitors (ICIs) are a key component of treating advanced
cancer patients, principally antibodies against CTLA-4 and PD-1 or PD-L1.
Durvalumab (MEDI4736) is a selective, high-affinity, human IgG1 monoclonal
antibody that blocks PD-L1, which binds to PD-1 and CD80, but not to PD-L2.
Single-agent durvalumab showed clinical efficacy and a manageable safety profile
in advanced non-small-cell lung cancer, particularly the ≥25% PD-L1+ population.
Durvalumab is under evaluation in early, locally advanced and advanced disease
as monotherapy and combined with ICIs, targeted therapies, chemotherapy and
radiotherapy. Impressive activity has been recently reported after
chemoradiation in locally advanced patients; promising activity was observed
with other ICI combinations, and potentially with other drugs including
platinum-based chemotherapy. In contrast, early data reveal lower response rates
in EGFR and ALK-positive patients. BACKGROUND: Lung cancer occupies the leading position of cancer incidence and
mortality worldwide, including in the Czech Republic. Despite significant
advances in systemic oncology treatments, lung cancer still has the worst
prognosis, which is driving the need for innovative therapies and methods to
treat this disease. Immunotherapy is a developing area of systemic oncology
treatment, which has recently begun to be significantly applied to patients with
lung carcinoma. The most useful type of immunotherapy currently employs
checkpoint inhibitors, including CTLA-4 inhibitors (ipilimumab and tremelimumab)
and PD-1/PD-L1 inhibitors (nivolumab, pembrolizumab, durvalumab, and avelumab).
Except for monotherapy, different combinations of these inhibitors or
combinations between one more of these inhibitors and chemotherapy or targeted
treatment are being actively studied. Despite intensive investigations,
anti-tumor vaccines and cytokines have not had an important impact on the
treatment of lung cancer. Checkpoint inhibitors have yielded favorable results,
especially for the treatment of advanced (i.e., stage IIIB and IV) non-small
cell lung cancer (NSCLC) and are being extensively investigated for the
treatment of SCLC.
AIM: The aim of this review was to summarize the most important achievements,
possibilities, and perspectives of modern immunotherapy for the treatment of
patients with lung cancer.
CONCLUSION: Immunotherapy is an important tool in todays arsenal of oncology
treatments, and for patients with lung cancer it offers the hope of prolonging
life and img iprovints quality.Key words: immunotherapy - lung cancer - NSCLC -
SCLC - checkpoint inhibitors This work was supported by National Sustainability
Programme I No. LO1503 provided by Ministry of education, youth and sports and
program No. 17-30748A devided by The Ministry of Health of the Czech Republic.
The authors declare they have no potential conflicts of interest concerning
drugs, products, or services used in the study. The Editorial Board declares
that the manuscript met the ICMJE recommendation for biomedical
papers.Submitted: 31. 8. 2017Accepted: 7. 9. 2017. PURPOSE OF REVIEW: The therapeutic armamentarium for advanced non-small-cell
lung cancer has evolved considerably over the past years. Immune checkpoint
inhibitors targeting programmed cell death-1 such as pembrolizumab and nivolumab
or programmed cell death ligand 1 such as atezolizumab, durvalumab and avelumab
have shown favorable efficacy results in this patient population in the
first-line and second-line setting. These immunotherapies are associated with a
distinct toxicity profile based on autoimmune organ toxicity which is a new
challenge for supportive care during treatment with these drugs.
RECENT FINDINGS: The differential diagnosis of events occurring during immune
checkpoint inhibitor treatment is broad: they can be due to immune-related or
nonimmune-related adverse events, atypical tumor responses (pseudoprogression or
hyperprogression) or events related to comorbidities or other treatments.
SUMMARY: The management of these patients includes a thorough baseline clinical,
biological and radiologic evaluation, patient education, correct follow-up and
management by a multidisciplinary team with a central role for the medical
oncologist. Immune-related toxicities should be managed according to available
guidelines. BACKGROUND: Immune checkpoint inhibitors are a new standard of care for patients
with advanced non-small-cell lung cancer (NSCLC) without EGFR tyrosine kinase or
anaplastic lymphoma kinase (ALK) genetic aberrations (EGFR-/ALK-), but clinical
benefit in patients with EGFR mutations or ALK rearrangements (EGFR+/ALK+) has
not been shown. We assessed the effect of durvalumab (anti-PD-L1) treatment in
three cohorts of patients with NSCLC defined by EGFR/ALK status and tumour
expression of PD-L1.
METHODS: ATLANTIC is a phase 2, open-label, single-arm trial at 139 study
centres in Asia, Europe, and North America. Eligible patients had advanced NSCLC
with disease progression following at least two previous systemic regimens,
including platinum-based chemotherapy (and tyrosine kinase inhibitor therapy if
indicated); were aged 18 years or older; had a WHO performance status score of 0
or 1; and measurable disease per Response Evaluation Criteria in Solid Tumors
(RECIST) version 1.1. Key exclusion criteria included mixed small-cell lung
cancer and NSCLC histology; previous exposure to any anti-PD-1 or anti-PD-L1
antibody; and any previous grade 3 or worse immune-related adverse event while
receiving any immunotherapy agent. Patients in cohort 1 had EGFR+/ALK+ NSCLC
with at least 25%, or less than 25%, of tumour cells with PD-L1 expression.
Patients in cohorts 2 and 3 had EGFR-/ALK- NSCLC; cohort 2 included patients
with at least 25%, or less than 25%, of tumour cells with PD-L1 expression, and
cohort 3 included patients with at least 90% of tumour cells with PD-L1
expression. Patients received durvalumab (10 mg/kg) every 2 weeks, via
intravenous infusion, for up to 12 months. Retreatment was allowed for patients
who benefited but then progressed after completing 12 months. The primary
endpoint was the proportion of patients with increased tumour expression of
PD-L1 (defined as ≥25% of tumour cells in cohorts 1 and 2, and ≥90% of tumour
cells in cohort 3) who achieved an objective response, assessed in patients who
were evaluable for response per independent central review according to RECIST
version 1.1. Safety was assessed in all patients who received at least one dose
of durvalumab and for whom any post-dose data were available. The trial is
ongoing, but is no longer open to accrual, and is registered with
ClinicalTrials.gov, number NCT02087423.
FINDINGS: Between Feb 25, 2014, and Dec 28, 2015, 444 patients were enrolled and
received durvalumab: 111 in cohort 1, 265 in cohort 2, and 68 in cohort 3. Among
patients with at least 25% of tumour cells expressing PD-L1 who were evaluable
for objective response per independent central review, an objective response was
achieved in 9 (12·2%, 95% CI 5·7-21·8) of 74 patients in cohort 1 and 24 (16·4%,
10·8-23·5) of 146 patients in cohort 2. In cohort 3, 21 (30·9%, 20·2-43·3) of 68
patients achieved an objective response. Grade 3 or 4 treatment-related adverse
events occurred in 40 (9%) of 444 patients overall: six (5%) of 111 patients in
cohort 1, 22 (8%) of 265 in cohort 2, and 12 (18%) of 68 in cohort 3. The most
common treatment-related grade 3 or 4 adverse events were pneumonitis (four
patients [1%]), elevated gamma-glutamyltransferase (four [1%]), diarrhoea (three
[1%]), infusion-related reaction (three [1%]), elevated aspartate
aminotransferase (two [<1%]), elevated transaminases (two [<1%]), vomiting (two
[<1%]), and fatigue (two [<1%]). Treatment-related serious adverse events
occurred in 27 (6%) of 444 patients overall: five (5%) of 111 patients in cohort
1, 14 (5%) of 265 in cohort 2, and eight (12%) of 68 in cohort 3. The most
common serious adverse events overall were pneumonitis (five patients [1%]),
fatigue (three [1%]), and infusion-related reaction (three [1%]).
Immune-mediated events were manageable with standard treatment guidelines.
INTERPRETATION: In patients with advanced and heavily pretreated NSCLC, the
clinical activity and safety profile of durvalumab was consistent with that of
other anti-PD-1 and anti-PD-L1 agents. Responses were recorded in all cohorts;
the proportion of patients with EGFR-/ALK- NSCLC (cohorts 2 and 3) achieving a
response was higher than the proportion with EGFR+/ALK+ NSCLC (cohort 1)
achieving a response. The clinical activity of durvalumab in patients with EGFR+
NSCLC with ≥25% of tumour cells expressing PD-L1 was encouraging, and further
investigation of durvalumab in patients with EGFR+/ALK+ NSCLC is warranted.
FUNDING: AstraZeneca. Lung cancer is the most common cancer worldwide and the most common cause of
cancer-related death. Non-small-cell lung cancer comprises ~87% of newly
diagnosed cases of lung cancer, and nearly one-third of these patients have
stage III disease. Despite improvements in the treatment of stage IV lung
cancer, particularly with the introduction and dissemination of checkpoint
inhibitors, very little progress has been made in the treatment of stage III
lung cancer. In this article, we discuss the general staging criteria and
treatment options for stage III lung cancer. We review how concurrent radiation
and chemotherapy can have immunomodulatory effects, supporting the rationale for
incorporating immunotherapy into existing treatment paradigms. Finally, we
discuss the results of the PACIFIC trial and implications for the treatment of
stage III lung cancer. In the PACIFIC trial, adding durvalumab as a maintece
therapy following the completion of chemoradiotherapy improved progression-free
survival in patients with locally advanced unresectable stage III lung cancer.
On the strength of these results, durvalumab has been approved by the US Food
and Drug Administration for use in this setting, representing the first advance
in the treatment of stage III lung cancer in nearly a decade. In non-small cell lung cancer (NSCLC), immunotherapy is one of today's most
important and ground-breaking systemic treatments, mainly represented by
antibodies against cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) and
programmed death protein 1 or ligand 1 (PD-1/PD-L1). Durvalumab (MEDI4736) is a
high-affinity human IgG1 monoclonal antibody that binds to PD-1 and CD80,
blocking PD-L1, but not PD-L2. Areas covered: In advanced NSCLC patients,
durvalumab has demonstrated activity and acceptable tolerability, particularly
with ≥25% PD-L1 tumor expression in the EGFR and ALK wild-type population.
However, preliminary data have shown lower efficacy in EGFR mutant and
ALK-positive patients. The results from the recent PACIFIC study in locally
advanced patients have placed durvalumab as standard of care in consolidation
after chemoradiation, leading to Food and Drug Administration (FDA) approval.
Expert commentary: Early data suggest promising activity for durvalumab with the
CTLA-4 inhibitor tremelimumab, regardless of PD-L1 expression, and potentially
in combination with other drugs such as platinum-doublet chemotherapy. However,
treatment-related toxicity associated with the combinations is an important
aspect of the benefit-risk evaluation in the decision-making process. Results of
ongoing phase III trials will provide illuminating data to confirm the place of
durvalumab in the management of NSCLC patients. New data from the phase III PACIFIC trial of durvalumab in patients with stage
III non-small cell lung cancer show that the drug increases the odds of
surviving for 24 months. The study also confirms that progression-free survival
and time to death or distant metastasis are longer for patients treated with
durvalumab than for patients who received a placebo. PURPOSE OF REVIEW: Despite aggressive treatment based on definitive
chemoradiotherapy, 5-year overall survival in unresectable stage III nonsmall
cell lung cancer remains poor (15-20%). The novel immunotherapy based on immune
checkpoint inhibitors (ICIs) presents as the therapeutic 'Holly Grail' in lung
cancer treatment.
RECENT FINDINGS: Preclinical models provide evidence of
immunotherapy-radiotherapy (IM-RT) synergy. The exposure to ionizing radiation
turns tumor in an in-situ vaccine, primes the innate immune system, increases
immunotherapy efficacy by overcoming the immunosuppressive microenvironment of
immune-resistant tumors and promotes a systemic, out-of-field antitumor
T-cell-mediated response called abscopal effect. The immunomodulatory and
abscopal effects of radiotherapy can be further enhanced by combining with
systemic immunotherapies. The phase III START trial proved that liposomal
vaccine - tecemotide (L-BLP25) administered as maintece therapy after
concurrent chemoradiotherapy (CRT) in LA-NSCLC prolongs survival. In the phase
III PACIFIC trial consolidation with durvalumab, an anti-PDL-1 antibody, was
associated with survival benefit in patients diagnosed with LA-NSCLC who
responded to concurrent chemoradiotherapy.
SUMMARY: PACIFIC trial results are expected to definitely establish durvalumab
as standard consolidation strategy in LA-NSCLC. Many clinical trials are ongoing
in the field of immunoradiotherapy in LA-NSCLC to define the optimal conditions
for this therapeutic combination. |
Is LRP1 interacting with Urokinase receptor? | Yes | Low-density lipoprotein receptor-related protein (LRP) mediates internalization
of urokinase:plasminogen activator inhibitor complexes (uPA:PAI-1) and the
urokinase receptor (uPAR). Here we investigated whether direct interaction
between uPAR, a glycosyl-phosphatidylinositol-anchored protein, and LRP, a
transmembrane receptor, is required for clearance of uPA:PAI-1, regeneration of
unoccupied uPAR, activation of plasminogen, and the ability of HT1080 cells to
invade extracellular matrix. We found that in the absence of uPA:PAI-1, uPAR is
randomly distributed along the plasma membrane, whereas uPA:PAI-1 promotes
formation of uPAR-LRP complexes and initiates redistribution of occupied uPAR to
clathrin-coated pits. uPAR-LRP complexes are endocytosed via clathrin-coated
vesicles and traffic together to early endosomes (EE) because they can be
coimmunoprecipitated from immunoisolated EE, and internalization is blocked by
depletion of intracellular K(+). Direct binding of domain 3 (D3) of uPAR to LRP
is required for clearance of uPA-PAI-1-occupied uPAR because internalization is
blocked by incubation with recombit D3. Moreover, uPA-dependent plasmin
generation and the ability of HT1080 cells to migrate through Matrigel-coated
invasion chambers are also inhibited in the presence of D3. These results
demonstrate that GPI-anchored uPAR is endocytosed by piggybacking on LRP and
that direct binding of occupied uPAR to LRP is essential for internalization of
occupied uPAR, regeneration of unoccupied uPAR, plasmin generation, and invasion
and migration through extracellular matrix. BACKGROUND: The urokinase receptor (uPAR/CD87) is highly expressed in maligt
tumours. uPAR, as a GPI anchored protein, is preferentially located at the cell
surface, where it interacts with its ligands urokinase (uPA) and the
extracellular matrix protein vitronectin, thus promoting plasmin generation,
cell-matrix interactions and intracellular signalling events. Interaction with a
complex formed by uPA and its inhibitor PAI-1 induces cell surface down
regulation and recycling of the receptor via the clathrin-coated pathway, a
process dependent on the association to LRP-1.
METHODOLOGY/PRINCIPAL FINDINGS: In this study, we have found that along with the
ligand-induced down-regulation, uPAR also internalizes and recycles
constitutively through a second pathway that is independent of LRP-1 and
clathrin but shares some properties with macropinocytosis. The
ligand-independent route is amiloride-sensitive, does not require uPAR
partitioning into lipid rafts, is independent of the activity of small GTPases
RhoA, Rac1 and Cdc42, and does not require PI3K activity. Constitutively
endocytosed uPAR is found in EEA1 positive early/recycling endosomes but does
not reach lysosomes in the absence of ligands. Electron microscopy analysis
reveals the presence of uPAR in ruffling domains at the cell surface, in
macropinosome-like vesicles and in endosomal compartments.
CONCLUSIONS/SIGNIFICANCE: These results indicate that, in addition to the
ligand-induced endocytosis of uPAR, efficient surface expression and membrane
trafficking might also be driven by an uncommon macropinocytic mechanism coupled
with rapid recycling to the cell surface. |
Is obesity related to cognitive decline? | Obesity is a common medical illness that is increasingly recognised as conferring risk of decline in cognitive performance, independent of other comorbid medical conditions. Overweight and obesity are associated with an increased risk of subnormal intellectual performance in young adult males. Subjects with low birth weight and adolescent overweight/obesity are at particular risk of subnormal performance. | BACKGROUND: Overweight and obesity are risk factors for cardiovascular disease.
There is also an association between body mass index (BMI) and cognitive
ability. Since low birth weight is associated with adult metabolic disease,
particularly in obese subjects, the question emerges whether obesity has an
additional negative effect on cognitive function in subjects with low birth
weight.
OBJECTIVES: The aim was to analyse whether overweight or obesity influence
intellectual performance in young adults with particular focus on those with a
low birth weight.
METHODS: Data were collected from the Swedish Medical Birth Register on 620,834
males born between 1973 and 1988 and matched to results on intellectual
performance and BMI at conscription.
RESULTS: The risk for low intellectual performance was higher for those with
high BMI compared to those with normal. The highest risk was found among
subjects with low birth weight and overweight or obesity in young adulthood
(odds ratios, 1.98 [1.73-2.22] and 2.59 [2.00-3.34], respectively). However,
subjects with further high birth weight and a high BMI at conscription had no
further increased risk.
CONCLUSIONS: Overweight and obesity are associated with an increased risk of
subnormal intellectual performance in young adult males. Subjects with low birth
weight and adolescent overweight/obesity are at particular risk of subnormal
performance. A high birth weight increases the risk for obesity, but a high
adult BMI does not further increase the risk for subnormal performance. INTRODUCTION: Previous studies investigating the relationship between obesity
and cognition as well as gender differences in these relationships reported
equivocal results. Here, we examined age, years of education, schizophrenia, and
gender differences which might affect the relationship between obesity and
cognition.
METHODS: 1012 healthy controls and 707 participants with schizophrenia were
recruited. Information on body mass index (BMI) was obtained and a
neurocognitive battery was administered. Structural equation modeling (SEM) was
performed to examine the relationship between BMI, schizophrenia, cognition and
its covariates.
RESULTS: No significant direct effect of BMI on cognition was found when
cognition was regressed on age, years of education, diagnosis of schizophrenia
and BMI. Instead, two SEM models indicated that indirect effects between BMI and
cognition exist. The indirect effect of BMI on cognition through schizophrenia
was present in both genders, while the indirect effect of cognition on BMI
through schizophrenia was only found in females. BMI affecting cognition through
age, years of education and schizophrenia appears to be the most plausible model
that explains the data. This indirect effect was larger in females and was
masked by diagnosis of schizophrenia.
CONCLUSION: With increased rates of obesity in schizophrenia, it is important to
highlight the potentially deleterious effect of obesity on cognition. BMI could
be used as a candidate risk marker to identify people at higher risk of
cognitive deficits, and as an intervention target for modifications of cognitive
outcomes. Changes in food composition and availability have contributed to the dramatic
increase in obesity over the past 30-40 years in developed and, increasingly, in
developing countries. The brain plays a critical role in regulating energy
balance. Some human studies have demonstrated increased preference for high fat
and high sugar foods in people reporting greater stress exposure. We have
examined neurochemical changes in the brain in rodent models during the
development of obesity, including the impact of obesity on cognition, reward
neurocircuitry and stress responsiveness. Using supermarket foods high in fat
and sugar, we showed that such a diet leads to changes in neurotransmitters
involved in the hedonic appraisal of foods, indicative of an addiction-like
capacity of foods high in fat and/or sugar. Importantly, withdrawal of the
palatable diet led to a stress-like response. Furthermore, access to this
palatable diet attenuated the physiological effects of acute stress (restraint),
indicating that it could act as a comfort food. In more chronic studies, the
diet also attenuated anxiety-like behavior in rats exposed to stress (maternal
separation) early in life, but these rats may suffer greater metabolic harm than
rats exposed to the early life stressor but not provided with the palatable
diet. Impairments in cognitive function have been associated with obesity in
both people and rodents. However, as little as 1 week of exposure to a high fat,
high sugar diet selectively impaired place but not object recognition memory in
the rat. Excess sugar alone had similar effects, and both diets were linked to
increased inflammatory markers in the hippocampus, a critical region involved in
memory. Obesity-related inflammatory changes have been found in the human brain.
Ongoing work examines interventions to prevent or reverse diet-induced cognitive
impairments. These data have implications for minimizing harm caused by
unhealthy eating. OBJECTIVES: This review focuses on the relationship between obesity and aging
and how these interact to affect cognitive function. The topics covered are
guided by the Scaffolding Theory of Aging and Cognition (STAC [Park and
Reuter-Lorenz. Annu Rev Psychol 2009;60:173-96]-a conceptual model designed to
relate brain structure and function to one's level of cognitive ability.
METHODS: The initial literature search was focused on normal aging and was
guided by the key words, "aging, cognition, and obesity" in PubMed. In a second
search, we added key words related to neuropathology including words
"Alzheimer's disease," "vascular dementia," and "mild cognitive impairment."
RESULTS: The data suggest that being overweight or obese in midlife may be more
detrimental to subsequent age-related cognitive decline than being overweight or
obese at later stages of the life span. These effects are likely mediated by the
accelerated effects obesity has on the integrity of neural structures, including
both gray and white matter. Further epidemiological studies have provided
evidence that obesity in midlife is linked to an increased risk for Alzheimer's
disease and vascular dementia, most likely via an increased accumulation of
Alzheimer's disease pathology.
CONCLUSIONS: Although it is clear that obesity negatively affects cognition,
more work is needed to better understand how aging plays a role and how brain
structure and brain function might mediate the relationship of obesity and age
on cognition. Guided by the STAC and the STAC-R models, we provide a roadmap for
future investigations of the role of obesity on cognition across the life span. Diabetes and obesity, two major public health concerns, are associated with
increased risk for problems in multiple organ systems, including the central
nervous system. The adverse effects of diabetes and obesity on cognitive
functioning are increasingly well recognized. This special issue of
Psychosomatic Medicine features the latest research linking diabetes, obesity,
and brain structure, function, and metabolism and follows a special meeting on
this topic organized by the American Psychosomatic Society in October 2013.
Evidence for the increased prevalence of diabetes and obesity is reviewed as it
relates to cognitive decline. These articles indicate that the age of onset of
Type 1 diabetes may be relevant to future cognitive function and that disease
duration of Type 2 diabetes and sociocultural factors are related to cognitive
decline during the aging process. The hypothalamus and other neural circuits,
notably the dopaminergic system that underlies feeding and reward-related
aspects of food intake, are among the key factors involved in obesity. Research
on the associations between obesity and cognitive function is described using
the positive effects of weight reduction following bariatric surgery or
behavioral methods. This special issue concludes with a conceptual framework for
linking obesity and diabetes with accelerated cognitive decline as related to
the aging process. The collection of articles highlights the importance of using
a life span perspective to understand the influence of both Type 1 and Type 2
diabetes on brain metabolism, function, and structure. Moreover, these studies
show that distressing environmental circumstances can adversely influence
neurocognitive dysfunction associated with obesity and diabetes. OBJECTIVE: To test the hypothesis that obesity is associated with impaired
cognitive outcomes in the pre-school years.
METHODS: Associations were examined between weight status at age 3-5 years and
cognitive performance at age 5 years. Cognitive outcome measures were tests of
pattern construction (visuospatial skills), naming vocabulary (expressive
language skills), and picture similarity (reasoning skills). The sample was the
UK Millennium Cohort Study (n = 12,349 participants).
RESULTS: Boys with obesity at 3 years had significantly lower performance in
pattern construction at age 5 years compared to those of a healthy weight, even
after controlling for confounders (β = -0.029, P = 0.03). Controlling for
confounders, boys who developed obesity between the ages of 3 and 5 years had
lower scores in pattern construction (β = -0.03, P = 0.03). "Growing out" of
obesity had a positive association with picture similarity performance in girls
(β = 0.03, P = 0.04).
CONCLUSIONS: Obesity in the pre-school years was associated with poorer outcomes
for some cognitive measures in this study. Stronger relationships between
obesity and cognition or educational attainment may emerge later in childhood. INTRODUCTION: Obesity is a common medical illness that is increasingly
recognised as conferring risk of decline in cognitive performance, independent
of other comorbid medical conditions. Individuals with mood disorders (bipolar
disorder (BD) or major depressive disorder (MDD)) display an increased
prevalence of both obesity and risk factors for cardiovascular diseases.
Moreover, BD and MDD are associated with impairment in cognitive functioning
across multiple domains. The independent contribution of obesity to cognitive
decline in this population has not been explored. This study examines the impact
of obesity on cognition by comparing neuropsychological performance in obese
individuals, with or without a mood disorder before and after undergoing
bariatric surgery.
METHODS AND ANALYSIS: This study compares measures of declarative memory,
executive functioning and attention in obese individuals (body mass index >35
kg/m(2)) with BD or MDD, and 2 control populations (obese individuals without a
psychiatric illness and healthy non-obese controls) prior to and following
bariatric surgery. Participants (ages 18-60) receive a psychiatric diagnosis via
the Structured Clinical Interview for the Diagnostic and Statistical Manual of
Mental Disorders, Fourth Edition (DSM-IV; SCID). Mood ratings, physical
measurements, nutritional and health questionnaires are also administered. A
standardised battery of neuropsychological tests aimed at establishing
performance in areas of declarative memory, executive functioning and attention
are administered. Warrington's Recognition Memory Task (RMT) and an N-Back Task
are performed in a 3 T functional MRI to investigate patterns of neural
activation during cognitive performance. Additionally, anatomical MRI data are
obtained to investigate potential changes in neural structures. Baseline data
will be analysed for between-group differences and later compared with
postsurgical data to investigate cognitive change.
ETHICS AND DISSEMINATION: This study has been approved by the Hamilton
Integrated Research Ethics Board (09-3254). Results will be available in
peer-reviewed scientific publications and scientific meetings presentations, and
released in lay form to media. There is increasing evidence for important roles of key cognitive processes,
including attention, memory and learning, in the short-term decision making
about eating. There is parallel evidence that people who are overweight or obese
tend to perform worse on a variety of cognitive tasks. In this review, the
evidence for these two ideas is summarised and then the idea that
overconsumption of Western-style high-fat (HF)-high-sugar diets may underlie the
association between obesity and poorer cognitive performance is explored. In
particular, evidence in animals and human subjects that repeated consumption of
HF or HF and sugar (HFS) diets leads to specific impairments in the functioning
of the hippocampus, which underpin the consequent changes in cognition is
summarised. These findings lead into the vicious cycle model (VCM), which
suggests that these cognitive changes have knock-on negative effects for future
appetite control, and evidence that altered hippocampal function is also
associated with impaired appetite control is explored. The review concludes that
there is consistent evidence in the animal literature and emerging evidence from
human studies that supports this VCM. It is also noted, however, that to date
studies lack the nutritional specificity needed to be able to translate these
basic research findings into clear nutritional effects, and concludes that there
is an urgent need for additional research to clarify the precise nature of the
apparent effects of consuming HFS diets on cognition. BACKGROUND: Obesity has been implicated in the pathophysiology of major
depressive disorder (MDD), which prompted us to examine the possible association
of obesity with cognitive function and brain structure in patients with MDD.
METHODS: Three hundred and seven patients with MDD and 294 healthy participants,
matched for age, sex, ethnicity (Japanese), and handedness (right) were
recruited for the study. Cognitive function was assessed using the Brief
Assessment of Cognition in Schizophrenia (BACS). Gray and white matter
structures were analyzed using voxel-based morphometry and diffusion tensor
imaging in a subsample of patients (n = 114) whose magnetic resoce imaging
(MRI) data were obtained using a 1.5 T MRI system.
RESULTS: Verbal memory, working memory, motor speed, attention, executive
function, and BACS composite scores were lower for the MDD patients than for the
healthy participants (p < 0.05). Among the patient group, working memory, motor
speed, executive function, and BACS composite scores were lower in obese
patients (body mass index ≥ 30, n = 17) than in non-obese patients (n = 290, p <
0.05, corrected). MRI determined frontal, temporal, thalamic, and hippocampal
volumes, and white matter fractional anisotropy values in the internal capsule
and left optic radiation were reduced in obese patients (n = 7) compared with
non-obese patients (n = 107, p < 0.05, corrected).
LIMITATIONS: Sample size for obese population was not very large.
CONCLUSIONS: Obesity is associated with decreased cognitive function, reduced
gray matter volume, and impaired white matter integrity in cognition-related
brain areas in patients with MDD. |
Describe the mechanism of action of ibalizumab. | Ibalizumab is a humanized monoclonal antibody that acts as post-attachment inhibitor by binding CD4 2nd domain of T lymphocyte and preventing HIV connection to CCR5 or CXCR4. It has been recently approved by Food and Drug Administration as a new intravenous antiretroviral agent for heavily treated HIV adults with multi -drug resistant infection. | Ibalizumab (formerly TNX-355) is a humanized monoclonal antibody that binds CD4,
the primary receptor for human immunodeficiency virus type 1 (HIV-1), and
inhibits the viral entry process. A phase lb multidose study of the safety,
pharmacokinetics, and antiviral activity of ibalizumab was conducted with 22
HIV-1-infected patients. Nineteen patients were randomized to receive either 10
mg/kg of body weight weekly (arm A) or a 10-mg/kg loading dose followed by 6
mg/kg every 2 weeks (arm B) intravenously for 9 weeks. Three patients were
assigned to receive 25 mg/kg every 2 weeks for five doses (arm C). During the
study, the patients remained off other antiretrovirals or continued a stable
failing regimen. Treatment with ibalizumab resulted in substantial reductions in
HIV-1 RNA levels (0.5 to 1.7 log(10)) in 20 of 22 subjects. In most patients,
HIV-1 RNA fell to nadir levels after 1 to 2 weeks of treatment and then returned
to baseline despite continued treatment. Baseline viral isolates were
susceptible to ibalizumab in vitro, regardless of coreceptor tropism. Emerging
resistance to ibalizumab was manifested by reduced maximal percent inhibition in
a single-cycle HIV infectivity assay. Resistant isolates remained CD4 dependent
and were susceptible to enfuvirtide in vitro. Complete coating of CD4(+) T-cell
receptors was correlated with serum ibalizumab concentrations. There was no
evidence of CD4(+) T-cell depletion in ibalizumab-treated patients. Ibalizumab
was not immunogenic, and no serious drug-related adverse effects occurred. In
conclusion, ibalizumab administered either weekly or biweekly was safe and well
tolerated and demonstrated antiviral activity. Further studies with ibalizumab
in combination with standard antiretroviral treatments are warranted. Ibalizumab is a humanized monoclonal antibody that binds human CD4, the primary
receptor for human immunodeficiency virus type 1 (HIV-1). With its unique
specificity for domain 2 of CD4, this antibody potently and broadly blocks HIV-1
infection in vitro by inhibiting a postbinding step required for viral entry but
without interfering with major histocompatibility complex class II
(MHC-II)-mediated immune function. In clinical trials, ibalizumab has
demonstrated anti-HIV-1 activity in patients without causing immunosuppression.
Thus, a characterization of the ibalizumab epitope was conducted in an attempt
to gain insight into the underlying mechanism of its antiviral activity as well
as its safety profile. By studying mouse/human chimeric CD4 molecules and
site-directed point mutants of CD4, amino acids L96, P121, P122, and Q163 in
domain 2 were found to be important for ibalizumab binding, with E77 and S79 in
domain 1 also contributing. All these residues appear to cluster on the
interface between domains 1 and 2 of human CD4 on a surface opposite the site
where gp120 and the MHC-II molecule bind on domain 1. Separately, the epitope of
M-T441, a weakly neutralizing mouse monoclonal antibody that competes with
ibalizumab, was localized entirely within domain 2 on residues 123 to 125 and
138 to 140. The results reported herein not only provide an appreciation for why
ibalizumab has not had significant adverse immunological consequences in
infected patients to date but also raise possible steric hindrance mechanisms by
which this antibody blocks HIV-1 entry into a CD4-positive cell. Ibalizumab is a humanized, anti-CD4 monoclonal antibody. It potently blocks
HIV-1 infection and targets an epitope in the second domain of CD4 without
interfering with immune functions mediated by interaction of CD4 with major
histocompatibility complex (MHC) class II molecules. We report here the crystal
structure of ibalizumab Fab fragment in complex with the first two domains
(D1-D2) of CD4 at 2.2 Å resolution. Ibalizumab grips CD4 primarily by the
BC-loop (residues 121-125) of D2, sitting on the opposite side of gp120 and
MHC-II binding sites. No major conformational change in CD4 accompanies binding
to ibalizumab. Both monovalent and bivalent forms of ibalizumab effectively
block viral infection, suggesting that it does not need to crosslink CD4 to
exert antiviral activity. While gp120-induced structural rearrangements in CD4
are probably minimal, CD4 structural rigidity is dispensable for ibalizumab
inhibition. These results could guide CD4-based immunogen design and lead to a
better understanding of HIV-1 entry. Ibalizumab (formerly TNX-355) is a first-in-class, monoclonal antibody inhibitor
of CD4-mediated human immunodeficiency type 1 (HIV-1) entry. Multiple clinical
trials with HIV-infected patients have demonstrated the antiviral activity,
safety, and tolerability of ibalizumab treatment. A 9-week phase Ib study adding
ibalizumab monotherapy to failing drug regimens led to transient reductions in
HIV viral loads and the evolution of HIV-1 variants with reduced susceptibility
to ibalizumab. This report characterizes these variants by comparing the
phenotypic susceptibilities and envelope (env) sequences of (i) paired baseline
and on-treatment virus populations, (ii) individual env clones from selected
paired samples, and (iii) env clones containing site-directed mutations. Viruses
with reduced susceptibility to ibalizumab were found to exhibit reduced
susceptibility to the anti-CD4 antibody RPA-T4. Conversely, susceptibility to
soluble CD4, which targets the HIV-1 gp120 envelope protein, was enhanced. No
changes in susceptibility to the fusion inhibitor enfuvirtide or the CCR5
antagonist maraviroc were observed. Functionally, viruses with reduced
ibalizumab susceptibility also displayed high levels of infectivity relative to
those of paired baseline viruses. Individual env clones exhibiting reduced
ibalizumab susceptibility contained multiple amino acid changes in different
regions relative to the paired baseline clones. In particular, clones with
reduced susceptibility to ibalizumab contained fewer potential asparagine-linked
glycosylation sites (PNGSs) in variable region 5 (V5) than did paired
ibalizumab-susceptible clones. The reduction in ibalizumab susceptibility due to
the loss of V5 PNGSs was confirmed by site-directed mutagenesis. Taken together,
these findings provide important insights into resistance to this new class of
antiretroviral drug. OBJECTIVES: Passive immunization for the prevention of HIV-1 infection is
currently being reenergized. The anti-CD4 monoclonal antibody ibalizumab has
demonstrated safety and efficacy in phase 1 and 2 clinical trials for treatment
of HIV-1 infection and is undergoing a phase 1 clinical trial in HIV-1
uninfected individuals for prevention. Here, we sought to assess ibalizumab
antiviral breadth and potency and to identify determits of natural
preexisting resistance.
METHODS: Ibalizumab breadth and potency was assessed against a large clinically
relevant panel of HIV-1 pseudoviruses (n = 116) commonly used to assess vaccine
candidates. Determits of resistance were assessed by sequence analysis.
RESULTS: Ibalizumab neutralized 92% and 66% of viruses as defined by 50% and 80%
inhibition, respectively. Median in vitro neutralization potency by IC50 was
0.03 μg/mL, substantially lower than the broadly neutralizing mAbs, PG9, or
VRC01. The domit determit of resistance was the absence of a potential
N-linked glycosylation site (PNGS) at the V5 N-terminus (P < 0.001), with the V2
loop length possibly influencing the degree of resistance afforded by the
absence of the V5 N-terminal PNGS (P = 0.001). Other significant independent
correlates of resistance included PNGS at position 386 and the side chain length
of residue 375. Ibalizumab exhibited complementary resistance to VRC01 (P =
0.006) and sCD4 (P < 0.001), in part mediated by the V5 PNGS.
CONCLUSIONS: Ibalizumab breadth and potency compared favorably with broadly
neutralizing anti-HIV-1 monoclonal antibodies, supporting the clinical
development of ibalizumab, alone or in combination, for HIV-1 prevention. BACKGROUND: Although broadly neutralizing monoclonal antibodies (bNAbs) have
always been considered to be a potential therapeutic option for the prophylaxis
and treatment of HIV infection, their lack of breadth against all HIV variants
has been one of the limiting factors. To provide sufficient neutralization
breadth and potency against diverse viruses, including neutralization escape
mutants, strategies to combine different bNAbs have been explored recently.
METHODS: We rationally designed and engineered a novel bispecific
HIV-1-neutralizing antibody (bibNAb), iMabm36. The potency and breadth of
iMabm36 against HIV were extensively characterized in vitro.
RESULTS: iMabm36 comprises the anti-CD4 Ab ibalizumab (iMab) linked to 2 copies
of the single-domain Ab m36, which targets a highly conserved CD4-induced
epitope. iMabm36 neutralizes a majority of a large, multiclade panel of
pseudoviruses (96%, n = 118) at an IC50 concentration of less than 10 µg/mL,
with 83% neutralized at an IC50 concentration of less than 0.1 µg/mL. In
addition, iMabm36 neutralizes a small panel of replication-competent
transmitted-founder viruses to 100% inhibition at a concentration of less than
0.1 µg/mL in a peripheral blood mononuclear cell-based neutralizing assay.
Mechanistically, the improved antiviral activity of iMabm36 is dependent on both
the CD4-binding activity of the iMab component and the CD4i-binding activity of
the m36 component. After characterizing that viral resistance to iMabm36
neutralization was due to mutations residing in the bridging sheet of gp120, an
optimized m36 variant was engineered that, when fused to iMab, improved
antiviral activity significantly.
CONCLUSIONS: The interdependency of this dual mechanism of action enables
iMabm36 to potently inhibit HIV-1 entry. These results demonstrate that
mechanistic-based design of bibNAbs can generate potential preventive and
therapeutic candidates for HIV/AIDS. Antibody drugs are very useful tools for the treatment of many chronic diseases.
Recently, however, patients and doctors have encountered the problem of drug
resistance. How to improve the affinity of antibody drugs has therefore become a
pressing issue. Ibalizumab is a humanized monoclonal antibody that binds human
CD4, the primary receptor for human immunodeficiency virus type 1. This study
investigates the mutation residues of the complementarity determining regions of
Ibalizumab. We propose using the wild and mutations of Ibalizumab-human CD4
receptor complex structures, molecular dynamics techniques, alanine-scanning
mutagenesis calculations and solvated interaction energies methods to predict
the binding free energy of the Ibalizumab-human CD4 receptor complex structures.
This work found that revealed three key positions (31th, 32th and 33th in
HCDR-1) of the residues may play an important role in Ibalizumab-human CD4
receptor complex interactions. Therefore, bioengineering substitutions of the
three key positions and increasing number of intermolecular interactions (HCDR-1
of Ibalizumab/human CD4 receptor) might improve the binding affinities of this
complex structure. Conflict of interest statement: FUNDING: The preparation of this review was not
supported by any external funding. CONFLICT OF INTEREST: During the peer review
process the manufacturer of the agent under review was offered an opportunity to
comment on the article. Changes resulting from any comments received were made
by the author on the basis of scientific completeness and accuracy. A. Markham,
a contracted employee of Adis/Springer, is responsible for the article content
and declares no relevant conflicts of interest. Over the past 30 years, antiretroviral drug regimens for treating HIV infection
have become more effective, safer, and more convenient. Despite 31 currently
approved drugs, the pipeline of investigational HIV drugs remains full.
Investigational antiretroviral drugs include the nucleoside analogue reverse
transcriptase translocation inhibitor (NRTTI) MK-8591, a long-acting compound
that could be dosed once weekly. Investigational nonnucleoside analogue reverse
transcriptase inhibitors (NNRTIs) include doravirine, which is active in vitro
against NNRTI-resistant HIV and was potent and well-tolerated when used in
combination with a dual-nucleoside analogue RTI (nRTI) backbone in
treatment-naive individuals.New integrase strand transfer inhibitors (InSTIs)
include recently approved bictegravir, which is active against InSTI-resistant
viral strains in vitro and was potent and well-tolerated in combination regimens
in treatment-naive individuals, and investigational cabotegravir, which is being
studied with monthly parenteral dosing for HIV maintece treatment and with
bimonthly dosing for HIV preexposure prophylaxis (PrEP). Investigational HIV
entry inhibitors include the new CD4 attachment inhibitor fostemsavir, which
targets HIV envelope glycoprotein 120, and recently approved ibalizumab, which
binds the CD4 receptor. This article summarizes presentations by Roy M. Gulick,
MD, MPH, at the IAS-USA continuing education program, Improving the Management
of HIV Disease, held in Los Angeles, California, in April 2017, and at the 2017
Ryan White HIV/AIDS Program Clinical Conference, held in San Antonio, Texas, in
August 2017. |
Describe information obtained by immunophenotyping. | Mass cytomety enables comprehensive single-cell immunophenotyping and functional assessments, capturing the complexity of the immune system, and the molecularly heterogeneous consequences of primary immunodeficiency defects.
Circulating B, T, and dendritic cells were defined using flow cytometric analysis as recommended by the Human Immunology Project Consortium.
Clinical applications of flow cytometry currently utilized in the laboratory include cell surface antigen determinations or immunophenotyping of hematologic cells, DNA analysis of hematopoietic malignancies and solid tumors, and measurement of CD4 (T helper/inducer cell) absolute counts and T helper/T suppressor (CD4/CD8) ratios in the evaluation of immune deficiency. | INTRODUCTION: The workup of lymphoproliferative disorders (LPDs) involves the
combined use of flow cytometry (FC) and immunohistochemistry (IHC). This often
results in duplicate immunophenotypic testing and adds costs that may not be
eligible for reimbursement based on the Medicare National Correct Coding
Initiative. We aimed to establish a cost-effective diagnostic algorithm based on
initial FC categorization to reduce repetitive immunophenotyping.
METHODS: We retrospectively reviewed 242 cases of suspected LPDs with concurrent
FC and IHC testing over a 12-month period. We correlated FC with surgical
diagnoses and evaluated the frequency of repeat IHC testing.
RESULTS: Repetitive immunophenotyping was common; overall, 85% of cases had at
least one marker repeated. Concordant cases were significantly less likely to
have markers repeated than discordant cases. Of concordant B cell maligcies,
57% represented recurrent disease; however, repeat marker usage was not
decreased as compared to new diagnoses. The most frequently repeated markers
were CD3, CD5, CD10, and CD20.
CONCLUSIONS: We propose that in concordant cases, CD5 and CD10 should not be
repeated by IHC; this would decrease the use of these markers by 80% and 76%,
respectively. We developed an algorithmic approach to IHC usage that has
improved incorporation of FC data at our institution and may reduce healthcare
costs. BACKGROUND: The United Kingdom National External Quality Assessment Service (UK
NEQAS) for Leucocyte Immunophenotyping Immune Monitoring Programme, provides
external quality assessment (EQA) to non-U.S. laboratories affiliated with the
NIH NIAID Division of AIDS (DAIDS) clinical trials networks. Selected
laboratories are required to have oversight, performance monitoring, and
remediation undertaken by Immunology Quality Assessment (IQA) staff under the
DAIDS contract. We examined whether laboratory accuracy improves with longer EQA
participation and whether IQA remediation is effective.
METHODS: Laboratory accuracy, defined by the measurement residuals from trial
sample medians, was measured on four outcomes: both CD4+ absolute counts
(cells/μL) and percentages; and CD8+ absolute counts (cells/μL) and percentages.
Three laboratory categories were defined: IQA monitored (n = 116), United
Kingdom/non-DAIDS (n = 137), and non-DAIDS/non-UK (n = 1034). For absolute count
outcomes, the groups were subdivided into single platform and dual platform
users.
RESULTS: Increasing EQA duration was found to be associated with increasing
accuracy for all groups in all four lymphocyte subsets (P < 0.0001). In the
percentage outcomes, the typical IQA group laboratory improved faster than
laboratories from the other two groups (P < 0.005). No difference in the overall
rate of improvement was found between groups for absolute count outcomes.
However, in the DPT subgroup the IQA group ultimately showed greater
homogeneity.
CONCLUSIONS: EQA participation coupled with effective laboratory monitoring and
remedial action is strongly associated with improved laboratory accuracy, both
incrementally and in the proportion of laboratories meeting suggested standards.
Improvement in accuracy provides more reliable laboratory information
facilitating more appropriate patient treatment decisions. © 2017 International
Clinical Cytometry Society. OBJECTIVE: To elucidate the diversity of systemic lupus erythematosus (SLE)
based on immunophenotyping.
METHODS: Peripheral blood mononuclear cells were obtained from 143 SLE patients
and 49 healthy individuals. Circulating B, T, and dendritic cells were defined
using flow cytometric analysis as recommended by the Human Immunology Project
Consortium. Based on these results, immunophenotypes were distinguished by
principal components analysis (PCA), and cluster analysis was used to classify
SLE patients into subgroups.
RESULTS: The proportions of Treg and follicular helper T (Tfh) cells were higher
in SLE patients than in healthy controls, whereas Th1 and Th17 cell proportions
did not differ. Proportions of class-switched memory B cells and IgD-CD27- B
cells were increased in SLE patients as well. The largest difference compared to
the control group was observed in the proportion of plasmablasts, which was
higher in SLE patients and correlated with disease activity as assessed with the
British Isles Lupus Assessment Group index. PCA indicated that the
immunophenotype of SLE patients consisted of abnormalities of the T and B cell
axes. Cluster analysis showed that the SLE patients could be stratified into 3
subgroups (with high proportions of plasmablasts in all groups): patients who
did not show the characteristic features (T cell-independent group), patients
with a high percentage of Tfh cells (Tfh-domit group), and patients with a
high percentage of memory Treg cells (Treg-domit group). The percentage of
patients whose SLE was resistant to treatment was highest among the Tfh-domit
group.
CONCLUSION: Our study indicates that patients with active SLE can be divided
into 3 subgroups based on T cell heterogeneity. Further immunophenotyping
studies should help elucidate the pathogenesis of SLE and provide important
information for the development of new therapies. |
What is the mechanism of action of Emicizumab? | Emicizumab (Hemlibra®) is a bispecific humanized monoclonal antibody that restores the function of missing activated FVIII by bridging activated FIX and FX to facilitate effective haemostasis in patients with haemophilia A. | BACKGROUND: In patients with severe hemophilia A, standard treatment is regular
prophylactic and episodic intravenous infusions of factor VIII. However, these
treatments are burdensome, especially for children, and may lead to the
formation of anti-factor VIII alloantibodies (factor VIII inhibitors).
Emicizumab (ACE910), a humanized bispecific antibody mimicking the cofactor
function of factor VIII, was developed to abate these problems.
METHODS: We enrolled 18 Japanese patients with severe hemophilia A (with or
without factor VIII inhibitors) in an open-label, nonrandomized, interindividual
dose-escalation study of emicizumab. The patients received subcutaneous
emicizumab weekly for 12 weeks at a dose of 0.3, 1.0, or 3.0 mg per kilogram of
body weight (cohorts 1, 2, and 3, respectively). The end points were safety and
pharmacokinetic and pharmacodynamic profiles. An additional, exploratory end
point was the annualized bleeding rate, calculated as 365.25 times the number of
bleeding episodes, divided by the number of days in the treatment period as
compared with the 6 months before enrollment.
RESULTS: Emicizumab was associated with neither serious adverse events nor
clinically relevant coagulation abnormalities. Plasma concentrations of
emicizumab increased in a dose-dependent manner. Activated
partial-thromboplastin times remained short throughout the study. The median
annualized bleeding rates in cohorts 1, 2, and 3 decreased from 32.5 to 4.4,
18.3 to 0.0, and 15.2 to 0.0, respectively. There was no bleeding in 8 of 11
patients with factor VIII inhibitors (73%) and in 5 of 7 patients without factor
VIII inhibitors (71%). Episodic use of clotting factors to control bleeding was
reduced. Antibodies to emicizumab did not develop.
CONCLUSIONS: Once-weekly subcutaneous administration of emicizumab markedly
decreased the bleeding rate in patients who had hemophilia A with or without
factor VIII inhibitors. (Funded by Chugai Pharmaceutical; JapicCTI number,
121934.). The development of inhibitors to factor VIII (FVIII) or factor IX (FIX) remains
a major treatment complication encountered in the treatment of haemophilia. Not
all patients with even the same severity and genotype develop inhibitors
suggesting an underlying mechanism of tolerance against FVIII- or FIX-related
immunity. One mechanism may be central tolerance observed in patients in whom
the FVIII mutation enables some production of the protein. The other is a
peripheral tolerance mechanism which may be evident in patients with null
mutation. Recently, recombit porcine FVIII (rpFVIII, Obixur, OBI-1, BAX801)
has been developed for the haemostatic treatment of both congenital haemophilia
with inhibitor (CHAWI) and acquired haemophilia A (AHA). In 28 subjects with AHA
with life-/limb-threatening bleeding, rpFVIII reduced or stopped bleeding in all
patients within 24 h. The cross-reactivity of anti-human FVIII antibodies to
rpFVIII remains around 30-50%. Recently, new therapeutics based on the quite
novel concepts have been developed and clinical studies are ongoing. These are
humanized asymmetric antibody mimicking FVIIIa function by maintaining a
suitable interaction between FIXa and FX (Emicizumab, ACE910), and small
interfering RNAs (siRNA, ALN-AT3) suppress liver production of AT through
post-transcriptional gene silencing and a humanized anti-TFPI monoclonal
antibody (Concizumab). Their main advantages are longer half-life, subcutaneous
applicability and efficacy irrespective of the presence of inhibitors which will
make it easier to initiate more effective treatment especially early childhood. Emicizumab, a humanised bispecific antibody recognising factors (F) IX/IXa and
X/Xa, can accelerate FIXa-catalysed FX activation by bridging FIXa and FX in a
manner similar to FVIIIa. However, details of the emicizumab-antigen
interactions have not been reported so far. In this study, we first showed by
surface plasmon resoce analysis that emicizumab bound FIX, FIXa, FX, and FXa
with moderate affinities (KD = 1.58, 1.52, 1.85, and 0.978 µM, respectively). We
next showed by immunoblotting analysis that emicizumab recognised the antigens'
epidermal growth factor (EGF)-like domains. We then performed KD-based
simulation of equilibrium states in plasma for quantitatively predicting the
ways that emicizumab would interact with the antigens. The simulation predicted
that only a small part of plasma FIX, FX, and emicizumab would form
antigen-bridging FIX-emicizumab-FX ternary complex, of which concentration would
form a bell-shaped relationship with emicizumab concentration. The bell-shaped
concentration dependency was reproduced by plasma thrombin generation assays,
suggesting that the plasma concentration of the ternary complex would correlate
with emicizumab's cofactor activity. The simulation also predicted that at
10.0-100 µg/ml of emicizumab-levels shown in a previous study to be clinically
effective-the majority of plasma FIX, FX, and emicizumab would exist as
monomers. In conclusion, emicizumab binds FIX/FIXa and FX/FXa with micromolar
affinities at their EGF-like domains. The KD-based simulation predicted that the
antigen-bridging ternary complex formed in circulating plasma would correlate
with emicizumab's cofactor activity, and the majority of FIX and FX would be
free and available for other coagulation reactions. During the last decade, the development of improved and novel approaches for the
treatment of hemophilia A has expanded tremendously. These approaches include
factor VIII (FVIII) with extended half-life (eg, FVIII-Fc and PEGylated FVIII),
monoclonal antibodies targeting tissue factor pathway inhibitor, small
interfering RNA to reduce antithrombin expression and the bispecific antibody
ACE910/emicizumab. Emicizumab is a bispecific antibody recognizing both the
enzyme factor IXa and the substrate factor X. By simultaneously binding enzyme
and substrate, emicizumab mimics some part of the function exerted by the
original cofactor, FVIII, in that it promotes colocalization of the
enzyme-substrate complex. However, FVIII and the bispecific antibody are
fundamentally different proteins and subject to different modes of regulation.
Here, we will provide an overview of the similarities and dissimilarities
between FVIII and emicizumab from a biochemical and mechanistical perspective.
Such insight might be useful in the clinical decision making for those who apply
emicizumab in their practice now or in the future, particularly in view of the
thrombotic complications that have been reported when emicizumab is used in
combination with FVIII-bypassing agents. Emicizumab (ACE910), a recombit humanized bispecific monoclonal antibody,
provides factor VIII (FVIII) cofactor bridging function to restore hemostasis in
people with hemophilia A. In a phase 1 trial involving 18 Japanese patients with
severe hemophilia A, once-weekly subcutaneous administration of emicizumab 0.3,
1, or 3 mg/kg (cohorts 1, 2, and 3, respectively) was well tolerated and
substantially reduced annualized bleeding rates (ABRs) in the presence or
absence of FVIII inhibitors. The current study represents an open-label,
long-term extension of the previously reported 12-week phase 1 study, in which
16 of 18 patients continued to receive emicizumab for up to 33.3 months.
Long-term emicizumab treatment was well tolerated, with no thromboembolic events
reported and no neutralizing antiemicizumab antibodies developing during the
course of the study. Plasma concentrations of emicizumab increased in a
dose-proportional manner, with activated partial thromboplastin times remaining
short. In cohorts 1, 2, and 3, respectively, median ABRs remained low at 1.4,
0.2, and 0 compared with 4.4, 0, and 0 in the 12-week study. Overall, 8 patients
experienced no bleeding events (6 patients with and 2 patients without FVIII
inhibitors); dose up-titration resulted in further reduction in ABRs in patients
with suboptimal bleeding control; and the episodic use of clotting factors to
control bleeding was reduced. In conclusion, long-term emicizumab treatment
demonstrated a favorable safety profile with encouraging efficacy, irrespective
of the presence of FVIII inhibitors, in patients with hemophilia A. This study
was registered at www.clinicaltrials.jp as #JapicCTI-132195. Essentials The activated partial prothrombin time (aPTT) cannot predict the
activity of emicizumab (Emi). Adjusted clot waveform analyses using a
prothrombin time (PT)/aPTT initiator were developed. Activity of Emi in the
co-presence of factor VIII or bypassing agents was quantified. This assay is
useful for assessing coagulation potential in Emi-treated hemophilia A.
SUMMARY: Background Emicizumab is an anti-activated factor IX/FX bispecific
antibody that mimics activated FVIII cofactor function. Emicizumab does not
require activation by thrombin, and its effect on shortening the activated
partial thromboplastin time (APTT) is much greater than that of FVIII.
Therefore, the APTT has limited utility in hemophilia A (HA) patients treated
with emicizumab. Aim To evaluate the global coagulation potential of emicizumab.
Methods Clot waveform analysis (CWA) with prothrombin time (PT)/APTT mixed
reagents was used to define hemostatic monitoring protocols in HA patients. A
modified parameter, adjusted-|min1| (Ad|min1|), was developed. Maximum and
minimum percentage transmittance were defined as 100% and 0% in the
precoagulation and postcoagulation phases, respectively. Ad|min1| was calculated
as an index of the maximum velocity of the coagulation process. Results Ad|min1|
obtained with mixed-trigger reagent (PT/APTT/buffer, 1 : 15 : 135) in the
presence of emicizumab optimally corresponded to the conversion rate estimated
in animals; 0.2-0.4 IU dL-1 equivalent FVIII per 1 μg mL-1 emicizumab). Ex vivo
addition of emicizumab to HA plasma with or without inhibitors resulted in
concentration-dependent increases in Ad|min1|, with some individual variations.
The addition of various concentrations of FVIII to HA plasma mixed with
emicizumab resulted in dose-dependent increases in Ad|min1|. Similarly, mixtures
of activated prothrombin complex concentrate and emicizumab added to HA plasma
resulted in dose-dependent increases in Ad|min1|. In contrast, enhanced
coagulation potential appeared to be better defined by the clot time than by
Ad|min1| in experiments using recombit activated FVII. Conclusion The PT/APTT
reagent-triggered adjusted CWA could provide a useful means of assessing global
coagulation potential in emicizumab-treated HA patients, with enhanced activity
neither masking nor being masked by FVIII or bypassing agents. Hemophilia and von Willebrand disease are the most common congenital bleeding
disorders. Treatment of these disorders has focused on replacement of the
missing coagulation factor to prevent or treat bleeding. New technologies and
insights into hemostasis have driven the development of many promising new
therapies for hemophilia and von Willebrand disease. Emerging bypass agents
including zymogen-like factor IXa and Xa molecules are in development and a
bispecific antibody, emicizumab, demonstrated efficacy in a phase 3 trial in
people with hemophilia A and inhibitors. Tissue factor pathway inhibitor, the
protein C/S system, and antithrombin are targets of novel compounds in
development to alter the hemostatic balance and new approaches using modified
factor VIII molecules are being tested for prevention and eradication of
inhibitor antibodies in hemophilia A. The first recombit von Willebrand
factor (VWF) product has been approved and has unique VWF multimer content and
does not contain factor VIII. These new approaches may offer better routes of
administration, improved dosing regimens, and better efficacy for prevention and
treatment of bleeding in congenital bleeding disorders. Essentials Patients with hemophilia A and inhibitors receiving emicizumab
experience breakthrough bleeding. Safety concerns may exist when combining
emicizumab with bypassing agents. Combined bypassing agent and bispecific
antibody increased thrombin generation up to 17-fold. Thrombotic effects should
be considered when combining emicizumab with plasma bypassing agent.
SUMMARY: Background Investigational non-factor products such as emicizumab offer
a treatment option for patients with hemophilia and inhibitors. However, their
mechanism of action raises questions regarding safety when they are combined
with treatments for breakthrough bleeding. Objectives To evaluate in vitro
thrombin generation (TG) and clot formation for combinations of activated
prothrombin complex concentrate (aPCC), recombit activated factor VII
(rFVIIa), and a sequence-identical analog of emicizumab (SIA). Methods
Therapeutic concentrations of SIA (20-600 nm) alone or with aPCC (0.05-1 U mL-1
), isolated aPCC components or rFVIIa (0.88-5.25 μg mL-1 ) were tested for TG
and compared with reference ranges for healthy donor plasma. Coagulation of
FVIII-inhibited blood was determined with a widely established method, i.e.
rotational thromboelastometry (ROTEM), and confirmed with the Total
Thrombus-formation Analysis System. Results and conclusions SIA (600 nm) or aPCC
(0.5 U mL-1 ) alone resulted in peak thrombin levels of 21.4 nm and 38.6 nm,
respectively, both of which are lower than normal (83.7 ± 29.8 nm). SIA plus
aPCC (0.5 U mL-1 ) increased the peak thrombin level 17-fold over SIA alone,
exceeding the reference plasma value by 4.2-fold. This hypercoagulable effect
occurred with 600 nmSIA combined with as little as 0.25 U mL-1 aPCC, confirmed
by ROTEM. FIX was the main driver for enhanced TG. SIA plus rFVIIa (1.75 μg mL-1
) induced a 1.8-fold increase in the peak thrombin level in platelet-rich
plasma, but it did not reach the normal range. These in vitro experiments
demonstrate excessive TG after administration of a combination of aPCC and SIA
at clinically relevant doses. Careful judgement may be required when
breakthrough bleeding is treated in patients receiving emicizumab. Hemophilia is a serious bleeding disorder characterized by repeated bleeding
episodes into joints and muscles which can lead to permanent disabilities.
Treatment with factor replacement therapy has proven to be effective at
preventing these complications; however, it can lead to formation of
neutralizing antibodies termed inhibitors which significantly complicate the
management of the disorder. These inhibitor patients suffer from increased
morbidity and mortality and there has been a major unmet need for novel
therapeutic approaches. Recently, one such therapy, emicizumab, has been
licensed in the United States. Areas covered: This manuscript contains a
detailed discussion of the mechanism of action, the clinical trial development
program as well as a review of the benefits and risks of this novel agent. In
addition, practical considerations for the use of the agent are also described.
Expert commentary: Emicizumab represents a new class of medication for the
treatment of hemophilia A which in the past has relied on factor replacement
therapy and bypassing agent (alternative factor) therapy. Emicizumab fulfills
two major unmet needs in patients with hemophilia who have FVIII inhibitors.
First, it provides for a much more effective therapy for the prevention of
bleeding and second it substantially reduces the treatment burden. Hemophilia A, characterized by impaired or absent expression of factor VIII, has
long been managed via direct factor replacement. Functionally, factor VIII acts
as a cofactor for factor IXa and allows activation of factor X, which, in
combination with factor V, generates thrombin. Bispecific antibodies such as
emicizumab are recombit, monoclonal antibodies capable of recognizing and
binding to two distinct antigenic targets simultaneously; emicizumab binds
factors IXa and X, resulting in spatial approximation and activation of factor
X, thereby mimicking the actions of factor VIII. Critically, the presence of
antifactor VIII antibodies, for example, inhibitors, impacts neither the
mechanism nor the efficacy by which emicizumab functions. The results and
interim analyses of the emicizumab clinical trials, HAVEN 1, 2, 3, and 4, are
additionally reviewed and discussed. INTRODUCTION: Emicizumab-kywh (ACE910) is a recombit, humanized, asymmetric
bispecific antibody that functions to bring activated FIX (FIXa) and zymogen FX
into an appropriate steric conformation to medicate the activation of FX to FXa
thereby mimicking the cofactor function of FVIIIa.
AIM: The objective of this manuscript was to review the development and
potential role for emicizumab in the treatment of patients with haemophilia A
with and without inhibitors.
METHODS: A Cochrane Library and PubMed (MEDLINE) search focusing on emicizumab
in haemophilia was conducted.
RESULTS: In total, 37 citations were retrieved and serve as the database for the
literature reviewed herein. Once-weekly subcutaneous injection of emicizumab at
three dose levels has been shown to be effective as prophylaxis to prevent
bleeding in a majority haemophilia A patients with inhibitors to FVIII.
Likewise, prevention of bleeding was also observed in more than two thirds of
patients without inhibitors to FVIII. One antidrug antibody to emicizumab has
been reported in over 600 treated patients, two have developed thromboembolic
events and three thrombotic microangiopathy. These thrombotic complications have
occurred in conjunction with FVIII-bypassing agents, and none have been observed
following recommendations from the manufacturer regarding concomitant use of
bypassing agents. The median annual treated bleeding rates were decreased in
patients with as well as those without an inhibitor to FVIII.
CONCLUSION: The principal advantage of emicizumab is subcutaneous administration
and effectiveness irrespective of the presence of inhibitors. Emicizumab could
conceivably represent a new epoch in the treatment of people with haemophilia A. Essentials Emicizumab mimics factor (F)VIIIa cofactor function, augments the
intrinsic tenase activity. We assessed the emicizumab-driven hemostatic function
in FXI-deficient plasmas. Emicizumab improved the coagulation potentials in
severe FXI-deficient plasma. Emicizumab may provide a possibility for clinical
application in patients with FXI deficiency. SUMMARY: Background Patients with
factor (F)XI deficiency commonly present with markedly prolonged activated
partial thromboplastin times (APTT), although bleeding phenotypes are
heterogeneous. Emicizumab, a bispecific monoclonal antibody to FIX/FIXa and
FX/FXa, mimics FVIIIa cofactor function on phospholipid (PL) surfaces. Antibody
reactions were designed, therefore, to augment mechanisms during the propagation
phase of blood coagulation. Aim To assess emicizumab-driven hemostatic function
in FXI-deficient plasmas. Methods and Results Standard ellagic acid
(Elg)/PL-based APTTs of different FXI-deficient plasmas (n = 13; FXI activity,
< 1 IU dl-1 ) were markedly shortened dose dependently by the presence of
emicizumab. To further analyze the effects of emicizumab, clot waveform analysis
(CWA) in FXI-deficient plasmas with emicizumab, triggered by tissue factor
(TF)/Elg demonstrated improvements in both clot times, reflecting the initiation
phase, and coagulation velocity, which represents the propagation phase.
Emicizumab also enhanced the TF/Elg-triggered thrombin generation in
FXI-deficient plasmas dose-dependently although the degree of enhancement varied
in individual cases. Thrombin generation with either FVII-deficient plasma or
FIX-deficient plasma treated with anti-FXI antibody showed little or no increase
by the co-presence of emicizumab, suggesting that the accelerated thrombin
generation in FXI-deficient plasmas by emicizumab should depend on the
FIXa-involved coagulation propagation initially triggered by FVIIa/TF. The
ex vivo addition of emicizumab to whole blood from three patients with severe
FXI deficiency demonstrated modest, dose-dependent improvements in Ca2+
-triggered thromboelastograms (NATEM mode). Conclusion Emicizumab appeared to
improve coagulation function in severe FXI-deficient plasma, and might provide
possibilities for clinical application in patients with FXI deficiency. Patients affected by hemophilia A often require frequent prophylactic and
therapeutic self-infusion. For those who develop inhibitors, treatment options
are limited and mortality is increased. Emicizumab, a bispecific antibody to
Factors IXa and X that carries out the function of Factor VIII (FVIII),
represents a novel therapeutic approach. Areas covered: We review the clinical
trials and key laboratory assay research for emicizumab. Emicizumab reduced the
annualized bleeding rate by 87% compared to placebo in patients with inhibitors.
For patients without inhibitors, emicizumab reduced the annualized bleeding rate
96-97% compared to no prophylaxis and 68% compared to prior FVIII prophylaxis.
Three patients developed a thrombotic microangiopathy (TMA) and two patients had
thrombotic events while on emicizumab in combination with activated prothrombin
complex concentration (aPCC) alone or concurrent with activated recombit
factor FVII (rFVIIa). Expert opinion: Emicizumab represents a much-needed
alternative approach to managing Factor VIII deficiency, especially for those
with inhibitors or limited ability to self-infuse. For patients with inhibitors,
thrombotic complications including TMA, not seen with other bypassing agents,
raises concern about the use of emicizumab in combination with aPCC and how
patients who have breakthrough bleeding can be safely managed. |
What is the genetic cause of Roberts syndrome? | Roberts syndrome (RBS) is a human developmental disorder caused by mutations in the cohesin acetyltransferase ESCO2. | |
What is DiseaseEnhancer? | DiseaseEnhancer is a manually curated resource of human disease-associated enhancer catalog. As of July 2017, DiseaseEnhancer includes 847 disease-associated enhancers in 143 human diseases. Database features include basic enhancer information (i.e. genomic location and target genes); disease types; associated variants on the enhancer and their mediated phenotypes (i.e. gain/loss of enhancer and the alterations of transcription factor bindings). | |
Is Tisagenlecleucel effective for B-Cell Lymphoma? | Yes, CD19-targeting CAR T-cell therapy tisagenlecleucel produces durable responses in patients with relapsed and refractory diffuse large B-cell lymphoma. | The phase II JULIET trial suggests that the CD19-targeting CAR T-cell therapy
tisagenlecleucel produces durable responses in patients with relapsed and
refractory diffuse large B-cell lymphoma. Three months after the therapy, 32% of
the patients showed complete responses and 6% showed partial responses. After 6
months, those rates were 30% and 7%. Author information:
(1)From the Departments of Pediatrics (S.L.M., S.A.G.) and Pathology and
Laboratory Medicine (C.H.J., B.L.L.), Perelman School of Medicine, and Abramson
Cancer Center (C.H.J., B.L.L.), University of Pennsylvania, and the Division of
Oncology, Center for Childhood Cancer Research and Cancer Immunotherapy Program,
Children's Hospital of Philadelphia (S.L.M., S.A.G.) - all in Philadelphia; the
Department of Pediatrics and Harold C. Simmons Comprehensive Cancer Center,
University of Texas Southwestern Medical Center, and the Pauline Allen Gill
Center for Cancer and Blood Disorders, Children's Health, Dallas (T.W.L.); the
Department of Pediatric Hematology and Oncology, Oslo University Hospital, Oslo
(J.B.); the Department of Pediatric Hematology and Oncology, Hospital Sant Joan
de Deu Barcelona, Barcelona (S.R.); the Department of Pediatrics and Internal
Medicine, University of Utah, Salt Lake City (M.B.); the Department of
Pediatrics, Faculty of Medicine, University of Montreal, and the Hematology
Oncology Division and Charles-Bruneau Cancer Center, Centre Hospitalier
Universitaire Sainte-Justine Research Center, Montreal (H.B.), and the Division
of Haematology/Oncology/Bone Marrow Transplantation, Hospital for Sick Children,
Toronto (J.K.) - all in Canada; the Division of Stem Cell Transplantation and
Immunology, Hospital for Children and Adolescents, University Hospital
Frankfurt, Frankfurt, Germany (P.B.); the Division of Pediatric Blood and Marrow
Transplant, University of Minnesota, Minneapolis (M.R.V., H.E.S.); Children's
Mercy Hospital and Clinics, Kansas City, MO (G.D.M.); Aflac Cancer and Blood
Disorders Center, Emory University, Atlanta (M.Q.); the Department of Pediatric
Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital,
and the Cancer Research Institute Ghent (CRIG), Ghent, Belgium (B.D.M.); the
Department of Pediatrics, Graduate School of Medicine Kyoto University, Kyoto,
Japan (H.H.); the Department of Pediatrics, Stanford University School of
Medicine, Stanford (K. Schlis, K.L.D.), and the Division of Hematology,
Oncology, Blood and Marrow Transplant, Children's Hospital Los Angeles, USC Keck
School of Medicine, Los Angeles (M.A.P.) - all in California; the Division of
Pediatric Blood and Marrow Transplant, Duke University Medical Center, Durham,
NC (P.L.M.); Oregon Health and Science University, Portland (E.R.N.); C.S. Mott
Children's Hospital, Ann Arbor, MI (G.A.Y.); the Stem Cell Transplantation Unit,
St. Anna Children's Hospital, Vienna (C.P.); University Hospital Robert Debré
and University Paris Diderot (A. Baruchel), and Saint-Louis Hospital and
University Paris Diderot (N.B.), Paris; the Royal Children's Hospital,
Melbourne, VIC, Australia (F.M.); Clinica Pediatrica Universita degli Studi di
Milano Bicocca, Monza, Italy (A. Balduzzi); and Novartis Pharmaceuticals (P.W.,
T.T., M.L., Y.Z., K. Sen, D.L.) and Novartis Institutes for Biomedical Research
(K.T.M.) - both in East Hanover, NJ. On August 30, 2017, the U.S. Food and Drug Administration (FDA) approved
Novartis' tisagenlecleucel (CTL-019, Kymriah), which is a synthetic bioimmune
product of anti-CD19 chimeric antigen receptor (CAR) T cells, for the treatment
of relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL). This was a
milestone in tumor immunology on account of the significant antitumor effect of
tisagenlecleucel for the treatment of relapsed/refractory B-ALL patients.
Conventional standard therapies for B-ALL have high failure rates, thus
developing new therapies is crucial for patients with B-ALL. Results from
clinical trials indicate that anti-CD19 CAR T-cell therapies could successfully
induce high response rates in B-ALL patients. However, related toxicities, such
as cytokine release syndrome and CAR T-cell-related encephalopathy syndrome, may
be severe or even fatal, and the management of such toxicities is therefore
vital. This review will focus on the clinical application of anti-CD19 CAR
T-cell therapy in B-ALL treatment, including design features of CAR constructs,
therapeutic use of tisagenlecleucel, CAR T-cell therapy clinical trials and
related toxicity, and prospects for cancer immunotherapy. BACKGROUND: Anti-CD19 CAR T cell therapy has demonstrated high response rates in
patients with relapsed or refractory (r/r) B cell maligcies but is associated
with significant toxicity. Cytokine release syndrome (CRS) is the most
significant complication associated with CAR T cell therapy, and it is critical
to have a reproducible and easy method to grade CRS after CAR T cell infusions.
DISCUSSION: The Common Terminology Criteria for Adverse Events scale is
inadequate for grading CRS associated with cellular therapy. Clinical experience
with the anti-CD19 CAR T cell therapy tisagenlecleucel at the University of
Pennsylvania (Penn) was used to develop the Penn grading scale for CRS. The Penn
grading scale depends on easily accessible clinical features; does not rely on
location of care or quantitation of supportive care; assigns grades to guide CRS
management; distinguishes between mild, moderate, severe, and life-threatening
CRS; and applies to both early-onset and delayed-onset CRS associated with T
cell therapies. Clinical data from 55 pediatric patients with r/r B cell acute
lymphoblastic leukemia and 42 patients with r/r chronic lymphocytic lymphoma
treated with tisagenlecleucel were used to demonstrate the current application
of the Penn grading scale.
CONCLUSION: We show that the Penn grading scale provides reproducible CRS
grading that can be useful to guide therapy and that can be applied across
clinical trials and treatment platforms. Conflict of interest statement: Conflict-of-interest disclosure: M.S. provides
consultancy for Abbvie, Genentech, and Sound Biologics; is on the advisory board
for Abbvie, Genentech, and Verastem; and receives research funding from Mustang
Biopharma, Pharmacyclics, Gilead, Genentech, TG Therapeutics, Bigene, Acerta,
Emergent, and Merck. A.K.G. reports grants and nonficial support from Teva,
Bristol-Myers Squibb, Merck, Takeda, TG Therapeutics, and Effector; grants,
personal fees, and nonficial support from Seattle Genetics, Pfizer, Janssen,
Gilead, Spectrum, and Incyte; and personal fees from Aptevo, BRIM Bio, Seattle
Genetics, and Sanofi. V.A.C. declares no competing ficial interests. PURPOSE: Tisagenlecleucel is an anti-CD19 chimeric antigen receptor (CAR19)
T-cell therapy approved for the treatment of children and young adults with
relapsed/refractory (r/r) B-cell acute lymphoblastic leukemia (B-ALL).
PATIENTS AND METHODS: We evaluated the cellular kinetics of tisagenlecleucel,
the effect of patient factors, humoral immunogenicity, and manufacturing
attributes on its kinetics, and exposure-response analysis for efficacy, safety
and pharmacodynamic endpoints in 79 patients across two studies in pediatric
B-ALL (ELIANA and ENSIGN).
RESULTS: Using quantitative polymerase chain reaction to quantify levels of
tisagenlecleucel transgene, responders (N = 62) had ≈2-fold higher
tisagenlecleucel expansion in peripheral blood than nonresponders (N = 8; 74%
and 104% higher geometric mean Cmax and AUC0-28d, respectively) with persistence
measurable beyond 2 years in responding patients. Cmax increased with occurrence
and severity of cytokine release syndrome (CRS). Tisagenlecleucel continued to
expand and persist following tocilizumab, used to manage CRS. Patients with
B-cell recovery within 6 months had earlier loss of the transgene compared with
patients with sustained clinical response. Clinical responses were seen across
the entire dose range evaluated (patients ≤50 kg: 0.2 to 5.0 × 106/kg; patients
>50 kg: 0.1 to 2.5 × 108 CAR-positive viable T cells) with no relationship
between dose and safety. Neither preexisting nor treatment-induced antimurine
CAR19 antibodies affected the persistence or clinical response.
CONCLUSIONS: Response to tisagenlecleucel was associated with increased
expansion across a wide dose range. These results highlight the importance of
cellular kinetics in understanding determits of response to chimeric antigen
receptor T-cell therapy. Relapsed or refractory aggressive B-cell lymphoma has an extremely poor
prognosis and efforts to develop novel therapies for these patients have failed
for almost four decades until the advent of chimeric antigen receptor (CAR)
T-cell therapy. Within the last one year, two anti-CD19 CAR T-cell therapy
products, axicabtagene ciloleucel and tisagenlecleucel, were approved by the
United States Food and Drug Administration for the treatment of relapsed or
refractory large B-cell lymphoma after at least two lines of systemic therapy
based on multicenter single-arm phase two clinical trials. Here, we will discuss
the different components of the CAR construct and their mechanisms of action,
the role of conditioning chemotherapy, the efficacy and toxicity observed with
anti-CD19 CAR T-cell therapies in aggressive B-cell lymphomas, and emerging
strategies to further improve the safety and efficacy of these highly promising
approaches. Tisagenlecleucel (Kymriah; Novartis Pharmaceuticals) is a CD19-directed
genetically modified autologous T-cell immunotherapy. On August 30, 2017, the
FDA approved tisagenlecleucel for treatment of patients up to 25 years of age
with B-cell precursor acute lymphoblastic leukemia (ALL) that is refractory in
second or later relapse. Approval was based on the complete remission (CR) rate,
durability of CR, and minimal residual disease (MRD) <0.01% in a cohort of 63
children and young adults with relapsed or refractory ALL treated on a
single-arm trial (CCTL019B2202). Treatment consisted of fludarabine and
cyclophosphamide followed 2 to 14 days later by a single dose of
tisagenlecleucel. The CR rate was 63% (95% confidence interval, 50%-75%), and
all CRs had MRD <0.01%. With a median follow-up of 4.8 months, the median
duration of response was not reached. Cytokine release syndrome (79%) and
neurologic events (65%) were serious toxicities reported in the trial. With
implementation of a Risk Evaluation and Mitigation Strategy, the benefit-risk
profile was considered acceptable for this patient population with such
resistant ALL. A study of safety with 15 years of follow-up is required as a
condition of the approval.See related commentary by Geyer, p. 1133. |
What is the function of GFRAL? | GFRAL (orphan receptor of the glial-derived neurotrophic factor (GDNF) receptor α family) is a high-affinity receptor for GDF15.
GFRAL expression is limited to hindbrain neurons and not present in peripheral tissues, which suggests that GDF15-GFRAL-mediated regulation of food intake is by a central mechanism. | Growth differentiation factor 15 (GDF15), a distant member of the transforming
growth factor (TGF)-β family, is a secreted protein that circulates as a 25-kDa
dimer. In humans, elevated GDF15 correlates with weight loss, and the
administration of GDF15 to mice with obesity reduces body weight, at least in
part, by decreasing food intake. The mechanisms through which GDF15 reduces body
weight remain poorly understood, because the cognate receptor for GDF15 is
unknown. Here we show that recombit GDF15 induces weight loss in mice fed a
high-fat diet and in nonhuman primates with spontaneous obesity. Furthermore, we
find that GDF15 binds with high affinity to GDNF family receptor α-like (GFRAL),
a distant relative of receptors for a distinct class of the TGF-β superfamily
ligands. Gfral is expressed in neurons of the area postrema and nucleus of the
solitary tract in mice and humans, and genetic deletion of the receptor
abrogates the ability of GDF15 to decrease food intake and body weight in mice.
In addition, diet-induced obesity and insulin resistance are exacerbated in
GFRAL-deficient mice, suggesting a homeostatic role for this receptor in
metabolism. Finally, we demonstrate that GDF15-induced cell signaling requires
the interaction of GFRAL with the coreceptor RET. Our data identify GFRAL as a
new regulator of body weight and as the bona fide receptor mediating the
metabolic effects of GDF15, enabling a more comprehensive assessment of GDF15 as
a potential pharmacotherapy for the treatment of obesity. Growth/differentiation factor 15 (GDF15), also known as MIC-1, is a distant
member of the transforming growth factor-β (TGF-β) superfamily and has been
implicated in various biological functions, including cancer cachexia, renal and
heart failure, atherosclerosis and metabolism. A connection between GDF15 and
body-weight regulation was initially suggested on the basis of an observation
that increasing GDF15 levels in serum correlated with weight loss in individuals
with advanced prostate cancer. In animal models, overexpression of GDF15 leads
to a lean phenotype, hypophagia and other improvements in metabolic parameters,
suggesting that recombit GDF15 protein could potentially be used in the
treatment of obesity and type 2 diabetes. However, the signaling and mechanism
of action of GDF15 are poorly understood owing to the absence of a clearly
identified cognate receptor. Here we report that GDNF-family receptor α-like
(GFRAL), an orphan member of the GFR-α family, is a high-affinity receptor for
GDF15. GFRAL binds to GDF15 in vitro and is required for the metabolic actions
of GDF15 with respect to body weight and food intake in vivo in mice. Gfral-/-
mice were refractory to the effects of recombit human GDF15 on body-weight,
food-intake and glucose parameters. Blocking the interaction between GDF15 and
GFRAL with a monoclonal antibody prevented the metabolic effects of GDF15 in
rats. Gfral mRNA is highly expressed in the area postrema of mouse, rat and
monkey, in accordance with previous reports implicating this region of the brain
in the metabolic actions of GDF15 (refs. 4,5,6). Together, our data demonstrate
that GFRAL is a receptor for GDF15 that mediates the metabolic effects of GDF15. Growth differentiation factor 15 (GDF15; also known as MIC-1) is a divergent
member of the TGF-β superfamily and is associated with body-weight regulation in
humans and rodents. However, the cognate receptor of GDF15 is unknown. Here we
show that GDF15 binds specifically to GDNF family receptor α-like (GFRAL) with
high affinity, and that GFRAL requires association with the coreceptor RET to
elicit intracellular signaling in response to GDF15 stimulation. We also found
that GDF15-mediated reductions in food intake and body weight of mice with
obesity were abolished in GFRAL-knockout mice. We further found that GFRAL
expression was limited to hindbrain neurons and not present in peripheral
tissues, which suggests that GDF15-GFRAL-mediated regulation of food intake is
by a central mechanism. Lastly, given that GDF15 did not increase energy
expenditure in treated mice with obesity, the anti-obesity actions of the
cytokine are likely driven primarily by a reduction in food intake. Macrophage inhibitory cytokine-1/growth differentiation factor 15 (MIC-1/GDF15)
is a divergent transforming growth factor (TGFβ) superfamily cytokine implicated
in biological and disease processes including metabolism, cancer, and chronic
inflammation, but whose receptor has remained elusive. Four laboratories have
recently identified GFRAL, an orphan receptor of the glial-derived neurotrophic
factor (GDNF) receptor α family, as the receptor for MIC-1/GDF15, signaling
though the coreceptor Ret. These data identify a new systemic to central nervous
system (CNS) circuit that regulates metabolism in response to stress and which
could be targeted to treat both severe obesity and anorexia/cachexia syndrome. |
What is the role of ZCCHC17? | ZCCHC17 is a master regulator of synaptic gene expression in Alzheimer's disease. Master regulator analysis identifies ZCCHC17 as normally supporting the expression of a network of synaptic genes, and predicts that ZCCHC17 dysfunction in AD leads to lower expression of these genes. ZCCHC17 is normally expressed in neurons and is reduced early in the course of AD pathology. Its loss in rat neurons leads to lower expression of the majority of the predicted synaptic targets. | MOTIVATION: In an effort to better understand the molecular drivers of synaptic
and neurophysiologic dysfunction in Alzheimer's disease (AD), we analyzed
neuronal gene expression data from human AD brain tissue to identify master
regulators of synaptic gene expression.
RESULTS: Master regulator analysis identifies ZCCHC17 as normally supporting the
expression of a network of synaptic genes, and predicts that ZCCHC17 dysfunction
in AD leads to lower expression of these genes. We demonstrate that ZCCHC17 is
normally expressed in neurons and is reduced early in the course of AD
pathology. We show that ZCCHC17 loss in rat neurons leads to lower expression of
the majority of the predicted synaptic targets and that ZCCHC17 drives the
expression of a similar gene network in humans and rats. These findings support
a conserved function for ZCCHC17 between species and identify ZCCHC17 loss as an
important early driver of lower synaptic gene expression in AD.
AVAILABILITY AND IMPLEMENTATION: Matlab and R scripts used in this paper are
available at https://github.com/afteich/AD_ZCC.
CONTACT: [email protected].
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics
online. |
Is ADP-ribosylation a PTM? | Yes,
Poly-ADP-ribosylation (PARylation) is a protein posttranslational modification (PTM) that is critically involved in many biological processes that are linked to cell stress responses. | Posttranslational modifications (PTMs) regulate protein functions and
interactions. ADP-ribosylation is a PTM, in which ADP-ribosyltransferases use
nicotinamide adenine dinucleotide (NAD+) to modify target proteins with
ADP-ribose. This modification can occur as mono- or poly-ADP-ribosylation. The
latter involves the synthesis of long ADP-ribose chains that have specific
properties due to the nature of the polymer. ADP-Ribosylation is reversed by
hydrolases that cleave the glycosidic bonds either between ADP-ribose units or
between the protein proximal ADP-ribose and a given amino acid side chain. Here
we discuss the properties of the different enzymes associated with
ADP-ribosylation and the consequences of this PTM on substrates. Furthermore,
the different domains that interpret either mono- or poly-ADP-ribosylation and
the implications for cellular processes are described. MOTIVATION: ADP-ribosylation is a post-translational modification (PTM)
implicated in several crucial cellular processes, ranging from regulation of DNA
repair and chromatin structure to cell metabolism and stress responses. To date,
a complete understanding of ADP-ribosylation targets and their modification
sites in different tissues and disease states is still lacking. Identification
of ADP-ribosylation sites is required to discern the molecular mechanisms
regulated by this modification. This motivated us to develop a computational
tool for the prediction of ADP-ribosylated sites.
RESULTS: Here, we present ADPredict, the first dedicated computational tool for
the prediction of ADP-ribosylated aspartic and glutamic acids. This predictive
algorithm is based on (i) physicochemical properties, (ii) in-house designed
secondary structure-related descriptors and (iii) three-dimensional features of
a set of human ADP-ribosylated proteins that have been reported in the
literature. ADPredict was developed using principal component analysis and
machine learning techniques; its performance was evaluated both internally via
intensive bootstrapping and in predicting two external experimental datasets. It
outperformed the only other available ADP-ribosylation prediction tool, ModPred.
Moreover, a novel secondary structure descriptor, HM-ratio, was introduced and
successfully contributed to the model development, thus representing a promising
tool for bioinformatics studies, such as PTM prediction.
AVAILABILITY AND IMPLEMENTATION: ADPredict is freely available at
www.ADPredict.net.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics
online. |
Does epidural anesthesia for pain management during labor affect the Apgar score of the the infant? | Epidural analgesia for labor pain management did not appear to have an immediate effect on neonatal status as determined by Apgar scores or in admissions to neonatal intensive care. | BACKGROUND AND OBJECTIVES: The association of an opioid with a local anesthetic
improves the quality of labor analgesia and reduces the risk of systemic
toxicity of the local anesthetic. However, opioids are not devoid of side
effects. The aim of this study was to compare the side effects of subarachnoid
sufentanil associated with bupivacaine to those caused by epidural sufentanil
associated with ropivacaine in the doses used in the Anesthesiology Department
in pregt women undergoing labor analgesia.
METHODS: Sixty pregt women, ASA physical status I and II, ages between 15 and
42 years, at term and with healthy fetuses, undergoing labor analgesia were
enrolled in this study. They were randomly divided in two groups: G1 - combined
spinal epidural anesthesia - 0.5% bupivacaine (2.5 mg) and subarachnoid
sufentanil (5 microg); G2 - Epidural Block - 0.2% ropivacaine (20 mg), and
epidural sufentanil (10 microg). Complementary doses of 0.2% ropivacaine (12 mg)
were administered whenever necessary, and 1% ropivacaine (50 mg) was
administered for labor resolution. Patients were evaluated after analgesia (M1)
regarding the presence of hypotension, maternal bradycardia, pruritus, nausea,
vomiting, respiratory depression, and sedation. They were also evaluated
postoperatively (M2) regarding the presence of nausea, vomiting, pruritus,
sedation, urinary retention, and pain. Newborns were evaluated by the Apgar
score. The test t Student, Mann-Whitney test, and Chi-Square test were used for
the statistical analysis.
RESULTS: Both groups were similar regarding age, weight, height, duration of
labor after analgesia, Apgar score of the newborns, hypotension, maternal
bradycardia, nausea, vomiting, pruritus, and urinary retention. Sedation was
more frequent in patients in G2 at M1 (50%), which was statistically
significant.
CONCLUSION: Subarachnoid or epidural sufentanil, in the doses used in this
study, associated with local anesthetics, had the same effect on the duration of
labor after analgesia and in the Apgar score of newborns. Sedation was the most
frequent side effect in patients receiving epidural sufentanil. |
What is latex bead phagocytosis? | Macrophage scavenger function was assessed by an in vitro latex bead phagocytosis assay.
We developed a scanning cytometry-based high-throughput assay of macrophage phagocytosis that quantitates bound and internalized unopsonized latex beads. | A highly sensitive quantitative fluorometric assay for phagocytosis, previously
measured using fluorescence spectrophotometry or flow cytometry, has been
adapted for use with a 96-well fluorescence plate reader. The technique allows
rapid analysis of large numbers of samples, and requires only a small sample
volume. Comparison of plate types demonstrated that opaque white 96-well
luminostrips produced a 100 fold greater fluorescent output, and were more
sensitive than black fluoroplates. Intraplate variability was also significantly
lower using white luminostrips. For the phagocytic assay, fluorescein conjugated
polystyrene beads were incubated with macrophage monolayers in white
luminostrips. After incubation, cells were washed, lysed and phagocytosis
quantified by determining the fluorescent intensity using a fluorescence plate
reader. The number of beads phagocytized was determined from a standard curve of
bead number versus fluorescent output. The phagocytic activity of resident and
thioglycollate-elicited peritoneal macrophages was compared using this
technique. BACKGROUND: Scavenger receptors are important components of the innate immune
system in the lung, allowing alveolar macrophages to bind and phagocytose
numerous unopsonized targets. Mice with genetic deletions of scavenger
receptors, such as SR-A and MARCO, are susceptible to infection or inflammation
from inhaled pathogens or dusts. However, the signaling pathways required for
scavenger receptor-mediated phagocytosis of unopsonized particles have not been
characterized.
METHODS: We developed a scanning cytometry-based high-throughput assay of
macrophage phagocytosis that quantitates bound and internalized unopsonized
latex beads. This assay allowed the testing of a panel of signaling inhibitors
which have previously been shown to target opsonin-dependent phagocytosis for
their effect on unopsonized bead uptake by human in vitro-derived alveolar
macrophage-like cells. The non-selective scavenger receptor inhibitor poly(I)
and the actin destabilizer cytochalasin D were used to validate the assay and
caused near complete abrogation of bead binding and internalization,
respectively.
RESULTS: Microtubule destabilization using nocodazole dramatically inhibited
bead internalization. Internalization was also significantly reduced by
inhibitors of tyrosine kinases (genistein and herbimycin A), protein kinase C
(staurosporine, chelerythrine chloride and Gö 6976), phosphoinositide-3 kinase
(LY294002 and wortmannin), and the JNK and ERK pathways. In contrast, inhibition
of phospholipase C by U-73122 had no effect.
CONCLUSION: These data indicate the utility of scanning cytometry for the
analysis of phagocytosis and that phagocytosis of unopsonized particles has both
shared and distinct features when compared to opsonin-mediated phagocytosis. |
Is phospholipid hydroperoxide glutathione peroxidase a selenoprotein? | Yes,
the phospholipid hydroperoxide glutathione peroxidase (PHGPx/GPx4) is the major selenoprotein. | Spermatogenesis is a complex process of male germ cells proliferation and
maturation from diploid spermatogonia, through meiosis, to mature haploid
spermatozoa. The process involves dynamic interactions between the developing
germ cells and their supporting Sertoli cells. The gonadal tissue, with
abundance of highly unsaturated fatty acids, high rates of cell division, and
variety of testis enzymes results very vulnerable to the overexpression of
reactive oxygen species (ROS). In order to address this risk, testis has
developed a sophisticated array of antioxidant systems comprising both enzymes
and free radical scavengers. This chapter sets out the major pathways of testis
generation, the metabolism of ROS, and highlights the transcriptional regulation
by steroid receptors of antioxidant stress enzymes and their functional
implications. It also deals with of the advantages of the system biology for an
antioxidant under steroid control, the major selenoprotein expressed by germ
cells in the testis, the phospholipid hydroperoxide glutathione peroxidase
(PHGPx/GPx4) having multiple functions and representing the pivotal link between
selenium, sperm quality, and species preservation. Glutathione peroxidase (Gpx1) is the major selenoprotein in most tissues in
animals. Knockout (KO) of Gpx1 decreases Gpx1 activity to near zero and
substantially reduces liver selenium (Se) levels, but has no overt effects in
otherwise healthy mice. To investigate the impact of deletion of Gpx1 on Se
metabolism, Se flux, and apparent Se requirements, KO, Gpx1 heterozygous (Het),
and Gpx1 wild-type (WT) mice were fed Se-deficient diet for 17 weeks, then
repleted with graded levels of Se (0-0.3 μg Se/g as Na2SeO3) for 7 days, and
selenoprotein activities and transcripts were determined in blood, liver, and
kidney. Se deficiency decreased the activities of plasma Gpx3, liver Gpx1, liver
Txnrd, and liver Gpx4 to 3, 0.3, 11, and 50% of WT Se-adequate levels,
respectively, but the Gpx1 genotype had no effect on growth or changes in
activity or expression of selenoproteins other than Gpx1. Se repletion increased
selenoprotein transcripts to Se-adequate levels after 7 days; Se response curves
and apparent Se requirements for selenoprotein transcripts were similar to those
observed in studies starting with Se-adequate mice. With short-term Se
repletion, selenoenzyme activities resulted in three Se response curve patterns:
(1) liver and kidney Gpx1, Gpx4, and Txnrd activities were sigmoidal or
hyperbolic with breakpoints (0.08-0.19 μg Se/g) that were double those observed
in studies starting with Se-adequate mice; (2) red blood cell Gpx1 activity was
not significantly changed; and (3) plasma Gpx3 activity only increased
substantially with 0.3 μg Se/g. Plasma Gpx3 is secreted from kidney. In this
short-term study, kidney Gpx3 mRNA reached plateau levels at 0.1 μg Se/g, and
other kidney selenoenzyme activities reached plateau levels at ≤ 0.2 μg Se/g, so
sufficient Se should have been present in kidney. Thus, the delayed increase in
plasma Gpx3 activity suggests that newly synthesized and secreted kidney Gpx3 is
preferentially retained in kidney or rapidly cleared by binding to basement
membranes in kidney or in other tissues. This repletion study shows that loss of
capacity to incorporate Se into Gpx1 in Gpx1 KO mice does not dramatically alter
expression of other Se biomarkers, nor the short-term flux of Se from intestine
to liver to kidney. |
Describe CGmapTools | CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data. | MOTIVATION: DNA methylation is important for gene silencing and imprinting in
both plants and animals. Recent advances in bisulfite sequencing allow detection
of single nucleotide variations (SNVs) achieving high sensitivity, but
accurately identifying heterozygous SNVs from partially C-to-T converted
sequences remains challenging.
RESULTS: We designed two methods, BayesWC and BinomWC, that substantially
improved the precision of heterozygous SNV calls from ∼80% to 99% while
retaining comparable recalls. With these SNV calls, we provided functions for
allele-specific DNA methylation (ASM) analysis and visualizing the methylation
status on reads. Applying ASM analysis to a previous dataset, we found that an
average of 1.5% of investigated regions showed allelic methylation, which were
significantly enriched in transposon elements and likely to be shared by the
same cell-type. A dynamic fragment strategy was utilized for DMR analysis in
low-coverage data and was able to find differentially methylated regions (DMRs)
related to key genes involved in tumorigenesis using a public cancer dataset.
Finally, we integrated 40 applications into the software package CGmapTools to
analyze DNA methylomes. This package uses CGmap as the format interface, and
designs binary formats to reduce the file size and support fast data retrieval,
and can be applied for context-wise, gene-wise, bin-wise, region-wise and
sample-wise analyses and visualizations.
AVAILABILITY AND IMPLEMENTATION: The CGmapTools software is freely available at
https://cgmaptools.github.io/.
CONTACT: [email protected].
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics
online. |
Is inositol effective for trichotillomania? | No, inositol is not effective for trichotillomania | Trichotillomania is characterized by repetitive pulling that causes noticeable
hair loss. Data on the pharmacological treatment of trichotillomania are
limited, with no clear first-line agent. The aim of the current study was to
determine the efficacy and tolerability of inositol in adults with
trichotillomania. A total of 38 individuals (35 women; mean age: 28.9±11.4) with
trichotillomania entered a 10-week, double-blind, placebo-controlled trial to
evaluate the safety and efficacy of inositol (dosing ranging from 6 to
18 g/day). Patients were assessed using the Massachusetts General Hospital Hair
Pulling Scale, the NIMH Trichotillomania Severity Scale, Clinical Global
Impression Scale, and measures of depression, anxiety, and psychosocial
functioning. Outcomes were examined using a linear mixed-effects model. Patients
assigned to inositol failed to show significantly greater reductions on primary
or secondary outcomes measures compared with placebo (all P>0.05). At study
endpoint, 42.1% of patients were 'much or very much improved' on inositol
compared with 35.3% on placebo. This is the first study assessing the efficacy
of inositol in the treatment of trichotillomania, but found no differences in
symptom reductions between inositol and placebo. Future studies should examine
whether inositol may be beneficial in controlling pulling behavior in a subgroup
of individuals with trichotillomania. Context • Excoriation (skin picking) disorder is characterized by the need or
urge to pick, scratch, pinch, touch, rub, scrub, squeeze, bite, or dig the skin,
and it can be a perplexing condition for the inexperienced physician. Treatments
include pharmacotherapy, psychotherapy, and alternative therapies. Alternative
therapies for excoriation disorder and other body-focused repetitive behaviors
include yoga, aerobic exercise, acupuncture, biofeedback, hypnosis, and inositol
and N-acetylcysteine, among others. Objective • This review article intended to
review the current literature on the alternative therapies to provide a brief
update on their benefits for the treatment of excoriation disorder for use in
conjunction with psychotherapy and pharmacotherapy in the management of a
challenging group of patients. Design • This review (focusing on literature
published in the last 15 y, selected from a search of PubMed) critically
considers the evidence for the use of alternative therapies in the treatment of
excoriation disorder. Setting • This review was conducted at the National
University of Asunción (San Lorenzo, Paraguay). Results • Results for yoga were
as follows: This technique may influence the structure and functioning of the
areas of emotional processing involved in the pathophysiology of excoriation
disorder and other body-focused repetitive behaviors, such as trichotillomania.
Although still limited, the current research team's use of yoga as a treatment
has given useful results. Results for aerobic exercise were as follows: People
suffering from excoriation disorder and other-body focused repetitive behaviors
generally have a worsening of their behaviors in times of negative mood and
anxiety. As exercise has qualities that allow individuals to improve their mood
and reduce their anxiety, it is likely that it also can help reduce behaviors
like hair pulling or scratching, and it should be considered to be an adjunctive
therapy. Results for acupuncture were as follows: The mechanism of action of
acupuncture increases serotonergic activity and releases endorphins in the
hypothalamus and limbic region, which could be beneficial in patients with
trichotillomania and excoriation disorder. Results for biofeedback were as
follows: Several case reports have suggested the value of biofeedback in
reducing tics, which bear some psychophysiological similarities to body-focused
repetitive behaviors, such as trichotillomania and excoriation disorder. Results
for hypnosis were as follows: When used as a channel for other types of
interventions, such as psychotherapy, hypnosis can help counteract the stress
that triggers the picking behaviors in some patients. Results for inositol and
N-acetylcysteine were as follows: Although more research is needed, these are
promising drugs that may be helpful in reducing the picking behavior.
Conclusions • The review indicates that yoga, aerobic exercise, acupuncture,
biofeedback, hypnosis, and inositol and N-acetylcysteine all show promise in the
treatment of excoriation disorder and other body-focused repetitive behaviors,
such as trichotillomania. In the current research team's experience, mainly yoga
and aerobic exercise have been shown useful in combination with psychotherapy
and pharmacotherapy. Obtaining solid evidence about the long-term beneficial
effects of these alternative therapies for the treatment of excoriation disorder
requires more investigation. |
How is the Regulatory Trait Concordance (RTC) calculated? | Regulatory Trait Concordance (RTC) that accounts for local LD structure and integrates eQTLs and GWAS results in order to reveal the subset of association signals that are due to cis eQTLs. | The recent success of genome-wide association studies (GWAS) is now followed by
the challenge to determine how the reported susceptibility variants mediate
complex traits and diseases. Expression quantitative trait loci (eQTLs) have
been implicated in disease associations through overlaps between eQTLs and GWAS
signals. However, the abundance of eQTLs and the strong correlation structure
(LD) in the genome make it likely that some of these overlaps are coincidental
and not driven by the same functional variants. In the present study, we propose
an empirical methodology, which we call Regulatory Trait Concordance (RTC) that
accounts for local LD structure and integrates eQTLs and GWAS results in order
to reveal the subset of association signals that are due to cis eQTLs. We
simulate genomic regions of various LD patterns with both a single or two causal
variants and show that our score outperforms SNP correlation metrics, be they
statistical (r(2)) or historical (D'). Following the observation of a
significant abundance of regulatory signals among currently published GWAS loci,
we apply our method with the goal to prioritize relevant genes for each of the
respective complex traits. We detect several potential disease-causing
regulatory effects, with a strong enrichment for immunity-related conditions,
consistent with the nature of the cell line tested (LCLs). Furthermore, we
present an extension of the method in trans, where interrogating the whole
genome for downstream effects of the disease variant can be informative
regarding its unknown primary biological effect. We conclude that integrating
cellular phenotype associations with organismal complex traits will facilitate
the biological interpretation of the genetic effects on these traits. Author information:
(1)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York,
NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and
Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029,
USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New
York, NY 10029, USA; James J. Peters VA Medical Center, Mental Illness Research
Education and Clinical Center (MIRECC), 130 West Kingsbridge Road, Bronx, NY
10468, USA. Electronic address: [email protected].
(2)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York,
NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount
Sinai, New York, NY 10029, USA; Department of Neuroscience, Icahn School of
Medicine at Mount Sinai, New York, NY 10029, USA.
(3)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York,
NY 10029, USA; Friedman Brain Institute, Icahn School of Medicine at Mount
Sinai, New York, NY 10029, USA.
(4)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York,
NY 10029, USA.
(5)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York,
NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and
Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029,
USA.
(6)Department of Human Genetics and Disease Diversity, Graduate School of
Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo
230-0045, Japan; Laboratory for Statistical Analysis, RIKEN Center for
Integrative Medical Sciences, Yokohama 230-0045, Japan.
(7)Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G
1X5, Canada; Toronto General Research Institute, Toronto, ON M5G 2M9, Canada;
Department of Medicine, University of Toronto, Toronto, ON M5S 2J7, Canada.
(8)Arthritis Research UK Centre for Genetics and Genomics, Musculoskeletal
Research Centre, Institute for Inflammation and Repair, Manchester Academic
Health Science Centre, University of Manchester, Manchester M13 9NT, UK;
National Institute for Health Research, Manchester Musculoskeletal Biomedical
Research Unit, Central Manchester University Hospitals National Health Service
Foundation Trust, Manchester Academic Health Sciences Centre, Manchester M13
9NT, UK.
(9)Rheumatology Unit, Department of Medicine (Solna), Karolinska Institutet,
Stockholm 171 76, Sweden.
(10)The Feinstein Institute for Medical Research, North Shore-Long Island Jewish
Health System, Manhasset, NY 11030, USA.
(11)Division of Rheumatology, Immunology, and Allergy, Brigham and Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics,
Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA;
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
02142, USA.
(12)Division of Rheumatology, Immunology, and Allergy, Brigham and Women's
Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Genetics,
Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA;
Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
02142, USA; NIHR Manchester Musculoskeletal Biomedical Research Unit, Central
Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre,
Manchester M13 9NT, UK.
(13)Department of Genetics and Genomic Sciences, Icahn School of Medicine at
Mount Sinai, New York, NY 10029, USA; Institute for Genomics and Multiscale
Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
(14)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York,
NY 10029, USA; Department of Genetics and Genomic Sciences, Icahn School of
Medicine at Mount Sinai, New York, NY 10029, USA; Institute for Genomics and
Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029,
USA; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New
York, NY 10029, USA; Department of Neuroscience, Icahn School of Medicine at
Mount Sinai, New York, NY 10029, USA. Electronic address: [email protected]. |
What is filipin staining used for? | Intracellular and total cholesterol (TC) were measured using filipin staining. | Bisphenol A (BPA) is an endocrine disruptor used in a variety of consumer
products. Exposure to BPA leads to alterations in steroidogenesis of ovarian
granulosa cells. Here, we analyzed the mechanism by which BPA alters
progesterone biosynthesis in immature rat granulosa cells. BPA increased
expression of steroidogenic acute regulatory protein (StAR), cholesterol
side-chain cleavage enzyme and 3β-hydroxysteroid dehydrogenase in granulosa
cells; however, BPA prevented the basal and the FSH-induced progesterone
production. BPA caused sequestration of cholesterol to the perinuclear area, as
evident by the Filipin staining. BPA decreased mRNA expression of ATP binding
cassette transporter-A1 (Abca1) and increased level of sterol regulatory element
binding protein 1. Addition of exogenous cell-permeable cholesterol restored the
effect of BPA on Abca1 and Star mRNA expression and partially reversed BPA's
effect on progesterone production. These results indicate that exposure to BPA
disrupts cholesterol homeostasis leading to decreased progesterone production in
immature rat granulosa cells. Transient Receptor Potential (TRP) cation channels, like the TRP Vanilloid 1
(TRPV1) and TRP Ankyrin 1 (TRPA1), are expressed on primary sensory neurons.
These thermosensor channels play a role in pain processing. We have provided
evidence previously that lipid raft disruption influenced the TRP channel
activation, and a carboxamido-steroid compound (C1) inhibited TRPV1 activation.
Therefore, our aim was to investigate whether this compound exerts its effect
through lipid raft disruption and the steroid backbone (C3) or whether altered
position of the carboxamido group (C2) influences the inhibitory action by
measuring Ca2+ transients on isolated neurons and calcium-uptake on
receptor-expressing CHO cells. Membrane cholesterol content was measured by
filipin staining and membrane polarization by fluorescence spectroscopy. Both
the percentage of responsive cells and the magnitude of the intracellular Ca2+
enhancement evoked by the TRPV1 agonist capsaicin were significantly inhibited
after C1 and C2 incubation, but not after C3 administration. C1 was able to
reduce other TRP channel activation as well. The compounds induced cholesterol
depletion in CHO cells, but only C1 induced changes in membrane polarization.
The inhibitory action of the compounds on TRP channel activation develops by
lipid raft disruption, and the presence and the position of the carboxamido
group is essential. |
Is TIAM1 favoring tumor progression in colorectal cancer (CRC)? | No. In colorectal cancer (CRC) TIAM1 suppresses tumor progression by regulating YAP/TAZ activity. | |
Which database has been developed that contains experimentally-confirmed carbonylated proteins? | Protein carbonylation, a chemically diverse oxidative post-translational modification, is widely considered as the biomarker for oxidative stress and protein damage. CarbonylDB has been developed as a manually curated data-resource of experimentally-confirmed carbonylated proteins/sites. The CarbonylDB currently contains 1495 carbonylated proteins and 3781 sites from 21 species, with human, rat and yeast as the top three species. | MOTIVATION: Oxidative stress and protein damage have been associated with over
200 human ailments including cancer, stroke, neuro-degenerative diseases and
aging. Protein carbonylation, a chemically diverse oxidative post-translational
modification, is widely considered as the biomarker for oxidative stress and
protein damage. Despite their importance and extensive studies, no
database/resource on carbonylated proteins/sites exists. As such information is
very useful to research in biology/medicine, we have manually curated a
data-resource (CarbonylDB) of experimentally-confirmed carbonylated
proteins/sites.
RESULTS: The CarbonylDB currently contains 1495 carbonylated proteins and 3781
sites from 21 species, with human, rat and yeast as the top three species. We
have made further analyses of these carbonylated proteins/sites and presented
their occurrence and occupancy patterns. Carbonylation site data on serum
albumin, in particular, provides a fine model system to understand the dynamics
of oxidative protein modifications/damage.
AVAILABILITY AND IMPLEMENTATION: The CarbonylDB is available as a web-resource
and for download at http://digbio.missouri.edu/CarbonylDB/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics
online. |
What is the function of the Nup153 protein? | Nup153 is a large (153 kD) O-linked glyco-protein which is a component of the basket structure located on the nucleoplasmic face of nuclear pore complexes. Nup153 is a nucleoporin mediating nuclear import. In addition to being important to pore architecture, Nup153 is a key participant in both import and export. During the transition into mitosis, Nup153 directs proteins involved in membrane remodeling to the nuclear envelope. | Nup153 is a large (153 kD) O-linked glyco-protein which is a component of the
basket structure located on the nucleoplasmic face of nuclear pore complexes.
This protein exhibits a tripartite structure consisting of a zinc finger domain
flanked by large (60-70 kD) NH2- and COOH-terminal domains. When full-length
human Nup153 is expressed in BHK cells, it accumulates appropriately at the
nucleoplasmic face of the nuclear envelope. Targeting information for Nup153
resides in the NH2-terminal domain since this region of the molecule can direct
an ordinarily cytoplasmic protein, pyruvate kinase, to the nuclear face of the
nuclear pore complex. Overexpression of Nup153 results in the dramatic
accumulation of nuclear poly (A)+ RNA, suggesting an inhibition of RNA export
from the nucleus. This is not due to a general decline in nucleocytoplasmic
transport or to occlusion or loss of nuclear pore complexes since nuclear
protein import is unaffected. While overexpression of certain Nup153 constructs
was found to result in the formation of unusual intranuclear membrane arrays,
this structural phenotype could not be correlated with the effects on poly (A)+
RNA distribution. The RNA trafficking defect was, however, dependent upon the
Nup153 COOH-terminal domain which contains most of the XFXFG repeats. It is
proposed that this region of Nup153, lying within the distal ring of the nuclear
basket, represents a docking site for mRNA molecules exiting the nucleus. We determined the times when the nuclear membrane, nuclear pore complex (NPC)
components, and nuclear import function were recovered during telophase in
living HeLa cells. Simultaneous observation of fluorescently-labeled NLS-bearing
proteins, lamin B receptor (LBR)-GFP, and Hoechst33342-stained chromosomes
revealed that nuclear membranes reassembled around chromosomes by 5 minutes
after the onset of anaphase (early telophase) whereas nuclear import function
was recovered later, at 8 minutes. GFP-tagged emerin also accumulated on
chromosomes 5 minutes after the onset of anaphase. Interestingly, emerin and LBR
initially accumulated at distinct, separate locations, but then became uniform 8
minutes after the onset of anaphase, concurrent with the recovery of nuclear
import function. We further determined the timing of NPC assembly by
immunofluorescence staining of cells fixed at precise times after the onset of
anaphase. Taken together, these results showed that emerin, LBR, and several NPC
components (RanBP2, Nup153, p62), but not Tpr, reconstitute around chromosomes
very early in telophase prior to the recovery of nuclear import activity. We report that the fission yeast nucleoporin Nup124p is required for the nuclear
import of both, retrotransposon Tf1-Gag as well as the retroviral HIV-1 Vpr.
Failure to import Tf1-Gag into the nucleus in a nup124 null mutant resulted in
complete loss of Tf1 transposition. Similarly, nuclear import of HIV-1 Vpr was
impaired in nup124 null mutant strains and cells became resistant to Vpr's
cell-killing activity. On the basis of protein domain similarity, the human
nucleoporin Nup153 was identified as a putative homolog of Nup124p. We
demonstrate that in vitro-translated Nup124p and Nup153 coimmunoprecipitate
Tf1-Gag or HIV-1 Vpr. Though full-length Nup153 was unable to complement the Tf1
transposition defect in a nup124 null mutant, we provide evidence that both
nucleoporins share a unique N-terminal domain, Nup124p(AA264-454) and
Nup153(AA448-634) that is absolutely essential for Tf1 transposition. Epigenetic
overexpression of this domain in a wild-type (nup124(+)) background blocked Tf1
activity implying that sequences from Nup124p and the human Nup153 challenged
the same pathway affecting Tf1 transposition. Our results establish a unique
relationship between two analogous nucleoporins Nup124p and Nup153 wherein the
function of a common domain in retrotransposition is conserved. The vertebrate pore protein Nup153 plays pivotal roles in nuclear pore function.
In addition to being important to pore architecture, Nup153 is a key participant
in both import and export. The scope of Nup153 function also extends beyond the
canonical view of the pore as a trafficking gateway. During the transition into
mitosis, Nup153 directs proteins involved in membrane remodeling to the nuclear
envelope. As cells exit mitosis, Nup153 is recruited to the chromosomal surface,
where nuclear pores are formed anew in a complicated process still under much
experimental scrutiny. In addition, Nup153 is targeted for protease cleavage
during apoptosis and in response to certain viral infections, providing
molecular insight into pore reconfiguration during cell response. Overall, the
versatile nature of Nup153 underscores an emerging view of the nuclear pore at
the nexus of many key cellular processes. 53BP1 is a mediator of DNA damage response (DDR) and a tumor suppressor whose
accumulation on damaged chromatin promotes DNA repair and enhances DDR
signaling. Using foci formation of 53BP1 as a readout in two human cell lines,
we performed an siRNA-based functional high-content microscopy screen for
modulators of cellular response to ionizing radiation (IR). Here, we provide the
complete results of this screen as an information resource, and validate and
functionally characterize one of the identified 'hits': a nuclear pore component
NUP153 as a novel factor specifically required for 53BP1 nuclear import. Using a
range of cell and molecular biology approaches including live-cell imaging, we
show that knockdown of NUP153 prevents 53BP1, but not several other DDR factors,
from entering the nuclei in the newly forming daughter cells. This translates
into decreased IR-induced 53BP1 focus formation, delayed DNA repair and impaired
cell survival after IR. In addition, NUP153 depletion exacerbates DNA damage
caused by replication stress. Finally, we show that the C-terminal part of
NUP153 is required for effective 53BP1 nuclear import, and that 53BP1 is
imported to the nucleus through the NUP153-importin-β interplay. Our data define
the structure-function relationships within this emerging
53BP1-NUP153/importin-β pathway and implicate this mechanism in the maintece
of genome integrity. Nuclear pore complexes (NPCs) span the 2 membranes of the nuclear envelope (NE)
and facilitate nucleocytoplasmic exchange of macromolecules. NPCs have a roughly
tripartite structural organization with the so-called nuclear basket emanating
from the NPC scaffold into the nucleoplasm. The nuclear basket is composed of
the 3 nucleoporins Nup153, Nup50, and Tpr, but their specific role for the
structural organization of this NPC substructure is, however, not well
established. In this study, we have used thin-section transmission electron
microscopy to determine the structural consequences of altering the expression
of Nup153 in human cells. We show that the assembly and integrity of the nuclear
basket is not affected by Nup153 depletion, whereas its integrity is perturbed
in cells expressing high concentrations of the zinc-finger domain of Nup153.
Moreover, even mild over-expression of Nup153 is coinciding with massive changes
in nuclear organization and it is the excess of the zinc-finger domain of Nup153
that is sufficient to induce these rearrangements. Our data indicate a central
function of Nup153 in the organization of the nucleus, not only at the
periphery, but throughout the entire nuclear interior. AIMS: Beyond the control of nuclear-cytoplasmic trafficking nucleoporins
regulate gene expression and are involved in cardiac diseases. Notably, a number
of cardiovascular disorders have been linked to alterations in epigenetic
mechanisms. Here we aimed to determine the contribution of Nup153 to the
epigenetic alterations occurring in cardiomyopathy of dystrophin-deficient mdx
mice (C57BL/10ScSn-Dmd mdx /J).
METHODS AND RESULTS: Nup153 was lysine-acetylated and its expression was
significantly increased at protein level in mdx hearts compared with controls.
Accordingly, lysine acetyl transferase (KAT) activity associated with Nup153 was
higher in mdx hearts paralleling increased binding with the lysine acetylases
P300/CBP-associated factor (PCAF) and p300. Interestingly, Nup153 silencing in
mdx organotypic heart tissue slices caused a reduction in PCAF- and
p300-specific activities. Remarkably, the level of nitric oxide (NO), which is
reduced in mdx mice, was important for KAT-dependent regulation of Nup153. In
fact, treatment of mdx heart tissue with an NO donor or the KAT inhibitor
anacardic acid normalized Nup153 protein expression. Nup153 was recruited to
chromatin and regulated the transcription of genes involved in cardiac
remodelling, including the actin-binding protein nexilin. Accordingly, nexilin
protein expression was abrogated by Nup153 silencing in mdx organotypic
cultures. Electrophysiological and molecular experiments revealed that Nup153
overexpression in normal cardiomyocytes increases Ca v 1.2 calcium channel
expression and function. Alterations in Nup153 protein expression and
intracellular localization were also found in dystrophic cardiomyocytes derived
from patient-specific induced pluripotent stem cells. Importantly, Nup153
up-regulation and increased acetylation were also found in the heart of Duchenne
muscular dystrophy patients.
CONCLUSIONS: Our data indicate that Nup153 is an epigenetic regulator which,
upon altered NO signalling, mediates the activation of genes potentially
associated with early dystrophic cardiac remodelling. DNA double-strand breaks are typically repaired through either the high-fidelity
process of homologous recombination (HR), in which BRCA1 plays a key role, or
the more error-prone process of non-homologous end joining (NHEJ), which relies
on 53BP1. The balance between NHEJ and HR depends, in part, on whether 53BP1
predominates in binding to damage sites, where it protects the DNA ends from
resection. The nucleoporin Nup153 has been implicated in the DNA damage
response, attributed to a role in promoting nuclear import of 53BP1. Here, we
define a distinct requirement for Nup153 in 53BP1 intranuclear targeting to
damage foci and report that Nup153 likely facilitates the role of another
nucleoporin, Nup50, in 53BP1 targeting. The requirement for Nup153 and Nup50 in
promoting 53BP1 recruitment to damage foci induced by either etoposide or
olaparib is abrogated in cells deficient for BRCA1 or its partner BARD1, but not
in cells deficient for BRCA2. Together, our results further highlight the
antagonistic relationship between 53BP1 and BRCA1, and place Nup153 and Nup50 in
a molecular pathway that regulates 53BP1 function by counteracting
BRCA1-mediated events. |
Is pacritinib effective for treatment of myelofibrosis? | Yes. Pacritinib (PAC), a multi-kinase inhibitor with specificity for JAK2, FLT3, and IRAK1 but sparing JAK1, has demonstrated clinical activity in myelofibrosis with minimal myelosuppression. | Pacritinib (SB1518) is a Janus kinase 2 (JAK2), JAK2(V617F), and Fms-like
tyrosine kinase 3 inhibitor that does not inhibit JAK1. It demonstrated a
favorable safety profile with promising efficacy in phase 1 studies in patients
with primary and secondary myelofibrosis (MF). This multicenter phase 2 study
further characterized the safety and efficacy of pacritinib in the treatment of
patients with MF. Eligible patients had clinical splenomegaly poorly controlled
with standard therapies or were newly diagnosed with intermediate- or high-risk
Lille score. Patients with any degree of cytopenia were eligible. Thirty-five
patients were enrolled. At entry, 40% had hemoglobin <10 g/dL and 43% had
platelets <100 000× 10(9)/L. Up to week 24, 8 of 26 evaluable patients (31%)
achieved a ≥35% decrease in spleen volume determined by magnetic resoce
imaging and 14 of 33 (42%) attained a ≥50% reduction in spleen size by physical
examination. Median MF symptom improvement was ≥50% for all symptoms except
fatigue. Grade 1 or 2 diarrhea (69%) and nausea (49%) were the most common
treatment-emergent adverse events. The study drug was discontinued in 9 patients
(26%) due to adverse events (4 severe). Pacritinib is an active agent in
patients with MF, offering a potential treatment option for patients with
preexisting anemia and thrombocytopenia. This trial was registered at
www.clinicaltrials.gov as #NCT00745550. Myelofibrosis (MF) is a myeloid disorder caused by a clonal hematopoietic
stem-cell proliferation associated with activation of the Janus kinase (JAK)
signal transducer and activator of transcription (STAT) signaling pathways.
Patients with MF often develop severe splenomegaly, marked symptom burden and
significant cytopenias, with a consequent marked negative impact on quality of
life and survival. The management of MF patients has dramatically improved with
the development of a group of drugs that inhibit JAK signaling. The first of
these agents to be approved was ruxolitinib, a JAK1/JAK2 inhibitor, which has
been shown to improve both spleen size and symptoms in patients with MF.
However, myelotoxicity, particularly of the platelet lineage, significantly
limits the patient population who can benefit from this agent. Thus, there is an
unmet need for novel agents with limited myelotoxicity to treat MF. Pacritinib,
a JAK2 and FMS-like tyrosine kinase 3 (FLT3) inhibitor, has shown promising
results in early phase trials with limited myelotoxicity and clinical responses
that are comparable with those seen with ruxolitinib, even in patients with
severe thrombocytopenia. Currently there are two large phase III clinical trials
of pacritinib in MF, including patients with thrombocytopenia, and those
previously treated with ruxolitinib. If the encouraging results observed in
early phase clinical trials are confirmed, pacritinib will represent a new and
exciting treatment option for patients with MF and particularly patients with
significant cytopenias. The first-in-class JAK1/JAK2 inhibitor ruxolitinib inhibits JAK/STAT signaling,
inducing durable reductions in splenomegaly and constitutional symptoms in
patients with myelofibrosis. However, the association of ruxolitinib therapy
with myelosuppression indicates the continued need for optimal treatment choices
in myelofibrosis. Pacritinib, a dual JAK2 and FLT3 inhibitor, improves
disease-related symptoms and signs with manageable gastrointestinal toxicity in
patients with myelofibrosis with splenomegaly and high-risk features, without
causing overt myelosuppression, and therefore may provide an important treatment
option for a range of patients with myelofibrosis. This article examines the
role of JAK2 and FLT3 signaling in myelofibrosis and provides an overview of the
clinical development of pacritinib as a new therapy for myelofibrosis. INTRODUCTION: Myelofibrosis (MF) is a clonal haematological disease associated
with recurrent somatic gene mutations (JAK2V617F, MPL, CALR) and constitutive
activation of the Janus kinase (JAK)/Signal Transducer and Activator of
Transcription pathway. MF is often characterised by debilitating symptoms and
JAK inhibitors (JAKIs) have revolutionised available therapeutic options.
Ruxolitinib, a JAK1 and 2 inhibitor, is the only currently approved agent.
Several other JAKIs are undergoing evaluation in the clinical trial setting and
Pacritinib , a novel JAK2 and FLT3 inhibitor, is at an advanced stage of
investigation with recent completion of a Phase III trial and another ongoing.
AREAS COVERED: Within this article we focus on pacritinib, summarising the
development, preclinical and up-to-date results from the Phase I - III trials.
We present the most recent data on efficacy and safety and indirectly compare
this novel JAKI with ruxolitinib.
EXPERT OPINION: The kinome array data for pacritinib suggests that it has a
range of targets differing to those for ruxolitinib. Pacritinib appears to be an
effective agent for the control of MF-related symptoms and splenomegaly with
potentially fewer haematological side-effects when compared with ruxolitinib and
seems a particularly promising agent for anaemic and thrombocytopenic patients.
It is also an attractive drug for potential combination studies due to its good
tolerability. BACKGROUND: Pacritinib (SB1518) is a highly selective kinase inhibitor with
specificity for JAK2, FLT3, IRAK1, and CFS1R. This multicenter phase 1/2 study
evaluated the maximum tolerated dose (MTD), safety, and clinical activity of
pacritinib in patients with myelofibrosis (MF) and other advanced myeloid
maligcies.
METHODS: In the phase 1 dose-escalation part of the study, 43 adults with
advanced myeloid maligcies received pacritinib 100 to 600 mg once daily (QD).
In the phase 2 part of the study, 31 adults with refractory or intermediate- or
high-risk newly diagnosed MF and any degree of cytopenia received pacritinib
400 mg QD. The primary endpoint is a ≥35% reduction in spleen volume at week 24
as determined by magnetic resoce imaging.
RESULTS: Five patients (11.6%) experienced a dose-limiting toxicity during cycle
1 of phase 1. The clinical benefit rate was 86.0% (13 patients achieving
clinical improvement and 24 patients having stable disease). The MTD was
established at 500 mg QD, and the recommended phase 2 dose was 400 mg QD. In
phase 2, the primary endpoint was achieved by 23.5% of evaluable patients
(4/17), with 47.4% (9/19) achieving a ≥50% spleen length reduction at week 24 as
measured by physical examination. At week 24, 38.9% of evaluable patients (7/18)
achieved a ≥50% decrease in MF Quality of Life and Symptom Assessment total
score. Gastrointestinal toxicities were the most common adverse events and were
predomitly grade 1/2 in severity. Grade 3/4 anemia was reported in 5/31
patients and grade 3/4 thrombocytopenia was reported in 3/31 patients. The most
frequent AEs considered to be treatment related were diarrhea (28/31), nausea
(15/31), vomiting (9/31), and fatigue (4/31). Grade 3 treatment-related AEs were
reported in seven patients (22.6%), four of whom had diarrhea. No grade 4/5
treatment-related AEs were reported. No leukopenia, neutropenia, or lymphopenia
were reported.
CONCLUSIONS: Pacritinib was well tolerated and demonstrated clinical activity in
MF. The study suggests that pacritinib has unique characteristics, namely a lack
of substantial myelosuppression and manageable side effects, making it an
attractive target for further evaluation in MF.
TRIAL REGISTRATION: Retrospectively registered at www.clinicaltrials.gov (#
NCT00719836 ) on July 20, 2008. BACKGROUND: Available therapies for myelofibrosis can exacerbate cytopenias and
are not indicated for patients with severe thrombocytopenia. Pacritinib, which
inhibits both JAK2 and FLT3, induced spleen responses with limited
myelosuppression in phase 1/2 trials. We aimed to assess the efficacy and safety
of pacritinib versus best available therapy in patients with myelofibrosis
irrespective of baseline cytopenias.
METHODS: This international, multicentre, randomised, phase 3 trial (PERSIST-1)
was done at 67 sites in 12 countries. Patients with higher-risk myelofibrosis
(with no exclusions for baseline anaemia or thrombocytopenia) were randomly
assigned (2:1) to receive oral pacritinib 400 mg once daily or best available
therapy (BAT) excluding JAK2 inhibitors until disease progression or
unacceptable toxicity. Randomisation was stratified by risk category, platelet
count, and region. Treatment assignments were known to investigators, site
personnel, patients, clinical monitors, and pharmacovigilance personnel. The
primary endpoint was spleen volume reduction (SVR) of 35% or more from baseline
to week 24 in the intention-to-treat population as assessed by blinded,
centrally reviewed MRI or CT. We did safety analyses in all randomised patients
who received either treatment. Here we present the final data. This trial is
registered with ClinicalTrials.gov, number NCT01773187.
FINDINGS: Between Jan 8, 2013, and Aug 1, 2014, 327 patients were randomly
assigned to pacritinib (n=220) or BAT (n=107). Median follow-up was 23·2 months
(IQR 14·8-28·7). At week 24, the primary endpoint of SVR of 35% or more was
achieved by 42 (19%) patients in the pacritinib group versus five (5%) patients
in the BAT group (p=0·0003). 90 patients in the BAT group crossed over to
receive pacritinib at a median of 6·3 months (IQR 5·8-6·7). The most common
grade 3-4 adverse events through week 24 were anaemia (n=37 [17%]),
thrombocytopenia (n=26 [12%]), and diarrhoea (n=11 [5%]) in the pacritinib
group, and anaemia (n=16 [15%]), thrombocytopenia (n=12 [11%]), dyspnoea (n=3
[3%]), and hypotension (n=3 [3%]) in the BAT group. The most common serious
adverse events that occurred through week 24 were anaemia (10 [5%]), cardiac
failure (5 [2%]), pyrexia (4 [2%]), and pneumonia (4 [2%]) with pacritinib, and
anaemia (5 [5%]), sepsis (2 [2%]), and dyspnoea (2 [2%]) with BAT. Deaths due to
adverse events were observed in 27 (12%) patients in the pacritinib group and 14
(13%) patients in the BAT group throughout the duration of the study.
INTERPRETATION: Pacritinib therapy was well tolerated and induced significant
and sustained SVR and symptom reduction, even in patients with severe baseline
cytopenias. Pacritinib could be a treatment option for patients with
myelofibrosis, including those with baseline cytopenias for whom options are
particularly limited.
FUNDING: CTI BioPharma Corp. The treatment landscape for myelofibrosis (MF) has reached the molecular era by
targeting different pathways that are implied in this myeloproliferative
neoplasm. A few years ago, the first-in-class JAK1/JAK2 inhibitor ruxolitinib,
demonstrated reductions in both constitutional symptoms and splenomegaly,
leading to the US FDA approval. The development or worsening of cytopenias in
patients receiving ruxolitinib uncovered an unmet need that has been addressed
by alternative approaches. Pacritinib, a dual JAK2 and FLT3 inhibitor which also
inhibits IRAK1, has demonstrated the ability to favorably impact MF-associated
splenomegaly and symptom burden, while having limited myelosuppression with
manageable gastrointestinal toxicity. Herein, we provide an overview of
pacritinib, from early preclinical studies to the latest and ongoing PAC203
trial, as an emerging therapy for MF. IMPORTANCE: Myelofibrosis is a hematologic maligcy characterized by
splenomegaly and debilitating symptoms. Thrombocytopenia is a poor prognostic
feature and limits use of Janus kinase 1 (JAK1)/Janus kinase 2 (JAK2) inhibitor
ruxolitinib.
OBJECTIVE: To compare the efficacy and safety of JAK2 inhibitor pacritinib with
that of best available therapy (BAT), including ruxolitinib, in patients with
myelofibrosis and thrombocytopenia.
DESIGN, SETTING, AND PARTICIPANTS: For this phase 3 randomized international
multicenter study-the PERSIST-2 study-of pacritinib vs BAT, 311 patients with
myelofibrosis and platelet count 100 × 109/L or less were recruited for
analysis. Crossover from BAT was allowed after week 24 or for progression of
splenomegaly.
INTERVENTIONS: Patients were randomized 1:1:1 to pacritinib 400 mg once daily,
pacritinib 200 mg twice daily, or BAT.
MAIN OUTCOMES AND MEASURES: Coprimary end points were rates of patients
achieving 35% or more spleen volume reduction (SVR) and 50% or more reduction in
total symptom score (TSS) at week 24. Efficacy analyses were performed on the
intention-to-treat efficacy population, comprising all patients with a
randomization date allowing for week 24 data.
RESULTS: Overall, 311 patients (mean [SD] age, 63.70 [9.08] years; 171 men [55%]
and 140 women [45%]) were included in the study; 149 patients (48%) had prior
ruxolitinib. The most common BAT was ruxolitinib (44 patients [45%]); 19
patients (19%) received watchful-waiting only. The intention-to-treat efficacy
population included 75 patients randomized to pacritinib once daily; 74,
pacritinib twice daily, and 72, BAT. Pacritinib (arms combined) was more
effective than BAT for 35% or more SVR (27 patients [18%] vs 2 patients [3%];
P = .001) and had a nonsignificantly greater rate of 50% or more reduction in
TSS (37 patients [25%] vs 10 patients [14%]; P = .08). Pacritinib twice daily
led to significant improvements in both end points over BAT (≥35% SVR: 16
patients [22%] vs 2 patients [3%]; P = .001; ≥50% reduction in TSS: 24 patients
[32%] vs 10 patients [14%]; P = .01). Clinical improvement in hemoglobin and
reduction in transfusion burden were greatest with pacritinib twice daily. For
pacritinib once daily, pacritinib twice daily, and BAT, the most common (>10%)
grade 3 or 4 adverse events were thrombocytopenia (32 patients [31%], 34
patients [32%], 18 patients [18%]), and anemia (28 patients [27%], 23 patients
[22%], 14 patients [14%]). In the pacritinib once daily, twice daily, and BAT
arms, discontinuation owing to adverse events occurred in 15 patients (14%), 10
patients (9%), and 4 patients (4%).
CONCLUSIONS AND RELEVANCE: In patients with myelofibrosis and thrombocytopenia,
including those with prior anti-JAK therapy, pacritinib twice daily was more
effective than BAT, including ruxolitinib, for reducing splenomegaly and
symptoms.
TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT02055781. Myelofibrosis (MF) is a clinical manifestation of chronic BCR-ABL1-negative
chronic myeloproliferative neoplasms. Splenomegaly is one of the major clinical
manifestations of MF and is directly linked to splenic extramedullary
hematopoiesis (EMH). EMH is associated with abnormal trafficking patterns of
clonal hematopoietic cells due to the dysregulated bone marrow (BM)
microenvironment leading to progressive splenomegaly. Several recent data have
emphasized the role of several cytokines for splenic EMH. Alteration of
CXCL12/CXCR4 pathway could also lead to splenic EMH by migrated clonal
hematopoietic cells from BM to the spleen. Moreover, low Gata1 expression was
found to be significantly associated with the EMH. Several gene mutations were
found to be associated with significant splenomegaly in MF. In recent data,
JAK2V617F homozygous mutation was associated with a larger spleen size. In other
data, CALR mutations in MF were signigicantly associated with longer larger
splenomegaly-free survivals than others. In addition, MF patients with ≥1
mutations in AZXL1, EZH1 or IDH1/2 had significantly low spleen reduction
response in ruxolitinib treatment. Developments of JAK inhibitors, such as
ruxolitinib, pacritinib, momelotinib, and febratinib enabled the effective
management in MF patients. Especially, significant spleen reduction responses of
the drugs were demonstrated in several randomized clinical studies, although
those could not eradicate allele burdens of MF. Myeloproliferative neoplasms (MPNs) include essential thrombocythemia,
polycythemia vera (PV), and primary myelofibrosis (MF). Phenotype-driver
mutations of JAK2, CALR, and MPL genes are present in MPNs and can be variably
combined with additional mutations. Driver mutations entail a constitutive
activation of the JAK2/STAT pathway, the key signaling cascade in MPNs. Among
JAK2 inhibitors (JAKis), ruxolitinib (RUX) has been approved for the treatment
of intermediate and high-risk MF and for PV inadequately controlled by or
intolerant of hydroxyurea. Other JAKis, such as fedratinib and pacritinib,
proved to be useful in MF. The primary end points in MF trials were spleen
volume response (SVR) and symptom response, whereas in PV trials they were
hematocrit control with or without spleen response. In advanced MF, RUX achieved
a long lasting SVR of >35% in ∼60% of patients, establishing a new benchmark for
MF treatment. RUX efficacy in early MF is also remarkable and toxicity is mild.
In PV, RUX achieved hematocrit control in ∼60% of cases and SVR in 40%. Symptom
relief was evident in both conditions. In the long-term, however, many MF
patients lose their SVR. Indeed, the definition of RUX failure and the design of
new trials in this setting are unmet needs. Decrease of hemoglobin/platelet
levels and increased infection rates are the most common side effects of RUX,
and nonmelanoma skin tumors need to be monitored while on treatment. In
conclusion, the introduction of JAKis raises the bar of treatment goals in MF
and PV. BACKGROUND: Fibrotic diseases result from an exuberant response to chronic
inflammation. Myelofibrosis is the end result of inflammation in bone, caused by
an inflammatory process triggered by production of abnormal myeloid cells driven
by mutations affecting the JAK-STAT pathway. Inflammatory cytokine
overproduction leads to increased mesenchymal cell proliferation, culminating in
fibrosis. Although JAK2 inhibitors, such as the JAK1/2 inhibitor ruxolitinib and
the JAK2/FLT3/CSF1R/IRAK1 inhibitor pacritinib suppress abnormal clone expansion
in myelofibrosis, ruxolitinib does not appear to prevent or reverse bone-marrow
fibrosis in most patients. In two Phase III clinical trials, pacritinib,
however, demonstrated improvements in platelet counts and hemoglobin and
reductions in transfusion burden in some patients with baseline cytopenias,
suggesting it may improve bone-marrow function. Unlike ruxolitinib, pacritinib
suppresses signaling through IRAK1, a key control point for inflammatory and
fibrotic signaling.
PURPOSE: To investigate potential antifibrotic effects of pacritinib in an
animal model of liver fibrosis relevant to the observed course of human disease.
METHODS: Pacritinib, negative control (vehicle), and positive control (the
angiotensin 2-receptor antagonist and PPARγ partial agonist telmisartan) were
assessed in the murine Stelic animal model, which mimics the clinically observed
progression from hepatic steatosis to nonalcoholic steatohepatitis, liver
fibrosis, and hepatocellular carcinoma. Histopathological analysis used
hematoxylin and eosin staining. Body and liver weight changes, nonalcoholic
fatty-liver disease activity scores, and plasma cytokeratin 18 fragment levels
(a biomarker of hepatic necrosis) were measured.
RESULTS: Pacritinib-treated mice had significantly (P<0.01) reduced fibrotic
areas in liver compared to vehicle control and significantly (P<0.05) lower
levels of CK18. The antifibrotic effect of pacritinib was comparable to that of
telmisartan, but without significant effects on fat accumulation.
CONCLUSION: These results, the first to demonstrate hepatic antifibrotic effects
for pacritinib in an animal model of liver disease, provide preliminary support
for potential clinical applications of pacritinib in fibrotic diseases other
than myelofibrosis. |
How can PEGylation improve recombinant drugs? | PEGylation primarily improves pharmacokinetics and helps to prevent adverse drug reactions, by increasing the molecular mass of proteins and peptides and shielding them from proteolytic enzymes. | Protein and peptide drugs hold great promise as therapeutic agents. But there
are shortcomings: Many recombit proteins are quickly degraded by proteolytic
enzymes or are rapidly cleared by kidney filtration resulting in a short
circulating half-life. Additionally they are prone to be recognized by the
immune system resulting in the generation of neutralizing and non-neutralizing
antibodies. PEGylation, a process by which polyethylene glycol chains are
attached to protein and peptide drugs, can overcome these and other
shortcomings. By increasing the molecular mass of proteins and peptides and
shielding them from proteolytic enzymes, PEGylation primarily improves
pharmacokinetics and helps to prevent adverse drug reactions. |
Can exposure to heavy metals like lead(Pb) or cadmium(Cd) cause changes in DNA methylation patterns in Isoetes sinensis? | Changes in DNA methylation of the endangered plant, Isoetes sinensis, have be shown to be affected by both Pb and Cd | Because of the accumulation of heavy metals, Hydrilla verticillata (L.f.) Royle,
a rooted submerged perennial aquatic herb, is being developed as a potential
tool to clean the aquatic ecosystem polluted by heavy metals. However, its
physiological responses for heavy metal remain to be elucidated. Here, through
employing proteomics approach, we found that excess Cu significantly induced the
expressions of four DNA methylation related proteins in H. verticillata, which
were the homologues of two domains rearranged methyltransferases (DRM), a
methyltransferases chromomethylase (CMT) and a histone H3 lysine-9 specific
SUVH6-like (SUVH6). Consistently, a dramatic change in DNA methylation patterns
was detected in excess Cu-exposed H. verticillata. Surprisingly, administration
of the NADPH oxidase inhibitors, diphenylene iodonium (DPI) and imidazole (IMZ)
that block production of reactive oxygen species (ROS) could trigger the
remethylation of genomic sites that were demethylated by excess Cu, indicating
that Cu-induced ROS might be another way to affect DNA methylation. Further
analysis suggested this changed DNA methylation may be owing to the ROS-induced
DNA damage. Taken together, our findings demonstrate that two different ways to
influence DNA methylation in excess Cu-treated H. verticillata. |
Describe GeneCodeq | The exponential reduction in cost of genome sequencing has resulted in a rapid growth of genomic data. Most of the entropy of short read data lies not in the sequence of read bases themselves but in their Quality Scores-the confidence measurement that each base has been sequenced correctly. Lossless compression methods are now close to their theoretical limits and hence there is a need for lossy methods that further reduce the complexity of these data without impacting downstream analyses. GeneCodeq is a Bayesian method inspired by coding theory for adjusting quality scores to improve the compressibility of quality scores without adversely impacting genotyping accuracy. Its model leverages a corpus of k-mers to reduce the entropy of the quality scores and thereby the compressibility of these data (in FASTQ or SAM/BAM/CRAM files), resulting in compression ratios that significantly exceeds those of other methods. GeneCodeq can be combined with existing lossy compression schemes to further reduce entropy and allows the user to specify a reference panel of expected sequence variations to improve the model accuracy. | |
Has Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) been reported to be a plasminogen receptor in pathogenic bacteria? | Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) has been reported to be a plasminogen receptor in many pathogenic bacteria. | Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (EC 1.2.1.12) is an anchorless,
multifunctional protein displayed on the surface of several fungi and
Gram-positive pathogens, which contributes to their adhesion and virulence. To
date a role for extracellular GAPDH in the pathogenesis of Gram-negative
bacteria has not been described. The aim of this study was to analyze the
extracellular localization of GAPDH in enterohemorrhagic (EHEC) and
enteropathogenic (EPEC) Escherichia coli strains and to examine its interaction
with host components that could be related to the infection mechanism.
Recombit E. coli GAPDH was purified and polyclonal antibodies were obtained.
Western blotting and immunoelectron microscopy showed that GAPDH is located on
the bacterial surface and released to the culture medium of EHEC and EPEC
strains. GAPDH export in these Gram-negative pathogens depends on the external
medium, is not mediated by vesicles and leads to an extracellular active enzyme.
Non-pathogenic E. coli strains do not secrete GAPDH. Two-dimensional
electrophoresis analysis showed that in E. coli GAPDH is present at least in two
major forms with different isoelectric points. Of these forms, the more basic is
secreted. Purified GAPDH was found to bind human plasminogen and fibrinogen in
Far-Western blot and ELISA-based assays. In addition, GAPDH remained associated
with colonic Caco-2 epithelial cells after adhesion of EHEC or EPEC. These
observations indicate that exported GAPDH may act as a virulence factor which
could contribute to EHEC and EPEC pathogenesis. This is the first description of
an extracellular localization for this enzyme, with a function other than its
glycolytic role in Gram-negative pathogens. |
Which de novo truncating mutations in WASF1 cause intellectual disability? | De novo truncating mutations in WAS protein family member 1 (WASF1) were identified in five unrelated individuals with moderate to profound intellectual disability with autistic features and seizures. WASF1, also known as WAVE1, is part of the WAVE complex and acts as a mediator between Rac-GTPase and actin to induce actin polymerization. The three mutations connected by Matchmaker Exchange were c.1516C>T (p.Arg506Ter), which occurs in three unrelated individuals, c.1558C>T (p.Gln520Ter), and c.1482delinsGCCAGG (p.Ile494MetfsTer23). All three variants are predicted to partially or fully disrupt the C-terminal actin-binding WCA domain. Functional studies using fibroblast cells from two affected individuals with the c.1516C>T mutation showed a truncated WASF1 and a defect in actin remodeling. | Collaborators: Aitman T, Bennett D, Caulfield M, Chinnery P, Gale D, Koziell A,
Kuijpers TW, Laffan MA, Maher E, Markus HS, Morrell NW, Ouwehand WH, Perry DJ,
Raymond FL, Roberts I, Smith KGC, Thrasher A, Watkins H, Williamson C, Woods G,
Ashford S, Bradley JR, Fletcher D, Hammerton T, James R, Kingston N, Penkett CJ,
Stirrups K, Veltman M, Young T, Brown M, Clements-Brod N, Davis J, Dewhurst E,
Dolling H, Erwood M, Frary A, Linger R, Martin JM, Papadia S, Rehnstrom K, Stark
H, Allsup D, Austin S, Bakchoul T, Bariana TK, Bolton-Maggs P, Chalmers E,
Collins J, Collins P, Erber WN, Everington T, Favier R, Freson K, Furie B,
Gattens M, Gebhart J, Gomez K, Greene D, Greinacher A, Gresele P, Hart D,
Heemskerk JWM, Henskens Y, Kazmi R, Keeling D, Kelly AM, Lambert MP, Lentaigne
C, Liesner R, Makris M, Mangles S, Mathias M, Millar CM, Mumford A, Nurden P,
Payne J, Pasi J, Peerlinck K, Revel-Vilk S, Richards M, Rondina M, Roughley C,
Schulman S, Schulze H, Scully M, Sivapalaratnam S, Stubbs M, Tait RC, Talks K,
Thachil J, Toh CH, Turro E, Van Geet C, De Vries M, Warner TQ, Watson H,
Westbury S, Furnell A, Mapeta R, Rayner-Matthews P, Simeoni I, Staines S,
Stephens J, Watt C, Whitehorn D, Attwood A, Daugherty L, Deevi SVV, Halmagyi C,
Hu F, Matser V, Meacham S, Megy K, Shamardina O, Titterton C, Tuna S, Yu P, von
Ziegenweldt J, Astle W, Bleda M, Carss KJ, Gräf S, Haimel M, Lango-Allen H,
Richardson S, Calleja P, Rankin S, Turek W, Anderson J, Bryson C, Carmichael J,
McJannet C, Stock S, Allen L, Ambegaonkar G, Armstrong R, Arno G,
Bitner-Glindzicz M, Brady A, Canham N, Chitre M, Clement E, Clowes V, Deegan P,
Deshpande C, Doffinger R, Firth H, Flinter F, French C, Gardham A, Ghali N,
Gissen P, Grozeva D, Henderson R, Hensiek A, Holden S, Holder M, Holder S, Hurst
J, Josifova D, Krishnakumar D, Kurian MA, Lees M, MacLaren R, Maw A, Mehta S,
Michaelides M, Moore A, Murphy E, Park SM, Parker A, Patch C, Paterson J, Rankin
J, Reid E, Rosser E, Sanchis-Juan A, Sandford R, Santra S, Scott R, Sohal A,
Stein P, Thomas E, Thompson D, Tischkowitz M, Vogt J, Wakeling E, Wassmer E,
Webster A, Ali S, Ali S, Boggard HJ, Church C, Coghlan G, Cookson V, Corris PA,
Creaser-Myers A, DaCosta R, Dormand N, Eyries M, Gall H, Ghataorhe PK, Ghio S,
Ghofrani A, Gibbs JSR, Girerd B, Greenhalgh A, Hadinnapola C, Houweling AC,
Humbert M, In't Veld AH, Kennedy F, Kiely DG, Kovacs G, Lawrie A, Ross RVM,
Machado R, Masati L, Meehan S, Moledina S, Montani D, Othman S, Peacock AJ,
Pepke-Zaba J, Pollock V, Polwarth G, Ranganathan L, Rhodes CJ, Rue-Albrecht K,
Schotte G, Shipley D, Soubrier F, Southgate L, Scelsi L, Suntharalingam J, Tan
Y, Toshner M, Treacy CM, Trembath R, Vonk Noordegraaf A, Walker S, Wanjiku I,
Wharton J, Wilkins M, Wort SJ, Yates K, Alachkar H, Antrobus R, Arumugakani G,
Bacchelli C, Baxendale H, Bethune C, Bibi S, Booth C, Browning M, Burns S,
Chandra A, Cooper N, Davies S, Devlin L, Drewe E, Edgar D, Egner W, Ghurye R,
Gilmour K, Goddard S, Gordins P, Grigoriadou S, Hackett S, Hague R, Harper L,
Hayman G, Herwadkar A, Huissoon A, Jolles S, Kelleher P, Kumararatne D, Lear S,
Longhurst H, Lorenzo L, Maimaris J, Manson A, McDermott E, Murng S, Nejentsev S,
Noorani S, Oksenhendler E, Ponsford M, Qasim W, Quinti I, Richter A,
Samarghitean C, Sargur R, Savic S, Seneviratne S, Sewell C, Staples E, Stauss H,
Thaventhiran J, Thomas M, Welch S, Willcocks L, Yeatman N, Yong P, Ancliff P,
Babbs C, Layton M, Louka E, McGowan S, Mead A, Roy N, Chambers J, Dixon P, Estiu
C, Hague B, Marschall HU, Simpson M, Chong S, Emmerson I, Ginsberg L, Gosal D,
Hadden R, Horvath R, Mahdi-Rogers M, Manzur A, Marshall A, Matthews E, McCarthy
M, Reilly M, Renton T, Rice A, Themistocleous A, Vale T, Van Zuydam N, Walker S,
Ormondroyd L, Hudson G, Wei W, Yu Wai Man P, Whitworth J, Afzal M, Colby E,
Saleem M, Alavijeh OS, Cook HT, Johnson S, Levine AP, Wong EKS, Tan R, Boycott
KM, MacKenzie A, Majewski J, Brudno M, Bulman D, Dyment D. |
Can CPX-351 be used for the treatment of tuberculosis? | No, CPX-351 is a novel liposomal formulation of cytarabine and daunorubicin which has recently been FDA approved for treatment of acute myeloid leukemia (AML). | PURPOSE: CPX-351 is a novel liposomal formulation of cytarabine and daunorubicin
which has recently been FDA approved for treatment of acute myeloid leukemia
(AML). The current study investigated the pharmacokinetics (PK) of this
liposomal formulation.
METHODS: CPX-351 PK data (cytarabine, daunorubicin, and metabolites) from a
phase I study of relapsed and refractory AML were used for the analysis. Therapy
was given days 1, 3, and 5 of induction (3-134 units/m2). We developed a
population PK model to characterize CPX-351 disposition.
RESULTS: 39 patients (3589 samples) were evaluated. Liposomal cytarabine and
daunorubicin were modeled separately with their respective metabolites. A
one-compartment model fit the parent compounds well; the metabolites required
two-compartment models. Weight was an independent predictor of liposomal
volumes; mild renal and liver dysfunction were not predictors of clearance or
volume (maximum creatinine 1.6 mg/dL and total bilirubin 1.8 mg/dL). Liposomal
clearances of the two drugs were highly correlated and 1000-fold smaller than
published non-encapsulated values supporting prolonged encapsulation in the
liposome.
CONCLUSIONS: The PK model demonstrates prolonged exposure to cytarabine and
daunorubicin without increases in non-hematologic toxicity that indicates
retention of the drugs within the liposome. The unique pharmacology of this
formulation may allow for simplified regimens and improved outcomes. |
Which proteins form the nuclear pore basket in human cells? | Nup133 Is Required for Proper Nuclear Pore Basket Assembly and Dynamics in Embryonic Stem Cells. Moreover, the association of TREX-2 with the NPC requires the basket nucleoporins NUP153 and TPR, but is independent of transcription. The nucleoporin Nup153 is required for nuclear pore basket formation, nuclear pore complex anchoring and import of a subset of nuclear proteins | Nup153 is a large (153 kD) O-linked glyco-protein which is a component of the
basket structure located on the nucleoplasmic face of nuclear pore complexes.
This protein exhibits a tripartite structure consisting of a zinc finger domain
flanked by large (60-70 kD) NH2- and COOH-terminal domains. When full-length
human Nup153 is expressed in BHK cells, it accumulates appropriately at the
nucleoplasmic face of the nuclear envelope. Targeting information for Nup153
resides in the NH2-terminal domain since this region of the molecule can direct
an ordinarily cytoplasmic protein, pyruvate kinase, to the nuclear face of the
nuclear pore complex. Overexpression of Nup153 results in the dramatic
accumulation of nuclear poly (A)+ RNA, suggesting an inhibition of RNA export
from the nucleus. This is not due to a general decline in nucleocytoplasmic
transport or to occlusion or loss of nuclear pore complexes since nuclear
protein import is unaffected. While overexpression of certain Nup153 constructs
was found to result in the formation of unusual intranuclear membrane arrays,
this structural phenotype could not be correlated with the effects on poly (A)+
RNA distribution. The RNA trafficking defect was, however, dependent upon the
Nup153 COOH-terminal domain which contains most of the XFXFG repeats. It is
proposed that this region of Nup153, lying within the distal ring of the nuclear
basket, represents a docking site for mRNA molecules exiting the nucleus. Yeast and vertebrate nuclear pores display significant morphological similarity
by electron microscopy, but sequence similarity between the respective proteins
has been more difficult to observe. Herein we have identified a vertebrate
nucleoporin, Nup93, in both human and Xenopus that has proved to be an
evolutionarily related homologue of the yeast nucleoporin Nic96p. Polyclonal
antiserum to human Nup93 detects corresponding proteins in human, rat, and
Xenopus cells. Immunofluorescence and immunoelectron microscopy localize
vertebrate Nup93 at the nuclear basket and at or near the nuclear entry to the
gated channel of the pore. Immunoprecipitation from both mammalian and Xenopus
cell extracts indicates that a small fraction of Nup93 physically interacts with
the nucleoporin p62, just as yeast Nic96p interacts with the yeast p62
homologue. However, a large fraction of vertebrate Nup93 is extracted from pores
and is also present in Xenopus egg extracts in complex with a newly discovered
205-kDa protein. Mass spectrometric sequencing of the human 205-kDa protein
reveals that this protein is encoded by an open reading frame, KIAAO225, present
in the human database. The putative human nucleoporin of 205 kDa has related
sequence homologues in Caenorhabditis elegans and Saccharomyces cerevisiae. The
analyze the role of the Nup93 complex in the pore, nuclei were assembled that
lack the Nup93 complex after immunodepletion of a Xenopus nuclear reconstitution
extract. The Nup93-complex-depleted nuclei are clearly defective for correct
nuclear pore assembly. From these experiments, we conclude that the vertebrate
and yeast pore have significant homology in their functionally important cores
and that, with the identification of Nup93 and the 205-kDa protein, we have
extended the knowledge of the nearest-neighbor interactions of this core in both
yeast and vertebrates. Nup153 is a molecular constituent of the nuclear basket of the nuclear pore
complex (NPC) that plays a critical role in nuclear export of RNAs and proteins.
In an effort to map this nucleoporin more precisely within the nuclear basket we
have developed an experimental approach for localizing Nup153 expressed and
incorporated in vivo into Xenopus oocyte NPCs. This approach involves the
microinjection into the cytoplasm of Xenopus oocytes of in vitro synthesized
mRNA from a vector encoding an epitope-tagged cDNA. Here we present results
obtained by Western blots, fluorescence microscopy, and immuno-electron
microscopy, which clearly document that the heterologous protein is properly
expressed, targeted, and incorporated into preexisting Xenopus NPCs. This new
approach for localizing nucleoporins within the structure of the NPC overcomes
limitations of previous techniques and allows for greater specificity and
resolution than have been possible with previous methods. In cell-free extracts of Xenopus eggs that support the assembly of
replication-competent nuclei, we found that lamin B(3) specifically associates
with four polypeptides (termed SLAPs, soluble lamin associated proteins). Here,
one SLAP is identified as the nuclear pore complex protein Nup153, one member of
the F/GXFG motif-containing nucleoporins. In vitro translated Nup153 and lamin
B(3) co-immunoprecipitate, and lamin B(3) interacts specifically with the
C-terminal domain of Nup153. During nuclear envelope assembly, other
F/GXFG-containing nucleoporins are incorporated into the nuclear envelope
preceding lamina assembly. Incorporation of Nup153 occurs at the same time as
lamina assembly. When lamina assembly is prevented using the domit-negative
mutant XlaminB delta 2+, Nup153 does not appear at the nuclear envelope, while
other F/GXFG-containing nucleoporins and Nup93 are recruited normally. When the
lamina of pre-assembled nuclei is disrupted using the same domit-negative
mutant, the distribution of other nucleoporins is unaffected. However, Nup153
recruitment at the nuclear envelope is lost. Our results indicate that both the
recruitment and maintece of Nup153 at the pore are dependent upon the
integrity of the lamina. The nucleoporins Nup60p, Nup2p, and Nup1p form part of the nuclear basket
structure of the Saccharomyces cerevisiae nuclear pore complex (NPC). Here, we
show that these necleoporins can be isolated from yeast extracts by affinity
chromatography on karyopherin Kap95p-coated beads. To characterize Nup60p
further, Nup60p-coated beads were used to capture its interacting proteins from
extracts. We find that Nup60p binds to Nup2p and serves as a docking site for
Kap95p-Kap60p heterodimers and Kap123p. Nup60p also binds Gsp1p-GTP and its
guanine nucleotide exchange factor Prp20p, and functions as a Gsp1p guanine
nucleotide dissociation inhibitor by reducing the activity of Prp20p. Yeast
lacking Nup60p exhibit minor defects in nuclear export of Kap60p, nuclear import
of Kap95p-Kap60p-dependent cargoes, and diffusion of small proteins across the
NPC. Yeast lacking Nup60p also fail to anchor Nup2p at the NPC, resulting in the
mislocalization of Nup2p to the nucleoplasm and cytoplasm. Purified Nup60p and
Nup2p bind each other directly, but the stability of the complex is compromised
when Kap60p binds Nup2p. Gsp1p-GTP enhances by 10-fold the affinity between
Nup60p and Nup2p, and restores binding of Nup2p-Kap60p complexes to Nup60p. The
results suggest a dynamic interaction, controlled by the nucleoplasmic
concentration of Gsp1p-GTP, between Nup60p and Nup2p at the NPC. Traffic between the nucleus and cytoplasm takes place through a macromolecular
structure termed the nuclear pore complex. To understand how the vital process
of nucleocytoplasmic transport occurs, the contribution of individual pore
proteins must be elucidated. One such protein, the nucleoporin Nup153, is
localized to the nuclear basket of the pore complex and has been shown to be a
central component of the nuclear transport machinery. Perturbation of Nup153
function was demonstrated previously to block the export of several classes of
RNA cargo. Moreover, these studies also showed that Nup153 can stably associate
with RNA in vitro. In this study, we have mapped a domain within Nup153,
encompassing amino acids 250-400 in human Nup153, that is responsible for RNA
association. After cloning this region of Xenopus Nup153, we performed a
cross-species analysis. Despite variation in sequence conservation between
Drosophila, Xenopus, and human, this domain of Nup153 displayed robust RNA
binding activity in each case, indicating that this property is a hallmark
feature of Nup153 and pointing toward a subset of amino acid residues that are
key to conferring this ability. We have further determined that a recombit
fragment of Nup153 can bind directly to RNA and that this fragment can interact
with endogenous RNA targets. Our findings identify a functionally conserved
domain in Nup153 and suggest a role for RNA binding in Nup153 function at the
nuclear pore. The nuclear pore complex (NPC) is a large proteinaceous structure through which
bidirectional transport of macromolecules across the nuclear envelope (NE) takes
place. Nup153 is a peripheral NPC component that has been implicated in protein
and RNP transport and in the interaction of NPCs with the nuclear lamina. Here,
Nup153 is localized by immunogold electron microscopy to a position on the
nuclear ring of the NPC. Nuclear reconstitution is used to investigate the role
of Nup153 in nucleo- cytoplasmic transport and NPC architecture. NPCs assembled
in the absence of Nup153 lacked several nuclear basket components, were unevenly
distributed in the NE and, unlike wild-type NPCs, were mobile within the NE.
Importin alpha/beta-mediated protein import into the nucleus was strongly
reduced in the absence of Nup153, while transportin-mediated import was
unaffected. This was due to a reduction in import complex translocation rather
than to defective receptor recycling. Our results therefore reveal functions for
Nup153 in NPC assembly, in anchoring NPCs within the NE and in mediating
specific nuclear import events. Tpr is a coiled-coil protein found near the nucleoplasmic side of the pore
complex. Since neither the precise localization of Tpr nor its functions are
well defined, we generated antibodies to three regions of Tpr to clarify these
issues. Using light and EM immunolocalization, we determined that mammalian Tpr
is concentrated within the nuclear basket of the pore complex in a distribution
similar to Nup153 and Nup98. Antibody localization together with imaging of
GFP-Tpr in living cells revealed that Tpr is in discrete foci inside the nucleus
similar to several other nucleoporins but is not present in intranuclear
filamentous networks (Zimowska et al., 1997) or in long filaments extending from
the pore complex (Cordes et al., 1997) as proposed. Injection of anti-Tpr
antibodies into mitotic cells resulted in depletion of Tpr from the nuclear
envelope without loss of other pore complex basket proteins. Whereas nuclear
import mediated by a basic amino acid signal was unaffected, nuclear export
mediated by a leucine-rich signal was retarded significantly. Nuclear injection
of anti-Tpr antibodies in interphase cells similarly yielded inhibition of
protein export but not import. These results indicate that Tpr is a nucleoporin
of the nuclear basket with a role in nuclear protein export. The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of
protein subcomplexes forming a structure of eightfold radial symmetry. The NPC
core consists of globular subunits sandwiched between two coaxial ring-like
structures of which the ring facing the nuclear interior is capped by a fibrous
structure called the nuclear basket. By postembedding immunoelectron microscopy,
we have mapped the positions of several human NPC proteins relative to the NPC
core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153,
Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess
their contributions to NPC and basket architecture, the genes encoding Nup93,
Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA
interference (RNAi) in HeLa cells, complementing recent RNAi experiments on
Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC
proper that are essential for NPC assembly and docking of Nup153 and Tpr to the
NPC. Nup93 and Nup205 are other NPC core elements that are important for
long-term maintece of NPCs but initially dispensable for the anchoring of
Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential
labeling of NPC core regions, whereas Nup153 is shown to bind via its
amino-terminal domain to the nuclear coaxial ring linking the NPC core
structures and Tpr. The position of Tpr in turn is shown to coincide with that
of the nuclear basket, with different Tpr protein domains corresponding to
distinct basket segments. We propose a model in which Tpr constitutes the
central architectural element that forms the scaffold of the nuclear basket. The nuclear pore complex (NPC) is both the major conduit for nucleocytoplasmic
trafficking and a platform for organizing macromolecules at the nuclear
envelope. We report that yeast Esc1, a non-NPC nuclear envelope protein, is
required both for proper assembly of the nuclear basket, a structure extending
into the nucleus from the NPC, and for normal NPC localization of the Ulp1 SUMO
protease. In esc1Delta cells, Ulp1 and nuclear basket components Nup60 and Mlp1
no longer distribute broadly around the nuclear periphery, but co-localize in a
small number of dense-staining perinuclear foci. Loss of Esc1 (or Nup60) alters
SUMO conjugate accumulation and enhances ulp1 mutant defects. Similar to
previous findings with Mlp1, both Esc1 and Ulp1 help retain unspliced pre-mRNAs
in the nucleus. Therefore, these proteins are essential for proper nuclear
basket function, which includes mRNA surveillance and regulation of SUMO protein
dynamics. The results raise the possibility that NPC-localized protein
desumoylation may be a key regulatory event preventing inappropriate pre-mRNA
export. Nuclear pore complexes (NPCs) span the 2 membranes of the nuclear envelope (NE)
and facilitate nucleocytoplasmic exchange of macromolecules. NPCs have a roughly
tripartite structural organization with the so-called nuclear basket emanating
from the NPC scaffold into the nucleoplasm. The nuclear basket is composed of
the 3 nucleoporins Nup153, Nup50, and Tpr, but their specific role for the
structural organization of this NPC substructure is, however, not well
established. In this study, we have used thin-section transmission electron
microscopy to determine the structural consequences of altering the expression
of Nup153 in human cells. We show that the assembly and integrity of the nuclear
basket is not affected by Nup153 depletion, whereas its integrity is perturbed
in cells expressing high concentrations of the zinc-finger domain of Nup153.
Moreover, even mild over-expression of Nup153 is coinciding with massive changes
in nuclear organization and it is the excess of the zinc-finger domain of Nup153
that is sufficient to induce these rearrangements. Our data indicate a central
function of Nup153 in the organization of the nucleus, not only at the
periphery, but throughout the entire nuclear interior. Nuclear pore complexes (NPCs) form the gateway to the nucleus, mediating
virtually all nucleocytoplasmic trafficking. Assembly of a nuclear pore complex
requires the organization of many soluble sub-complexes into a final massive
structure embedded in the nuclear envelope. By use of a LacI/LacO reporter
system, we were able to assess nucleoporin (Nup) interactions, show that they
occur with a high level of specificity, and identify nucleoporins sufficient for
initiation of the complex process of NPC assembly in vivo. Eleven nucleoporins
from different sub-complexes were fused to LacI-CFP and transfected separately
into a human cell line containing a stably integrated LacO DNA array. The
LacI-Nup fusion proteins, which bound to the array, were examined for their
ability to recruit endogenous nucleoporins to the intranuclear LacO site. Many
could recruit nucleoporins of the same sub-complex and a number could also
recruit other sub-complexes. Strikingly, Nup133 and Nup107 of the Nup107/160
subcomplex and Nup153 and Nup50 of the nuclear pore basket recruited a near full
complement of nucleoporins to the LacO array. Furthermore, Nup133 and Nup153
efficiently targeted the LacO array to the nuclear periphery. Our data support a
hierarchical, seeded assembly pathway and identify Nup133 and Nup153 as
effective "seeds" for NPC assembly. In addition, we show that this system can be
applied to functional studies of individual nucleoporin domains as well as to
specific nucleoporin disease mutations. We find that the R391H cardiac
arrhythmia/sudden death mutation of Nup155 prevents both its subcomplex assembly
and nuclear rim targeting of the LacO array. Several nuclear pore-associated factors, including the SUMO-protease Ulp1, have
been proposed to prevent the export of intron-containing messenger
ribonucleoparticles (mRNPs) in yeast. However, the molecular mechanisms of this
nuclear pore-dependent mRNA quality control, including the sumoylated targets of
Ulp1, have remained unidentified. Here, we demonstrate that the apparent
'pre-mRNA leakage' phenotype arising upon ULP1 inactivation is shared by
sumoylation mutants of the THO complex, an early mRNP biogenesis factor.
Importantly, we establish that alteration of THO complex activity differentially
impairs the expression of intronless and intron-containing reporter genes,
rather than triggering bona fide 'pre-mRNA leakage'. Indeed, we show that the
presence of introns within THO target genes attenuates the effect of THO
inactivation on their transcription. Epistasis analyses further clarify that
different nuclear pore components influence intron-containing gene expression at
distinct stages. Ulp1, whose maintece at nuclear pores depends on the Nup84
complex, impacts on THO-dependent gene expression, whereas the nuclear
basket-associated Mlp1/Pml39 proteins prevent pre-mRNA export at a later stage,
contributing to mRNA quality control. Our study thus highlights the multiplicity
of mechanisms by which nuclear pores contribute to gene expression, and further
provides the first evidence that intronic sequences can alleviate early mRNP
biogenesis defects. Nup133 belongs to the Y-complex, a key component of the nuclear pore complex
(NPC) scaffold. Studies on a null mutation in mice previously revealed that
Nup133 is essential for embryonic development but not for mouse embryonic stem
cell (mESC) proliferation. Using single-pore detection and average
NE-fluorescence intensity, we find that Nup133 is dispensable for interphase and
postmitotic NPC scaffold assembly in pluripotent mESCs. However, loss of Nup133
specifically perturbs the formation of the nuclear basket as manifested by the
absence of Tpr in about half of the NPCs combined with altered dynamics of
Nup153. We further demonstrate that its central domain mediates Nup133's role in
assembling Tpr and Nup153 into a properly configured nuclear basket. Our
findings thus revisit the role of the Y-complex in pore biogenesis and provide
insights into the interplay between NPC scaffold architecture, nuclear basket
assembly, and the generation of heterogeneity among NPCs. The transcription factor MYC (also c-Myc) induces histone modification,
chromatin remodeling, and the release of paused RNA polymerase to broadly
regulate transcription. MYC is subject to a series of post-translational
modifications that affect its stability and oncogenic activity, but how these
control MYC's function on the genome is largely unknown. Recent work
demonstrates an intimate connection between nuclear compartmentalization and
gene regulation. Here, we report that Ser62 phosphorylation and PIN1-mediated
isomerization of MYC dynamically regulate the spatial distribution of MYC in the
nucleus, promoting its association with the inner basket of the nuclear pore in
response to proliferative signals, where it recruits the histone
acetyltransferase GCN5 to bind and regulate local gene acetylation and
expression. We demonstrate that PIN1-mediated localization of MYC to the nuclear
pore regulates MYC target genes responsive to mitogen stimulation that are
involved in proliferation and migration pathways. These changes are also present
at the chromatin level, with an increase in open regulatory elements in response
to stimulation that is PIN1-dependent and associated with MYC chromatin binding.
Taken together, our study indicates that post-translational modification of MYC
controls its spatial activity to optimally regulate gene expression in response
to extrinsic signals in normal and diseased states. |
Does lucatumumab bind to CD140? | No, lucatumumab is a fully humanized anti-CD40 antibody that blocks interaction of CD40L with CD40 and also mediates antibody-dependent cell-mediated cytotoxicity (ADCC). | Lucatumumab is a fully humanized anti-CD40 antibody that blocks interaction of
CD40L with CD40 and also mediates antibody-dependent cell-mediated cytotoxicity
(ADCC). We evaluated lucatumumab in a phase I clinical trial in chronic
lymphocytic leukemia (CLL). Twenty-six patients with relapsed CLL were enrolled
on five different dose cohorts administered weekly for 4 weeks. The maximally
tolerated dose (MTD) of lucatumumab was 3.0 mg/kg. Four patients at doses of 4.5
mg/kg and 6.0 mg/kg experienced grade 3 or 4 asymptomatic elevated amylase and
lipase levels. Of the 26 patients enrolled, 17 patients had stable disease (mean
duration of 76 days, range 29-504 days) and one patient had a nodular partial
response for 230 days. Saturation of CD40 receptor on CLL cells was uniform at
all doses post-treatment but also persisted at trough time points in the 3.0
mg/kg or greater cohorts. At the MTD, the median half-life of lucatumumab was 50
h following the first infusion, and 124 h following the fourth infusion. In
summary, lucatumumab had acceptable tolerability, pharmacokinetics that
supported chronic dosing and pharmacodynamic target antagonism at doses of 3.0
mg/kg, but demonstrated minimal single-agent activity. Future efforts with
lucatumumab in CLL should focus on combination-based therapy. |
What is the mechanism of action of arimoclomol? | Arimoclomol is a heat shock protein co-inducer that promotes nascent protein folding. It enhances the ability of differentiated neurons to survive heat shock. | Arimoclomol is an investigational drug for amyotrophic lateral sclerosis (ALS)
that amplifies heat shock protein gene expression during cell stress. The
objectives of the present study were to assess the safety, tolerability, and
pharmacokinetics of arimoclomol in ALS. Eighty-four participants with ALS
received arimoclomol at one of three oral doses (25, 50, or 100 mg three times
daily) or placebo. The primary outcome measure was safety and tolerability. A
subset of 44 participants provided serum and cerebrospinal fluid (CSF) samples
for pharmacokinetic analysis. Participants who completed 12 weeks of treatment
could enroll in a 6-month open-label study. Arimoclomol at doses up to 300
mg/day was well tolerated and safe. Arimoclomol resulted in dose-linear
pharmacologic exposures and the half-life did not change with continued
treatment. Arimoclomol CSF levels increased with dose. Arimoclomol was shown to
be safe, and it crosses the blood-brain barrier. Serum pharmacokinetic profiles
support dosing of three times per day. An efficacy study in ALS is planned. Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder
characterized by motoneuron degeneration, resulting in muscle paralysis and
death, typically within 1-5 years of diagnosis. Although the pathogenesis of ALS
remains unclear, there is evidence for the involvement of proteasome dysfunction
and heat shock proteins in the disease. We have previously shown that treatment
with a co-inducer of the heat shock response called arimoclomol is effective in
the SOD(G93A) mouse model of ALS, delaying disease progression and extending the
lifespan of SOD(G93A) mice (Kieran et al. 2004). However, this previous study
only examined the effects arimoclomol when treatment was initiated in pre- or
early symptomatic stages of the disease. Clearly, to be of benefit to the
majority of ALS patients, any therapy must be effective after symptom onset. In
order to establish whether post-symptomatic treatment with arimoclomol is
effective, in this study we carried out a systematic assessment of different
treatment regimes in SOD(G93A) mice. Treatment with arimoclomol from early (75
days) or late (90 days) symptomatic stages significantly improved muscle
function. Treatment from 75 days also significantly increased the lifespan of
SOD(G93A) mice, although treatment from 90 days has no significant effect on
lifespan. The mechanism of action of arimoclomol involves potentiation of the
heat shock response, and treatment with arimoclomol increased Hsp70 expression.
Interestingly, this up-regulation in Hsp70 was accompanied by a decrease in the
number of ubiquitin-positive aggregates in the spinal cord of treated SOD(G93A)
mice, suggesting that arimoclomol directly effects protein aggregation and
degradation. Pharmacological up-regulation of heat shock proteins (hsps) rescues motoneurons
from cell death in a mouse model of amyotrophic lateral sclerosis. However, the
relationship between increased hsp expression and neuronal survival is not
straightforward. Here we examined the effects of two pharmacological agents that
induce the heat shock response via activation of HSF-1, on stressed primary
motoneurons in culture. Although both arimoclomol and celastrol induced the
expression of Hsp70, their effects on primary motoneurons in culture were
significantly different. Whereas arimoclomol had survival-promoting effects,
rescuing motoneurons from staurosporin and H(2)O(2) induced apoptosis, celastrol
not only failed to protect stressed motoneurons from apoptosis under same
experimental conditions, but was neurotoxic and induced neuronal death.
Immunostaining of celastrol-treated cultures for hsp70 and activated caspase-3
revealed that celastrol treatment activates both the heat shock response and the
apoptotic cell death cascade. These results indicate that not all agents that
activate the heat shock response will necessarily be neuroprotective. Arimoclomol, an amplifier of heat shock protein expression involved in cellular
stress response, has emerged as a potential therapeutic candidate in amyotrophic
lateral sclerosis (ALS) in recent years. Treatment with arimoclomol was reported
to improve survival and muscle function in a mouse model of motor neuron
disease. Several single- and multiple-dose safety studies have been completed in
healthy control subjects. A 3-month Phase IIa study in people with ALS
demonstrated safety at dosages up to 300 mg/day and another study is currently
recruiting participants with familial ALS caused by mutations in the superoxide
dismutase gene. We review the rationale for testing arimoclomol in sporadic and
familial ALS in the context of available safety and pharmacokinetic data.
Published and unpublished literature relative to the drug in the past two
decades is discussed. The current review attempts to bring together our existing
understanding of the actions of arimoclomol with the disease profile of ALS. The
pharmacological profile of arimoclomol and the available preclinical data make
it a promising therapeutic possibility in ALS. Recent years have seen an explosion of research into increasingly prevalent
neurodegenerative diseases. Arimoclomol (BRX-220), being developed by CytRx
Corp, is an oral therapeutic candidate for the treatment of amyotrophic lateral
sclerosis (ALS), the most common form of motor neuron disease. ALS is a fatal,
incurable disorder, which can present as sporadic (90 to 95% of cases) or
familial (5 to 10% of cases) forms. The etiology of sporadic ALS remains unknown
and much of the understanding of ALS pathogenesis has been derived through study
of its familial forms; in particular, through study of autosomal domit
mutations in the SOD1 (copper/zinc superoxide dismutase) gene, which cause
approximately 20% of familial ALS cases. Under conditions of excessive stress,
arimoclomol induces amplification of the cytoprotective heat shock response in
order to protect motor neurons from death. Comprehensive in vivo and in vitro
studies demonstrated its effect in the prevention of neuronal loss and promotion
of motor neuron survival, even after symptom onset. Clinical trials have
reported good tolerability and safety. This paper discusses the rationale for
arimoclomol use in ALS, the preclinical and clinical evidence collected to date,
the likelihood of its promising preclinical results translating to humans, and
the relevance of this research for neurodegeneration as a whole. We investigated the effect of a heat-shock protein co-inducer, arimoclomol
(CytRx, LA, CA), on hypoxia-adaptive responses using a rat model of simulated
altitude exposure (hypobaric hypoxia).Cognitive function was measured using a
T-maze and an object recognition test.Motor function was measured using an
inclined-screen test and an adhesion removal test. Immunohistochemical analyses
were assessed in brain for heat-shock protein 70 (HSP 70), intercellular
adhesion molecule 1 (ICAM- 1) and apoptosis (TUNEL staining). Results show that
both cognitive and motor performances were improved in rats treated with
arimoclomol during hypoxic exposure; the hypoxia-induced expression of HSP70 and
ICAM-1, and TUNEL-positive cells were reduced in brain with the treatment.Our
data suggest that the arimoclomol treatment reduces the hypoxia-induced stress
in brain tissue, and also improves the behavioral performance in rats during
hypoxic adaptation. We undertook a longitudinal study of the histological and biochemical changes at
the neuromuscular junction (NMJ) in muscles of SOD1-G93A mice. We also assessed
these functions in mice treated with a known heat shock protein inducer,
arimoclomol. Tissue samples of treated and untreated mSOD mice were analysed for
AChE and ChAT enzyme activities as markers of neuromuscular function. Sections
of hindlimb muscles (TA, EDL and soleus) were also stained for succinate
dehydrogenase and silver cholinesterase activities as well as for
immunohistochemistry. Hsp70 levels were also measured from muscle samples using
ELISA. Results showed that denervation and nerve sprouting were present at
symptom onset in fast muscles, although slow muscles remained fully innervated.
Cholinergic enzyme activities were reduced prior to denervation and declined
further with disease progression. Reduction of endplate size, a slow to fast
shift in muscle phenotype was also observed. Treatment with arimoclomol delayed
the appearance of these changes, increased innervation, cholinergic enzyme
activities and endplate size and reversed muscle fibre transformation. These
beneficial effects of arimoclomol in muscles were accompanied by an increase in
Hsp70 expression. In conclusion, our results indicate that pharmacological
targeting of muscles at early stages of disease may be a successful strategy to
ameliorate disease progression in ALS. Spinal and bulbar muscular atrophy, also known as Kennedy's disease, is an
adult-onset hereditary neurodegenerative disorder caused by an expansion of the
polyglutamine repeat in the first exon in the androgen receptor gene.
Pathologically, the disease is defined by selective loss of spinal and bulbar
motor neurons causing bulbar, facial and limb weakness. Although the precise
disease pathophysiology is largely unknown, it appears to be related to abnormal
accumulation of the pathogenic androgen receptor protein within the nucleus,
leading to disruption of cellular processes. Using a mouse model of spinal and
bulbar muscular atrophy that exhibits many of the characteristic features of the
human disease, in vivo physiological assessment of muscle function revealed that
mice with the pathogenic expansion of the androgen receptor develop a motor
deficit characterized by a reduction in muscle force, abnormal muscle
contractile characteristics, loss of functional motor units and motor neuron
degeneration. We have previously shown that treatment with arimoclomol, a
co-inducer of the heat shock stress response, delays disease progression in the
mutant superoxide dismutase 1 mouse model of amyotrophic lateral sclerosis, a
fatal motor neuron disease. We therefore evaluated the therapeutic potential of
arimoclomol in mice with spinal and bulbar muscular atrophy. Arimoclomol was
administered orally, in drinking water, from symptom onset and the effects
established at 18 months of age, a late stage of disease. Arimoclomol
significantly improved hindlimb muscle force and contractile characteristics,
rescued motor units and, importantly, improved motor neuron survival and
upregulated the expression of the vascular endothelial growth factor which
possess neurotrophic activity. These results provide evidence that upregulation
of the heat shock response by treatment with arimoclomol may have therapeutic
potential in the treatment of spinal and bulbar muscular atrophy and may also be
a possible approach for the treatment of other neurodegenerative diseases. Retinitis pigmentosa (RP) is a group of inherited diseases that cause blindness
due to the progressive death of rod and cone photoreceptors in the retina. There
are currently no effective treatments for RP. Inherited mutations in rhodopsin,
the light-sensing protein of rod photoreceptor cells, are the most common cause
of autosomal-domit RP. The majority of mutations in rhodopsin, including the
common P23H substitution, lead to protein misfolding, which is a feature in many
neurodegenerative disorders. Previous studies have shown that upregulating
molecular chaperone expression can delay disease progression in models of
neurodegeneration. Here, we have explored the potential of the heat-shock
protein co-inducer arimoclomol to ameliorate rhodopsin RP. In a cell model of
P23H rod opsin RP, arimoclomol reduced P23H rod opsin aggregation and improved
viability of mutant rhodopsin-expressing cells. In P23H rhodopsin transgenic rat
models, pharmacological potentiation of the stress response with arimoclomol
improved electroretinogram responses and prolonged photoreceptor survival, as
assessed by measuring outer nuclear layer thickness in the retina. Furthermore,
treated animal retinae showed improved photoreceptor outer segment structure and
reduced rhodopsin aggregation compared with vehicle-treated controls. The
heat-shock response (HSR) was activated in P23H retinae, and this was enhanced
with arimoclomol treatment. Furthermore, the unfolded protein response (UPR),
which is induced in P23H transgenic rats, was also enhanced in the retinae of
arimoclomol-treated animals, suggesting that arimoclomol can potentiate the UPR
as well as the HSR. These data suggest that pharmacological enhancement of
cellular stress responses may be a potential treatment for rhodopsin RP and that
arimoclomol could benefit diseases where ER stress is a factor. Author information:
(1)Medical Research Council (MRC) Centre for Neuromuscular Diseases, University
College London (UCL) Institute of Neurology, Queen Square, London WC1N 3BG, UK.
Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of
Neurology, Queen Square, London WC1N 3BG, UK.
(2)Medical Research Council (MRC) Centre for Neuromuscular Diseases, University
College London (UCL) Institute of Neurology, Queen Square, London WC1N 3BG, UK.
(3)Department of Neurology, University of Kansas Medical Center, 3901 Rainbow
Boulevard, Mail Stop 2012, Kansas City, KS 66160, USA.
(4)Department of Biostatistics, University of Kansas Medical Center, Kansas
City, KS 66160, USA.
(5)Department of Health, Sport, and Exercise Science, The University of Kansas,
Lawrence, KS 66045-7567, USA.
(6)Victor Horsley Department of Neurosurgery, National Hospital for Neurology
and Neurosurgery, UCL Hospitals, Queen Square, London WC1N 3BG, UK.
(7)The Francis Crick Institute, Lincoln's Inn Fields Laboratory, 44 Lincoln's
Inn Fields, London WC2A 3LY, UK.
(8)Department of Cell & Molecular Biology, St. Jude Children's Research
Hospital, Memphis, TN 38105-3678, USA.
(9)Department of Neurology, University of Kansas Medical Center, 3901 Rainbow
Boulevard, Mail Stop 2012, Kansas City, KS 66160, USA. [email protected]
[email protected].
(10)Medical Research Council (MRC) Centre for Neuromuscular Diseases, University
College London (UCL) Institute of Neurology, Queen Square, London WC1N 3BG, UK.
Sobell Department of Motor Neuroscience and Movement Disorders, UCL Institute of
Neurology, Queen Square, London WC1N 3BG, UK. [email protected]
[email protected]. Few effective therapies exist for the treatment of neurodegenerative diseases
that have been characterized as protein misfolding disorders. Upregulation of
heat shock proteins (Hsps) mitigates against the accumulation of misfolded,
aggregation-prone proteins and synaptic dysfunction, which is recognized as an
early event in neurodegenerative diseases. Enhanced induction of a set of Hsps
in differentiated human SH-SY5Y neuronal cells was observed following
co-application of celastrol and arimoclomol, compared to their individual
application. The dosages employed did not affect cell viability or neuronal
process morphology. The induced Hsps included the little studied HSPA6
(Hsp70B'), a potentially neuroprotective protein that is present in the human
genome but not in rat and mouse and hence is missing in current animal models of
neurodegenerative disease. Enhanced induction of HSPA1A (Hsp70-1), DNAJB1
(Hsp40), HO-1 (Hsp32), and HSPB1 (Hsp27) was also observed. Celastrol activates
heat shock transcription factor 1 (HSF1), the master regulator of Hsp gene
transcription, and also exhibits potent anti-inflammatory and anti-oxidant
activities. Arimoclomol is a co-activator that prolongs the binding of activated
HSF1 to heat shock elements (HSEs) in the promoter regions of inducible Hsp
genes. Elevated Hsp levels peaked at 10 to 12 h for HSPA6, HSPA1A, DNAJB1, and
HO-1 and at 24 h for HSPB1. Co-application of celastrol and arimoclomol induced
higher Hsp levels compared to heat shock paired with arimoclomol. The
co-application strategy of celastrol and arimoclomol targets multiple
neurodegenerative disease-associated pathologies including protein misfolding
and protein aggregation, inflammatory and oxidative stress, and synaptic
dysfunction. Lysosomal storage diseases (LSDs) often manifest with severe systemic and
central nervous system (CNS) symptoms. The existing treatment options are
limited and have no or only modest efficacy against neurological manifestations
of disease. We demonstrate that recombit human heat shock protein 70 (HSP70)
improves the binding of several sphingolipid-degrading enzymes to their
essential cofactor bis(monoacyl)glycerophosphate in vitro. HSP70 treatment
reversed lysosomal pathology in primary fibroblasts from 14 patients with eight
different LSDs. HSP70 penetrated effectively into murine tissues including the
CNS and inhibited glycosphingolipid accumulation in murine models of Fabry
disease (Gla(-/-)), Sandhoff disease (Hexb(-/-)), and Niemann-Pick disease type
C (Npc1(-/-)) and attenuated a wide spectrum of disease-associated neurological
symptoms in Hexb(-/-) and Npc1(-/-) mice. Oral administration of arimoclomol, a
small-molecule coinducer of HSPs that is currently in clinical trials for
Niemann-Pick disease type C (NPC), recapitulated the effects of recombit
human HSP70, suggesting that heat shock protein-based therapies merit clinical
evaluation for treating LSDs. A new efficient chiral synthesis of etiopure arimoclomol (2) is reported from
(R)-(-)-glycidyl nosylate (11) with complete retention of chiral integrity.
Off-target pharmacology of arimoclomol (2) was evaluated against a
representative set of drug targets and showed modest binding to a few kinases.
Pharmacokinetic data was generated in vivo in mouse and showed a low
brain : plasma ratio. These studies will be helpful towards a better
understanding of the PK-PD relationship of 2 in disease models. OBJECTIVE: To examine the safety and tolerability as well as the preliminary
efficacy of arimoclomol, a heat shock protein co-inducer that promotes nascent
protein folding, in patients with rapidly progressive SOD1 amyotrophic lateral
sclerosis (ALS).
METHODS: This was a double-blind, placebo-controlled trial in which patients
with rapidly progressive SOD1-mutant ALS were randomized 1:1 to receive
arimoclomol 200 mg tid or matching placebo for up to 12 months. Study procedures
were performed using a mix of in-person and remote assessments. Primary outcome
was safety and tolerability. Secondary outcome was efficacy, with survival as
the principal measure. Additional efficacy measures were the rates of decline of
the Revised ALS Functional Rating Scale (ALSFRS-R) and percent predicted forced
expiratory volume in 6 seconds (FEV6), and the Combined Assessment of Function
and Survival (CAFS).
RESULTS: Thirty-eight participants were randomized. Thirty-six (19 placebo, 17
arimoclomol) were included in the prespecified intent-to-treat analysis. Apart
from respiratory function, groups were generally well-balanced at baseline.
Adverse events occurred infrequently, and were usually mild and deemed unlikely
or not related to study drug. Adjusting for riluzole and baseline ALSFRS-R,
survival favored arimoclomol with a hazard ratio of 0.77 (95% confidence
interval [CI] 0.32-1.80). ALSFRS-R and FEV6 declined more slowly in the
arimoclomol group, with treatment differences of 0.5 point/month (95% CI -0.63
to 1.63) and 1.24 percent predicted/month (95% CI -2.77 to 5.25), respectively,
and the CAFS similarly favored arimoclomol.
CONCLUSIONS: This study provides Class II evidence that arimoclomol is safe and
well-tolerated at a dosage of 200 mg tid for up to 12 months. Although not
powered for therapeutic effect, the consistency of results across the range of
prespecified efficacy outcome measures suggests a possible therapeutic benefit
of arimoclomol.
CLINICALTRIALSGOV IDENTIFIER: NCT00706147.
CLASSIFICATION OF EVIDENCE: This study provides Class II evidence that
arimoclomol is safe and well-tolerated at a dosage of 200 mg tid for up to 12
months. The study lacked the precision to conclude, or to exclude, an important
therapeutic benefit of arimoclomol. BACKGROUND: Gaucher Disease is caused by mutations of the GBA gene which encodes
the lysosomal enzyme acid beta-glucosidase (GCase). GBA mutations commonly
affect GCase function by perturbing its protein homeostasis rather than its
catalytic activity. Heat shock proteins are well known cytoprotective molecules
with functions in protein homeostasis and lysosomal function and their
manipulation has been suggested as a potential therapeutic strategy for GD. The
investigational drug arimoclomol, which is in phase II/III clinical trials, is a
well-characterized HSP amplifier and has been extensively clinically tested.
Importantly, arimoclomol efficiently crosses the blood-brain-barrier presenting
an opportunity to target the neurological manifestations of GD, which remains
without a disease-modifying therapy.
METHODS: We used a range of biological and biochemical in vitro assays to assess
the effect of arimoclomol on GCase activity in ex vivo systems of primary
fibroblasts and neuronal-like cells from GD patients.
FINDINGS: We found that arimoclomol induced relevant HSPs such as ER-resident
HSP70 (BiP) and enhanced the folding, maturation, activity, and correct cellular
localization of mutated GCase across several genotypes including the common
L444P and N370S mutations in primary cells from GD patients. These effects where
recapitulated in a human neuronal model of GD obtained by differentiation of
multipotent adult stem cells.
INTERPRETATION: These data demonstrate the potential of HSP-targeting therapies
in GCase-deficiencies and strongly support the clinical development of
arimoclomol as a potential therapeutic option for the neuronopathic forms of GD.
FUNDING: The research was funded by Orphazyme A/S, Copenhagen, Denmark. |
What are the effects of STEF depletion? | The mechanisms regulating the actin cap are currently poorly understood. STEF/TIAM2, a Rac1 selective guanine nucleotide exchange factor, localises at the nuclear envelope, co-localising with the key perinuclear proteins Nesprin-2G and Non-muscle myosin IIB (NMMIIB), where it regulates perinuclear Rac1 activity. STEF depletion reduces apical perinuclear actin cables (a phenotype rescued by targeting active Rac1 to the nuclear envelope), decreases nuclear stiffness and reduces expression of TAZ-regulated genes, indicating an alteration in mechanosensing pathways as a consequence of disruption of the actin cap. | The perinuclear actin cap is an important cytoskeletal structure that regulates
nuclear morphology and re-orientation during front-rear polarisation. The
mechanisms regulating the actin cap are currently poorly understood. Here, we
demonstrate that STEF/TIAM2, a Rac1 selective guanine nucleotide exchange
factor, localises at the nuclear envelope, co-localising with the key
perinuclear proteins Nesprin-2G and Non-muscle myosin IIB (NMMIIB), where it
regulates perinuclear Rac1 activity. We show that STEF depletion reduces apical
perinuclear actin cables (a phenotype rescued by targeting active Rac1 to the
nuclear envelope), increases nuclear height and impairs nuclear re-orientation.
STEF down-regulation also reduces perinuclear pMLC and decreases
myosin-generated tension at the nuclear envelope, suggesting that STEF-mediated
Rac1 activity regulates NMMIIB activity to promote stabilisation of the
perinuclear actin cap. Finally, STEF depletion decreases nuclear stiffness and
reduces expression of TAZ-regulated genes, indicating an alteration in
mechanosensing pathways as a consequence of disruption of the actin cap. |
Please list symptoms of measles. | The leading symptoms of the disease are high fever that presents after an incubation period of 9-10 days and the red rash that begins several days after the fever starts. Beyond specific generalized symptoms, measles may have ocular symptoms. The most commonly occuring satellite symptoms are conjunctivitis, coryza and cough. | This study reports on molecular analysis of a Measles virus (MV) isolate from a
patient who was infected in Japan but showed symptoms after arriving to Brazil.
This patient had typical clinical measles infection symptoms: fever, rash, cough
and coryza. After isolating the virus in B95a cells, a fragment of the
nucleoprotein (N) gene was amplified by reverse transcription-polymerase chain
reaction (RT-PCR) and subjected to direct nucleotide sequencing. The sequence
data showed that the MV isolate of concern is of the D5 genotype. Measles is a highly contagious viral infection associated with clinical symptoms
such as fever, cough, conjunctivitis, coryza, eruption and increased serum
immunoglobulin M (IgM) antibodies. A clinical diagnosis is easily established
when the chain of infection can be followed. However, Japan is currently
experiencing sporadic measles outbreaks, which complicate the establishment of
diagnosis. Furthermore, other exanthematous infections such as rubella, human
parvovirus B19, human herpesvirus 6 (HHV-6) and HHV-7 present with clinical
symptoms and IgM antibody levels similar to those in measles. Therefore,
real-time polymerase chain reaction virogene testing has been part of Japan's
standard diagnostic protocol for measles since 2010. This report presents two
pediatric cases clinically resembling measles that were diagnosed as HHV-6 based
on a virogene detection test. This underscores the importance of performing
pathogen testing to confirm a diagnosis when measles is suspected. The introduction of measles vaccination programs and broad coverage worldwide
has meant this infection a rare encounter for pediatricians. In Oman, with
almost 100% measles vaccination coverage for children, this infection
disappeared from the list of fever and rash differential diagnoses. Encephalitis
is a well-known complication of measles infection and sometimes can be the only
manifestation especially in adults. We report a seven-year-old Syrian immigrant
who was admitted to the Royal Hospital, Muscat, with acute encephalitis
secondary to wild measles infection. Although she had a classical presentation
of measle infection, the diagnosis was missed in the private and regional
hospital she attended before getting referred to Royal Hospital. She was later
identified to be exposed to an outbreak of the infection in an unvaccinated
population. Magnetic resoce imaging showed high signal intensity of both
basal ganglia suggestive of measles encephalitis. The diagnosis was confirmed by
detection of measles virus from her urine and blood, and a throat swab. The
isolated measles virus was D8 serotype, which was prevalent in Syria around the
same time. The child was treated with steroids and vitamin A. She achieved full
recovery despite her severe presentation. A high degree of suspicion for measles
infection should be maintained in unvaccinated children with a compatible
presentation of the infection or its complications. There might be a role for
steroid use in cases of acute measles encephalitis. BACKGROUND: In April 2015, Kamwenge District, western Uganda reported a measles
outbreak. We investigated the outbreak to identify potential exposures that
facilitated measles transmission, assess vaccine effectiveness (VE) and
vaccination coverage (VC), and recommend prevention and control measures.
METHODS: For this investigation, a probable case was defined as onset of fever
and generalized maculopapular rash, plus ≥1 of the following symptoms: Coryza,
conjunctivitis, or cough. A confirmed case was defined as a probable case plus
identification of measles-specific IgM in serum. For case-finding, we reviewed
patients' medical records and conducted in-home patient examination. In a
case-control study, we compared exposures of case-patients and controls matched
by age and village of residence. For children aged 9 m-5y, we estimated VC using
the percent of children among the controls who had been vaccinated against
measles, and calculated VE using the formula, VE = 1 - ORM-H, where ORM-H was
the Mantel-Haenszel odds ratio associated with having a measles vaccination
history.
RESULTS: We identified 213 probable cases with onset between April and August,
2015. Of 23 blood specimens collected, 78% were positive for measles-specific
IgM. Measles attack rate was highest in the youngest age-group, 0-5y
(13/10,000), and decreased as age increased. The epidemic curve indicated
sustained propagation in the community. Of the 50 case-patients and 200
controls, 42% of case-patients and 12% of controls visited health centers during
their likely exposure period (ORM-H = 6.1; 95% CI = 2.7-14). Among children aged
9 m-5y, VE was estimated at 70% (95% CI: 24-88%), and VC at 75% (95% CI:
67-83%). Excessive crowding was observed at all health centers; no patient
triage-system existed.
CONCLUSIONS: The spread of measles during this outbreak was facilitated by
patient mixing at crowded health centers, suboptimal VE and inadequate VC. We
recommended emergency immunization campaign targeting children <5y in the
affected sub-counties, as well as triaging and isolation of febrile or rash
patients visiting health centers. |
Does simvastatin improve outcomes of aneurysmal subarachnoid hemorrhage? | No. Simvastatin showed no benefits in decreasing the incidence of vasospasm, DCI, or all-cause mortality after aneurysmal subarachnoid hemorrhage. Patients with aneurysmal subarachnoid hemorrhage should not be treated routinely with simvastatin during the acute stage. | BACKGROUND AND PURPOSE: Experimental evidence has indicated the benefits of
simvastatin for the treatment of subarachnoid hemorrhage. Two randomized
placebo-controlled pilot trials that used the highest clinically approved dose
of simvastatin (80 mg daily) gave positive results despite the fact that a lower
dose of simvastatin (40 mg daily) did not improve clinical outcomes. We
hypothesized that a high dose of 80 mg of simvastatin daily for 3 weeks would
reduce the incidence of delayed ischemic deficits after subarachnoid hemorrhage
compared with a lower dose (40 mg of simvastatin daily) and lead to improved
clinical outcomes.
METHODS: The study design was a randomized controlled double-blinded clinical
trial. Patients with aneurysmal subarachnoid hemorrhage (presenting within 96
hours of the ictus) from 6 neurosurgical centers were recruited for 3 years. The
primary outcome measure was the presence of delayed ischemic deficits, and
secondary outcome measures included a modified Rankin disability score at 3
months and an analysis of cost-effectiveness.
RESULTS: No difference was observed between the groups treated with the higher
dose or the lower dose of simvastatin in the incidence of delayed ischemic
deficits (27% versus 24%; odds ratio, 1.2; 95% confidence interval, 0.7-2.0;
P=0.586) or in the rate of favorable outcomes (modified Rankin Scale score, 0-2)
at 3 months (73% versus 72%; odds ratio, 1.1; 95% confidence interval, 0.6-1.9;
P=0.770).
CONCLUSIONS: High-dose simvastatin treatment should not be prescribed routinely
for aneurysmal subarachnoid hemorrhage.
CLINICAL TRIAL REGISTRATION URL: http://www.clinicaltrials.gov. Unique
identifier: NCT01077206. OBJECTIVES: Experimental evidence has indicated the benefit of simvastatin in
the treatment of subarachnoid hemorrhage (SAH). Recently, acute simvastatin
treatment was not shown to be beneficial in neurological outcome using modified
Rankin Scale. Cognitive function is another important dimension of outcome
assessment and yet had not been investigated in statin studies for aneurysmal
subarachnoid hemorrhage. We therefore explored whether acute simvastatin
treatment would improve cognitive outcomes.
METHODS: The study recruited SAH patients with acute simvastatin treatment
enrolled in a randomized controlled double-blinded clinical trial
(ClinicalTrials.gov Identifier: NCT01038193). A control cohort of SAH patients
without simvastatin treatment was identified with propensity score matching of
age and admission grade. Primary outcome measure was Montreal Cognitive
Assessment (MoCA). Secondary outcome measures were delayed ischaemic deficit
(DID), delayed cerebral infarction, modified Rankin Scale (mRS), and Mini-Mental
State Examination (MMSE).
RESULTS: Fifty-one SAH patients with acute simvastatin treatment and 51 SAH
patients without simvastatin treatment were recruited for analysis. At 3 months,
there were no differences in MoCA scores (MoCA: 21+/-6 vs. 21+/-5, p=0.772).
MoCA-assessed cognitive impairment (MoCA<26) was not different (75% vs. 80%, OR
0.7, 95%CI 0.3 to 1.8, p=0.477). There were also no differences in DID, delayed
cerebral infarction, favorable mRS outcome, and MMSE scores, and MMSE-assessed
cognitive impairment between both groups.
CONCLUSIONS: The current study does not support that acute simvastatin treatment
improves cognitive outcome after aneurysmal subarachnoid hemorrhage. : The leading cause of morbidity and mortality after surviving the rupture of an
intracranial aneurysm is delayed cerebral ischaemia (DCI). We present an update
of recent literature on the current status of prevention and treatment
strategies for DCI after aneurysmal subarachnoid haemorrhage. A systematic
literature search of three databases (PubMed, ISI Web of Science, and Embase)
was performed. Human clinical trials assessing treatment strategies, published
in the last 5 yr, were included based on full-text analysis. Study data were
extracted using tables depicting study type, sample size, and outcome variables.
We identified 49 studies meeting our inclusion criteria. Clazosentan, magnesium,
and simvastatin have been tested in large high-quality trials but failed to show
a beneficial effect. Cilostazol, eicosapentaenoic acid, erythropoietin, heparin,
and methylprednisolone yield promising results in smaller, non-randomized or
retrospective studies and warrant further investigation. Topical application of
nicardipine via implants after clipping has been shown to reduce clinical and
angiographic vasospasm. Methods to improve subarachnoid blood clearance have
been established, but their effect on outcome remains unclear. Haemodynamic
management of DCI is evolving towards euvolaemic hypertension. Endovascular
rescue therapies, such as percutaneous transluminal balloon angioplasty and
intra-arterial spasmolysis, are able to resolve angiographic vasospasm, but
their effect on outcome needs to be proved. Many novel therapies for preventing
and treating DCI after aneurysmal subarachnoid haemorrhage have been assessed,
with variable results. Limitations of the study designs often preclude definite
statements. Current evidence does not support prophylactic use of clazosentan,
magnesium, or simvastatin. Many strategies remain to be tested in larger
randomized controlled trials.
CLINICAL TRIAL REGISTRATION: This systematic review was registered in the
international prospective register of systematic reviews.
PROSPERO: CRD42015019817. Objective The present study was performed to explore the therapeutic potential
of simvastatin in subarachnoid hemorrhage (SAH) in the context of the
Simvastatin in Aneurysmal Subarachnoid Hemorrhage (STASH) trial. Methods
MEDLINE, EMBASE, and the Cochrane Library were searched for all randomized
controlled trials (RCTs) investigating the therapeutic effect of simvastatin on
aneurysmal SAH. We applied a random-effects model to calculate the data. Results
Five RCTs involving 951 patients met the eligibility criteria. We found no
statistically significant effects on vasospasm detected by transcranial cerebral
Doppler (relative risk [RR], 0.91; 95% confidence interval [CI], 0.55-1.49),
delayed cerebral ischemia (DCI) (RR, 0.85; 95% CI, 0.63-1.14), or all-cause
mortality (RR, 1.02; 95% CI, 0.67-1.54). Subgroup analysis showed that these
consolidated results were stable at different doses, different times to start of
treatment, and different courses of treatment in all included RCTs. Sensitivity
analysis showed that the STASH trial, which had a large population, did not
influence the consolidated results of all three outcomes. Conclusions
Simvastatin showed no benefits in decreasing the incidence of vasospasm, DCI, or
all-cause mortality after aneurysmal SAH. We conclude that patients with SAH
should not be treated routinely with simvastatin during the acute stage. |
Which databases can exchange data using Matchmaker Exchange's API? | Matchmaker Exchange (MME) was created to establish a federated network connecting databases of genomic and phenotypic data using a common application programming interface (API). To date, seven databases can exchange data using the API: GeneMatcher, PhenomeCentral, DECIPHER, MyGene2, matchbox, Australian Genomics Health Alliance Patient Archive, and Monarch Initiative; the latter included for model organism matching. | Author information:
(1)McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University,
Baltimore, Maryland.
(2)The Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
(3)Centre for Computational Medicine, Hospital for Sick Children, Toronto,
Ontario, Canada.
(4)Department of Pediatrics, University of Washington, Seattle, Washington.
(5)Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridgeshire, United Kingdom.
(6)FS Consulting LLC, Seattle, Washington.
(7)Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research,
The Kinghorn Cancer Centre, Darlinghurst, New South Wales, Australia.
(8)St Vincent's Clinical School, Faculty of Medicine, University of New South
Wales, Darlinghurst, New South Wales, Australia.
(9)William Harvey Research Institute, Barts and The London School of Medicine
and Dentistry, Queen Mary University of London, London, United Kingdom.
(10)Department of Medical Informatics and Clinical Epidemiology, Oregon Health &
Science University, Portland, Oregon.
(11)Children's Hospital of Eastern Ontario Research Institute, University of
Ottawa, Ottawa, Ontario, Canada.
(12)McKusick-Nathans Institute of Genetic Medicine (IGM), Clinical Director,
IGM. Scientific Director, OMIM. Johns Hopkins University. Baltimore, Maryland. |
Is pazopanib an effective treatment of glioblastoma? | No. Pazopanib does not improve survival of glioblastoma patients. | The objective of this phase II single-arm study was to evaluate the efficacy and
safety of pazopanib, a multi-targeted tyrosine kinase inhibitor, against
vascular endothelial growth factor receptor (VEGFR)-1, -2, and -3,
platelet-derived growth factor receptor-alpha and -beta, and c-Kit, in recurrent
glioblastoma. Patients with < or =2 relapses and no prior anti-VEGF/VEGFR
therapy were treated with pazopanib 800 mg daily on 4-week cycles without
planned interruptions. Brain magnetic resoce imaging and clinical
reassessment were made every 8 weeks. The primary endpoint was efficacy as
measured by 6-month progression-free survival (PFS6). Thirty-five GBM patients
with a median age of 53 years and median Karnofsky performance scale of 90 were
accrued. Grade 3/4 toxicities included leukopenia (n = 1), lymphopenia (n = 2),
thrombocytopenia (n = 1), ALT elevation (n = 3), AST elevation (n = 1), CNS
hemorrhage (n = 1), fatigue (n = 1), and thrombotic/embolic events (n = 3); 8
patients required dose reduction. Two patients had a partial radiographic
response by standard bidimensional measurements, whereas 9 patients (6 at the
8-week point and 3 only within the first month of treatment) had decreased
contrast enhancement, vasogenic edema, and mass effect but <50% reduction in
tumor. The median PFS was 12 weeks (95% confidence interval [CI]: 8-14 weeks)
and only 1 patient had a PFS time > or =6 months (PFS6 = 3%). Thirty patients
(86%) had died and median survival was 35 weeks (95% CI: 24-47 weeks). Pazopanib
was reasonably well tolerated with a spectrum of toxicities similar to other
anti-VEGF/VEGFR agents. Single-agent pazopanib did not prolong PFS in this
patient population but showed in situ biological activity as demonstrated by
radiographic responses. ClinicalTrials.gov identifier: NCT00459381. PURPOSE: Increased mitogenic signaling and angiogenesis, frequently facilitated
by somatic activation of EGF receptor (EGFR; ErbB1) and/or loss of PTEN, and
VEGF overexpression, respectively, drive maligt glioma growth. We
hypothesized that patients with recurrent glioblastoma would exhibit
differential antitumor benefit based on tumor PTEN/EGFRvIII status when treated
with the antiangiogenic agent pazopanib and the ErbB inhibitor lapatinib.
EXPERIMENTAL DESIGN: A phase II study evaluated the antitumor activity of
pazopanib 400 mg/d plus lapatinib 1,000 mg/d in patients with grade 4 maligt
glioma and known PTEN/EGFRvIII status not receiving enzyme-inducing
anticonvulsants (EIAC). The phase II study used a two-stage Green-Dahlberg
design for futility. An independent, parallel phase I component determined the
maximum-tolerated regimen (MTR) of pazopanib and lapatinib in patients with
grade 3/4 glioma receiving EIACs.
RESULTS: The six-month progression-free survival (PFS) rates in phase II (n =
41) were 0% and 15% in the PTEN/EGFRvIII-positive and PTEN/EGFRvIII-negative
cohorts, respectively, leading to early termination. Two patients (5%) had a
partial response and 14 patients (34%) had stable disease lasting 8 or more
weeks. In phase I (n = 34), the MTR was not reached. On the basis of
pharmacokinetic and safety review, a regimen of pazopanib 600 mg plus lapatinib
1,000 mg, each twice daily, was considered safe. Concomitant EIACs reduced
exposure to pazopanib and lapatinib.
CONCLUSIONS: The antitumor activity of this combination at the phase II dose
tested was limited. Pharmacokinetic data indicated that exposure to lapatinib
was subtherapeutic in the phase II evaluation. Evaluation of intratumoral drug
delivery and activity may be essential for hypothesis-testing trials with
targeted agents in maligt glioma. |
What is the purpose of the Ottawa Ankle Rule? | Ottawa Ankle Rules is a clinical decision tool used to minimize unnecessary radiographs in ankle and foot injuries. It shows the areas of tenderness to be evaluated in ankle trauma patients to determine the need for imaging. | BACKGROUND: Foot and ankle injuries are frequent in emergency departments.
Although only a few patients with foot and ankle sprain present fractures and
the fracture patterns are almost always simple, lack of fracture diagnosis can
lead to poor functional outcomes.
AIM: The present study aims to evaluate the reliability of the Ottawa ankle
rules and the orthopedic surgeon subjective perception to assess foot and ankle
fractures after sprains.
SUBJECTS AND METHODS: A cross-sectional study was conducted from July 2012 to
December 2012. Ethical approval was granted. Two hundred seventy-four adult
patients admitted to the emergency department with foot and/or ankle sprain were
evaluated by an orthopedic surgeon who completed a questionnaire prior to
radiographic assessment. The Ottawa ankle rules and subjective perception of
foot and/or ankle fractures were evaluated on the questionnaire.
RESULTS: Thirteen percent (36/274) patients presented fracture. Orthopedic
surgeon subjective analysis showed 55.6% sensitivity, 90.1% specificity, 46.5%
positive predictive value and 92.9% negative predictive value. The general
orthopedic surgeon opinion accuracy was 85.4%. The Ottawa ankle rules presented
97.2% sensitivity, 7.8% specificity, 13.9% positive predictive value, 95%
negative predictive value and 19.9% accuracy respectively. Weight-bearing
inability was the Ottawa ankle rule item that presented the highest reliability,
69.4% sensitivity, 61.6% specificity, 63.1% accuracy, 21.9% positive predictive
value and 93% negative predictive value respectively.
CONCLUSION: The Ottawa ankle rules showed high reliability for deciding when to
take radiographs in foot and/or ankle sprains. Weight-bearing inability was the
most important isolated item to predict fracture presence. Orthopedic surgeon
subjective analysis to predict fracture possibility showed a high specificity
rate, representing a confident method to exclude unnecessary radiographic exams. The original and modified Ottawa Ankle Rules (OARs) were developed as clinical
decision rules for use in emergency departments. However, the OARs have not been
evaluated as an acute clinical evaluation tool.
OBJECTIVE: To evaluate the measures of diagnostic accuracy of the OARs in the
acute setting.
METHODS: The OARs were applied to all appropriate ankle injuries at 2 colleges
(athletics and club sports) and 21 high schools. The outcomes of OARs,
diagnosis, and decision for referral were collected by the athletic trainers
(ATs) at each of the locations. Contingency tables were created for evaluations
completed within 1 h for which radiographs were obtained. From these data the
sensitivity, specificity, positive and negative likelihood ratios, and positive
and negative predictive values were calculated.
RESULTS: The OARs met the criteria for radiographs in 100 of the 124 cases, of
which 38 were actually referred for imaging. Based on radiographic findings in
an acute setting, the OARs (n = 38) had a high sensitivity (.88) and are good
predictors to rule out the presence of a fracture. Low specificity (0.00)
results led to a high number of false positives and low positive predictive
values (.18).
CONCLUSION: When applied during the first hour after injury the OARs
significantly overestimate the need for radiographs. However, a negative finding
rules out the need to obtain radiographs. It appears the AT's decision making
based on the totality of the examination findings is the best filter in
determining referral for radiographs. BACKGROUND: A recent multicenter prospective Canadian study presented
prospective evidence supporting the Low Risk Ankle Rules (LRAR) as a means of
reducing the number of ankle radiographs ordered for children presenting with an
ankle injury while maintaining nearly 100% sensitivity. This is in contrast to a
previous prospective study which showed that this rule yielded only 87%
sensitivity.
OBJECTIVE: It is important to further investigate the LRAR and compare them with
the already validated Ottawa Ankle Rules (OAR) to potentially curb healthcare
costs and decrease unnecessary radiation exposure without compromising
diagnostic accuracy.
METHODS: We conducted a retrospective chart review of 980 qualifying patients
ages 12months to 18years presenting with ankle injury to a commonly staffed 310
bed children's hospital and auxiliary site pediatric emergency department.
RESULTS: There were 28 high-risk fractures identified. The Ottawa Ankle Rules
had a sensitivity of 100% (95% CI 87.7-100), specificity of 33.1% (95% CI
30.1-36.2), and would have reduced the number of ankle radiographs ordered by
32.1%. The Low Risk Ankle Rules had a sensitivity of 85.7% (95% CI 85.7-96),
specificity of 64.9% (95% CI 61.8-68), and would have reduced the number of
ankle radiographs ordered by 63.1%. The latter rule missed 4 high-risk
fractures.
CONCLUSION: The Low Risk Ankle Rules may not be sensitive enough for use in
Pediatric Emergency Departments, while the Ottawa Ankle Rules again demonstrated
100% sensitivity. Further research on ways to implement the Ottawa Ankle Rules
and maximize its ability to decrease wait times, healthcare costs, and improve
patient satisfaction are needed. BACKGROUND: Ankle decision rules are developed to expedite patient care and
reduce the number of radiographs of the ankle and foot. Currently, only three
systematic reviews have been conducted on the accuracy of the Ottawa Ankle and
Foot Rules (OAFR) in adults and children. However, no systematic review has been
performed to determine the most accurate ankle decision rule.
OBJECTIVES: The purpose of this study is to examine which clinical decision
rules are the most accurate for excluding ankle fracture after acute ankle
trauma.
METHODS: A systematic search was conducted in the databases PubMed, CINAHL,
PEDro, ScienceDirect, and EMBASE. The sensitivity, specificity, likelihood
ratios, and diagnostic odds ratio of the included studies were calculated. A
meta-analysis was conducted if the accuracy of a decision rule was available
from at least three different experimental studies.
RESULTS: Eighteen studies satisfied the inclusion criteria. These included six
ankle decision rules, specifically, the Ottawa Ankle Rules, Tuning Fork Test,
Low Risk Ankle Rule, Malleolar and Midfoot Zone Algorithms, and the Bernese
Ankle Rules. Meta-analysis of the Ottawa Ankle Rules (OAR), OAFR, Bernese Ankle
Rules, and the Malleolar Zone Algorithm resulted in a negative likelihood ratio
of 0.12, 0.14, 0.39, and 0.23, respectively.
CONCLUSION: The OAR and OAFR are the most accurate decision rules for excluding
fractures in the event of an acute ankle injury. BACKGROUND: The Ottawa Ankle Rules, Ottawa Knee Rule, and Canadian C-Spine
Rule-together known as The Ottawa Rules-are a set of internationally validated
clinical decision rules developed to decrease unnecessary diagnostic imaging in
the emergency department. In this study, we sought to develop and evaluate the
use of a mobile app version of The Ottawa Rules.
OBJECTIVE: The primary objective of this study was to determine acceptability of
The Ottawa Rules app among emergency department clinicians. The secondary
objective was to evaluate the effect of publicity efforts on uptake of The
Ottawa Rules app.
METHODS: The Ottawa Rules app was developed and publicly released for free on
iOS and Android operating systems in April 2016. Local and national news and
academic media coverage coincided with app release. This study was conducted at
a large tertiary trauma care center in Ottawa, Canada. The study was advertised
through posters and electronically by email. Emergency department clinicians
were approached in person to enroll via in-app consent for a 1-month study
during which time they were encouraged to use the app when evaluating patients
with suspected knee, foot, or neck injuries. A 23-question survey was
administered at the end of the study period via email to determine self-reported
frequency, perceived ease of use of the app, and participant Technology
Readiness Index scores.
RESULTS: A total of 108 emergency department clinicians completed the study
including 42 nurses, 33 residents, 20 attending physicians, and 13 medical
students completing emergency department rotations. The median Technology
Readiness Index for this group was 3.56, indicating a moderate degree of
openness for technological adoption. The majority of survey respondents
indicated favorable receptivity to the app including finding it helpful to
applying the rules (73/108, 67.6%), that they would recommend the app to
colleagues (81/108, 75.0%), and that they would continue using the app (73/108,
67.6%). Feedback from study participants highlighted a desire for access to more
clinical decision rules and a higher degree of interactivity of the app. Between
April 21, 2016, and June 1, 2017, The Ottawa Rules app was downloaded
approximately 4000 times across 89 countries.
CONCLUSIONS: We have found The Ottawa Rules app to be an effective means to
disseminate the Ottawa Ankle Rules, Ottawa Knee Rule, and Canadian C-Spine Rule
among all levels of emergency department clinicians. We have been successful in
monitoring uptake and access of the rules in the app as a result of our
publicity efforts. Mobile technology can be leveraged to improve the
accessibility of clinical decision tools to health professionals. Author information:
(1)Clinical Assistant Professor, Department of Orthopaedic Surgery, Stanford
University School of Medicine, Stanford, CA |
What is CIBERSORT used for? | CIBERSORT is a versatile computational method for characterizing cell composition of complex tissues from their gene expression profiles. | Author information:
(1)1] Institute for Stem Cell Biology and Regenerative Medicine, Stanford
University, Stanford, California, USA. [2] Department of Medicine, Division of
Oncology, Stanford Cancer Institute, Stanford University, Stanford, California,
USA.
(2)1] Department of Medicine, Division of Oncology, Stanford Cancer Institute,
Stanford University, Stanford, California, USA. [2] Center for Cancer Systems
Biology, Stanford University, Stanford, California, USA.
(3)1] Center for Cancer Systems Biology, Stanford University, Stanford,
California, USA. [2] Department of Radiology, Stanford University, Stanford,
California, USA.
(4)Department of Radiation Oncology, Stanford University, Stanford, California,
USA.
(5)Department of Cardiothoracic Surgery, Division of Thoracic Surgery, Stanford
University, Stanford, California, USA.
(6)1] Institute for Stem Cell Biology and Regenerative Medicine, Stanford
University, Stanford, California, USA. [2] Department of Radiation Oncology,
Stanford University, Stanford, California, USA. [3] Stanford Cancer Institute,
Stanford University, Stanford, California, USA.
(7)1] Institute for Stem Cell Biology and Regenerative Medicine, Stanford
University, Stanford, California, USA. [2] Department of Medicine, Division of
Oncology, Stanford Cancer Institute, Stanford University, Stanford, California,
USA. [3] Center for Cancer Systems Biology, Stanford University, Stanford,
California, USA. [4] Stanford Cancer Institute, Stanford University, Stanford,
California, USA. [5] Department of Medicine, Division of Hematology, Stanford
Cancer Institute, Stanford University, Stanford, California, USA. BACKGROUND: Not all breast cancer patients benefit from neoadjuvant or adjuvant
therapy, resulting in considerable undertreatment or overtreatment. New insights
into the role of tumor-infiltrating immune cells suggest that their composition,
as well as their functionality, might serve as a biomarker to enable optimal
patient selection for current systemic therapies and upcoming treatment options
such as immunotherapy.
METHODS: We performed several complementary unbiased in silico analyses on gene
expression profiles of 7270 unrelated tumor samples of nonmetastatic breast
cancer patients with known clinical follow-up. CIBERSORT was used to estimate
the fraction of 22 immune cell types to study their relations with pathological
complete response (pCR), disease-free survival (DFS), and overall survival (OS).
In addition, we used four previously reported immune gene signatures and a CD8+
T-cell exhaustion signature to assess their relationships with breast cancer
outcome. Multivariable binary logistic regression and multivariable Cox
regression were used to assess the association of immune cell-type fractions and
immune signatures with pCR and DFS/OS, respectively.
RESULTS: Increased fraction of regulatory T-cells in human epidermal growth
factor receptor 2 (HER2)-positive tumors was associated with a lower pCR rate
(odds ratio [OR] = 0.15, 95% confidence interval [CI] = 0.03 to 0.69), as well
as shorter DFS (hazard ratio [HR] = 3.13, 95% CI = 1.23 to 7.98) and OS
(HR = 7.69, 95% CI = 3.43 to 17.23). A higher fraction of M0 macrophages in
estrogen receptor (ER)-positive tumors was associated with worse DFS (HR = 1.66,
95% CI = 1.18 to 2.33) and, in ER-positive/HER2-negative tumors, with worse OS
(HR = 1.71, 95% CI = 1.12 to 2.61). Increased fractions of γδ T-cells in all
breast cancer patients related to a higher pCR rate (OR = 1.55, 95% CI = 1.01 to
2.38), prolonged DFS (HR = 0.68, 95% CI = 0.48 to 0.98), and, in HER2-positive
tumors, with prolonged OS (HR = 0.27, 95% CI = 0.10 to 0.73). A higher fraction
of activated mast cells was associated with worse DFS (HR = 5.85, 95% CI = 2.20
to 15.54) and OS (HR = 5.33, 95% CI = 2.04 to 13.91) in HER2-positive tumors.
The composition of relevant immune cell types frequently differed per breast
cancer subtype. Furthermore, a high CD8+ T-cell exhaustion signature score was
associated with shortened DFS in patients with ER-positive tumors regardless of
HER2 status (HR = 1.80, 95% CI = 1.07 to 3.04).
CONCLUSIONS: The main hypothesis generated in our unbiased in silico approach is
that a multitude of immune cells are related to treatment response and outcome
in breast cancer. BACKGROUND: Immune infiltration of breast tumours is associated with clinical
outcome. However, past work has not accounted for the diversity of functionally
distinct cell types that make up the immune response. The aim of this study was
to determine whether differences in the cellular composition of the immune
infiltrate in breast tumours influence survival and treatment response, and
whether these effects differ by molecular subtype.
METHODS AND FINDINGS: We applied an established computational approach
(CIBERSORT) to bulk gene expression profiles of almost 11,000 tumours to infer
the proportions of 22 subsets of immune cells. We investigated associations
between each cell type and survival and response to chemotherapy, modelling
cellular proportions as quartiles. We found that tumours with little or no
immune infiltration were associated with different survival patterns according
to oestrogen receptor (ER) status. In ER-negative disease, tumours lacking
immune infiltration were associated with the poorest prognosis, whereas in
ER-positive disease, they were associated with intermediate prognosis. Of the
cell subsets investigated, T regulatory cells and M0 and M2 macrophages emerged
as the most strongly associated with poor outcome, regardless of ER status.
Among ER-negative tumours, CD8+ T cells (hazard ratio [HR] = 0.89, 95% CI
0.80-0.98; p = 0.02) and activated memory T cells (HR 0.88, 95% CI 0.80-0.97; p
= 0.01) were associated with favourable outcome. T follicular helper cells (odds
ratio [OR] = 1.34, 95% CI 1.14-1.57; p < 0.001) and memory B cells (OR = 1.18,
95% CI 1.0-1.39; p = 0.04) were associated with pathological complete response
to neoadjuvant chemotherapy in ER-negative disease, suggesting a role for
humoral immunity in mediating response to cytotoxic therapy. Unsupervised
clustering analysis using immune cell proportions revealed eight subgroups of
tumours, largely defined by the balance between M0, M1, and M2 macrophages, with
distinct survival patterns by ER status and associations with patient age at
diagnosis. The main limitations of this study are the use of diverse platforms
for measuring gene expression, including some not previously used with
CIBERSORT, and the combined analysis of different forms of follow-up across
studies.
CONCLUSIONS: Large differences in the cellular composition of the immune
infiltrate in breast tumours appear to exist, and these differences are likely
to be important determits of both prognosis and response to treatment. In
particular, macrophages emerge as a possible target for novel therapies.
Detailed analysis of the cellular immune response in tumours has the potential
to enhance clinical prediction and to identify candidates for immunotherapy. BACKGROUND: Intra-sample cellular heterogeneity presents numerous challenges to
the identification of biomarkers in large Epigenome-Wide Association Studies
(EWAS). While a number of reference-based deconvolution algorithms have emerged,
their potential remains underexplored and a comparative evaluation of these
algorithms beyond tissues such as blood is still lacking.
RESULTS: Here we present a novel framework for reference-based inference, which
leverages cell-type specific DNAse Hypersensitive Site (DHS) information from
the NIH Epigenomics Roadmap to construct an improved reference DNA methylation
database. We show that this leads to a marginal but statistically significant
improvement of cell-count estimates in whole blood as well as in mixtures
involving epithelial cell-types. Using this framework we compare a widely used
state-of-the-art reference-based algorithm (called constrained projection) to
two non-constrained approaches including CIBERSORT and a method based on robust
partial correlations. We conclude that the widely-used constrained projection
technique may not always be optimal. Instead, we find that the method based on
robust partial correlations is generally more robust across a range of different
tissue types and for realistic noise levels. We call the combined algorithm
which uses DHS data and robust partial correlations for inference, EpiDISH
(Epigenetic Dissection of Intra-Sample Heterogeneity). Finally, we demonstrate
the added value of EpiDISH in an EWAS of smoking.
CONCLUSIONS: Estimating cell-type fractions and subsequent inference in EWAS may
benefit from the use of non-constrained reference-based cell-type deconvolution
methods. Tumor-infiltrating immune cells are highly relevant for prognosis and
identification of immunotherapy targets in hepatocellular carcinoma (HCC). The
recently developed CIBERSORT method allows immune cell profiling by
deconvolution of gene expression microarray data. By applying CIBERSORT, we
assessed the relative proportions of immune cells in 41 healthy human livers,
305 HCC samples and 82 HCC adjacent tissues. The obtained immune cell profiles
provided enumeration and activation status of 22 immune cell subtypes. Mast
cells were evaluated by immunohistochemistry in ten HCC patients. Activated mast
cells, monocytes and plasma cells were decreased in HCC, while resting mast
cells, total and naïve B cells, CD4+ memory resting and CD8+ T cells were
increased when compared to healthy livers. Previously described S1, S2 and S3
molecular HCC subclasses demonstrated increased M1-polarized macrophages in the
S3 subclass with good prognosis. Strong total immune cell infiltration into HCC
correlated with total B cells, memory B cells, T follicular helper cells and M1
macrophages, whereas weak infiltration was linked to resting NK cells,
neutrophils and resting mast cells. Immunohistochemical analysis of patient
samples confirmed the reduced frequency of mast cells in human HCC tumor tissue
as compared to tumor adjacent tissue. Our data demonstrate that deconvolution of
gene expression data by CIBERSORT provides valuable information about immune
cell composition of HCC patients. BACKGROUND: Elevated tumor-infiltrating lymphocytes (TILs) within the tumor
microenvironment is a known positive prognostic factor in colorectal cancer
(CRC). We hypothesized that since cytotoxic T cells release cytolytic proteins
such as perforin (PRF1) and pro-apoptotic granzymes (GZMA) to attack cancer
cells, a cytolytic activity score (CYT) would be a useful tool to assess
anticancer immunity.
METHODS: Genomic expression data were obtained from 456 patients from The Cancer
Genome Atlas (TCGA). CYT was defined by GZMA and PRF1 expression, and CIBERSORT
was used to evaluate intratumoral immune cell composition.
RESULTS: High CYT was associated with high microsatellite instability (MSI-H),
as well as high levels of activated memory CD4+T cells, gamma-delta T cells, and
M1 macrophages. CYT-high CRC patients had improved overall survival (p = 0.019)
and disease-free survival (p = 0.016) compared with CYT-low CRC patients,
especially in TIL-positive tumors. Multivariate analysis demonstrated that CYT-
high associates with improved survival independently after controlling for age,
lymphovascular invasion, colonic location, microsatellite instability, and TIL
positivity. The levels of immune checkpoint molecules (ICMs)-programmed death-1
(PD-1), programmed death-ligand 1 (PD-L1), cytotoxic T-lymphocyte-associated
protein 4 (CTLA4), lymphocyte-activation gene 3 (LAG3), T cell immunoglobulin
and mucin domain 3 (TIM3), and indoleamine 2,3-dioxygenase 1 (IDO1)-correlated
significantly with CYT (p < 0.0001); with improved survival in CYT-high and
ICM-low patients, and poorer survival in ICM-high patients.
CONCLUSIONS: High CYT within CRC is associated with improved survival, likely
due to increased immunity and cytolytic activity of T cells and M1 macrophages.
High CYT is also associated with high expression of ICMs; thus, further studies
to elucidate the role of CYT as a predictive biomarker of the efficacy of immune
checkpoint blockade are warranted. Interleukin-34 (IL-34) is a ligand for the CSF-1R and has also two additional
receptors, PTPRZ1 and syndecan-1. IL-34 plays a role in innate immunity,
inflammation, and cancer. However, the role of IL-34 in breast cancer is still
ill-defined. We analyzed IL-34 mRNA expression in breast cancer cell lines and
breast cancer patients and applied established computational approaches
(CIBERSORT, ESTIMATE, TIMER, TCIA), to analyze gene expression data from The
Cancer Genome Atlas (TCGA). Expression of IL-34 was associated with a favorable
prognosis in luminal and HER2 but not basal breast cancer patients. Gene
expression of CSF-1 and CSF-1R was strongly associated with myeloid cell
infiltration, while we found no or only weak correlations between IL-34, PTPRZ1,
syndecan-1 and myeloid cells. In vitro experiments showed that tyrosine
phosphorylation of CSF-1R, ERK, and FAK and cell migration are differentially
regulated by IL-34 and CSF-1 in breast cancer cell lines. Collectively, our data
suggest that correlation of IL-34 gene expression with survival is dependent on
the molecular breast cancer subtype. Furthermore, IL-34 is not associated with
myeloid cell infiltration and directly regulates breast cancer cell migration
and signaling. High grade gliomas, including glioblastoma (GB), are devastating maligcies
with very poor prognosis. Over the course of the last decade, there has been a
failure to develop new treatments for GB. Reasons for this failure include the
lack of validation of novel molecular targets, which are often characterized in
animal models and directly transposed to human trials. Here we build on our
previous findings, which describe how the multi-functional co-receptor
Neuropilin-1 (NRP1) signals through glioma associated microglia/macrophages
(GAMS) to promote murine glioma, and investigate NRP1 expression in human
glioma. Clinical and gene expression data were obtained via The Cancer Genome
Atlas (TCGA), and analyzed using R statistical software. Additionally, CIBERSORT
in silico deconvolution was used to determine fractions of immune cell
sub-populations within the gene expression datasets. We find that NRP1
expression is correlated with poor prognosis, glioma grade, and associates with
the mesenchymal GB subtype. In human GB, NRP1 expression is highly correlated
with markers of monocytes/macrophages, as well as genes that contribute to the
pro-tumorigenic phenotype of these cells. |
Are de novo mutations in regulatory elements responsible for neurodevelopmental disorders? | Yes. De novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. It is estimated that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. | We previously estimated that 42% of patients with severe developmental disorders
carry pathogenic de novo mutations in coding sequences. The role of de novo
mutations in regulatory elements affecting genes associated with developmental
disorders, or other genes, has been essentially unexplored. We identified de
novo mutations in three classes of putative regulatory elements in almost 8,000
patients with developmental disorders. Here we show that de novo mutations in
highly evolutionarily conserved fetal brain-active elements are significantly
and specifically enriched in neurodevelopmental disorders. We identified a
significant twofold enrichment of recurrently mutated elements. We estimate
that, genome-wide, 1-3% of patients without a diagnostic coding variant carry
pathogenic de novo mutations in fetal brain-active regulatory elements and that
only 0.15% of all possible mutations within highly conserved fetal brain-active
elements cause neurodevelopmental disorders with a domit mechanism. Our
findings represent a robust estimate of the contribution of de novo mutations in
regulatory elements to this genetically heterogeneous set of disorders, and
emphasize the importance of combining functional and evolutionary evidence to
identify regulatory causes of genetic disorders. |
Which molecule is targeted by Olaratumab? | Olaratumab is a recombinant human monoclonal antibody that binds to platelet-derived growth factor receptor-α (PDGFRα). It is used for treatment of soft tissue sarcoma. | PURPOSE: The platelet-derived growth factor receptor (PDGFR) has an important
role in tumorigenesis and tumor progression. Olaratumab (IMC-3G3) is a fully
human monoclonal antibody that selectively binds human PDGFRα and blocks ligand
binding. This phase I study assessed the safety, maximum tolerated dose (MTD),
recommended phase II dose (RP2D), pharmacokinetics, and preliminary antitumor
activity of olaratumab in patients with advanced solid tumors.
METHODS: Patients were enrolled into five dose-escalating cohorts of 3-6
patients each. Olaratumab was administered intravenously weekly at 4, 8, or 16
mg/kg (cohorts 1-3) or once every other week at 15 or 20 mg/kg (cohorts 4-5),
with 4 weeks/cycle.
RESULTS: Nineteen patients were treated in five cohorts. There were no
dose-limiting toxicities; the MTD was not identified with the doses studied. The
most common olaratumab-related adverse events (AE) were fatigue and infusion
reactions (10.5 % each). With the exception of 1 patient (20 mg/kg) experiencing
two grade 3 drug-related AEs after the dose-limiting toxicity assessment period,
all drug-related AEs were grade 1 or 2. The trough concentrations (C min) for 16
mg/kg weekly and 20 mg/kg biweekly were higher than 155 μg/mL, and the
concentration found to be efficacious in preclinical xenograft models. Twelve
patients (63.2 %) had a best response of stable disease [median duration of 3.9
months (95 % CI 2.3-8.7)].
CONCLUSIONS: Olaratumab was well tolerated and showed preliminary antitumor
activity. RP2Ds are 16 mg/kg weekly and 20 mg/kg biweekly. Phase II studies of
olaratumab as monotherapy and in combination are ongoing in several tumor types. Olaratumab (IMC-3G3) is a fully human IgG1 monoclonal antibody that selectively
binds the external domain of human platelet-derived growth factor receptor-α
with high affinity and blocks ligand binding. This was a single-center,
dose-escalation, phase I trial of olaratumab in Japanese patients with
advanced/refractory solid maligcies. Three to six patients were enrolled into
each of three cohorts: Patients received i.v. olaratumab: 10 mg/kg on days 1 and
8 every 3 weeks (cohort 1); 20 mg/kg every 2 weeks (cohort 2); and 15 mg/kg on
days 1 and 8 every 3 weeks (cohort 3). Doses were escalated from cohort 1
through cohort 3. The primary objective was to establish the safety and
pharmacokinetic profile of olaratumab. Sixteen patients were treated across
three cohorts. There were no dose-limiting toxicities, so the maximum tolerated
dose was not reached. The most common olaratumab-related treatment-emergent
adverse events (TEAEs) were proteinuria (25.0%) and elevated aspartate
transaminase (12.5%). One patient (cohort 2) had two olaratumab-related Grade 3
TEAEs (increased aspartate aminotransferase and tumor hemorrhage); otherwise,
olaratumab-related TEAEs were Grade 1/2. Seven patients (43.8%) had a best
response of stable disease. Based on the pharmacokinetic concentration profile
of olaratumab, the trough concentrations following single and multiple doses at
15 mg/kg on days 1 and 8 every 3 weeks (cohort 3) and multiple doses at 20 mg/kg
every 2 weeks (cohort 2) were above the 155 μg/mL target. Thus, these two doses
could represent an acceptable schedule for future trials in Japanese patients.
Olaratumab had an acceptable safety profile and was well tolerated. BACKGROUND: Treatment with doxorubicin is a present standard of care for
patients with metastatic soft-tissue sarcoma and median overall survival for
those treated is 12-16 months, but few, if any, novel treatments or chemotherapy
combinations have been able to improve these poor outcomes. Olaratumab is a
human antiplatelet-derived growth factor receptor α monoclonal antibody that has
antitumour activity in human sarcoma xenografts. We aimed to assess the efficacy
of olaratumab plus doxorubicin in patients with advanced or metastatic
soft-tissue sarcoma.
METHODS: We did an open-label phase 1b and randomised phase 2 study of
doxorubicin plus olaratumab treatment in patients with unresectable or
metastatic soft-tissue sarcoma at 16 clinical sites in the USA. For both the
phase 1b and phase 2 parts of the study, eligible patients were aged 18 years or
older and had a histologically confirmed diagnosis of locally advanced or
metastatic soft-tissue sarcoma not previously treated with an anthracycline, an
Eastern Cooperative Oncology Group (ECOG) performance status of 0-2, and
available tumour tissue to determine PDGFRα expression by immunohistochemistry.
In the phase 2 part of the study, patients were randomly assigned in a 1:1 ratio
to receive either olaratumab (15 mg/kg) intravenously on day 1 and day 8 plus
doxorubicin (75 mg/m(2)) or doxorubicin alone (75 mg/m(2)) on day 1 of each
21-day cycle for up to eight cycles. Randomisation was dynamic and used the
minimisation randomisation technique. The phase 1b primary endpoint was safety
and the phase 2 primary endpoint was progression-free survival using a two-sided
α level of 0.2 and statistical power of 0.8. This study was registered with
ClinicalTrials.gov, number NCT01185964.
FINDINGS: 15 patients were enrolled and treated with olaratumab plus doxorubicin
in the phase 1b study, and 133 patients were randomised (66 to olaratumab plus
doxorubicin; 67 to doxorubicin alone) in the phase 2 trial, 129 (97%) of whom
received at least one dose of study treatment (64 received olaratumab plus
doxorubicin, 65 received doxorubicin). Median progression-free survival in phase
2 was 6.6 months (95% CI 4.1-8.3) with olaratumab plus doxorubicin and 4.1
months (2.8-5.4) with doxorubicin (stratified hazard ratio [HR] 0.67; 0.44-1.02,
p=0.0615). Median overall survival was 26.5 months (20.9-31.7) with olaratumab
plus doxorubicin and 14.7 months (9.2-17.1) with doxorubicin (stratified HR
0.46, 0.30-0.71, p=0.0003). The objective response rate was 18.2% (9.8-29.6)
with olaratumab plus doxorubicin and 11.9% (5.3-22.2) with doxorubicin
(p=0.3421). Steady state olaratumab serum concentrations were reached during
cycle 3 with mean maximum and trough concentrations ranging from 419 μg/mL
(geometric coefficient of variation in percentage [CV%] 26.2) to 487 μg/mL (CV%
33.0) and from 123 μg/mL (CV% 31.2) to 156 μg/mL (CV% 38.0), respectively.
Adverse events that were more frequent with olaratumab plus doxorubicin versus
doxorubicin alone included neutropenia (37 [58%] vs 23 [35%]), mucositis (34
[53%] vs 23 [35%]), nausea (47 [73%] vs 34 [52%]), vomiting (29 [45%] vs 12
[18%]), and diarrhoea (22 [34%] vs 15 [23%]). Febrile neutropenia of grade 3 or
higher was similar in both groups (olaratumab plus doxorubicin: eight [13%] of
64 patients vs doxorubicin: nine [14%] of 65 patients).
INTERPRETATION: This study of olaratumab with doxorubicin in patients with
advanced soft-tissue sarcoma met its predefined primary endpoint for
progression-free survival and achieved a highly significant improvement of 11.8
months in median overall survival, suggesting a potential shift in the treatment
of soft-tissue sarcoma.
FUNDING: Eli Lilly and Company. Olaratumab (Lartruvo™) is a fully human IgG1 monoclonal antibody targeted
against the human platelet-derived growth factor (PDGF) receptor α (PDGFRα). It
was developed by Eli Lilly and Co. (previously ImClone Systems) after PDGFRα was
identified as a potential therapeutic target in a variety of cancers. Olaratumab
acts by selectively binding PDGFRα, thereby blocking PDGF ligand binding and
inhibiting PDGFRα activation and downstream signalling. In October 2016,
olaratumab received its first global approval, in the USA, for use in
combination with doxorubicin for the treatment of adult patients with soft
tissue sarcoma. The approval was granted by the US FDA under its Accelerated
Approval Program based on the results of the JGDG phase II trial (NCT01185964).
In addition, the EMA granted conditional approval for olaratumab in this
indication in November 2016 following a review under the EMA's Accelerated
Assessment Program. An international, confirmatory phase III trial in patients
with soft tissue sarcoma is ongoing (ANNOUNCE; NCT02451943). Olaratumab has also
been investigated in phase II trials in several other cancers. This article
summarizes the milestones in the development of olaratumab leading to this first
approval, for use in combination with doxorubicin for the treatment of soft
tissue sarcoma in adults. Lartruvo (olaratumab) is a monoclonal antibody against the extracellular domain
of PDGFRA. Olaratumab blocks ligand binding and thereby inhibits activation of
PDGFRA kinase activity. Pre-clinically, this antibody inhibited PDGFRA-dependent
tumor growth. In a randomized Phase II study, adding olaratumab to doxorubicin
chemotherapy significantly improved overall survival, leading to FDA approval. Olaratumab is a humanized IgG1 monoclonal antibody that blocks the
platelet-derived growth factor receptor alpha (PDGFRα). Its antagonistic
behavior inhibits the receptor's tyrosine kinase activity, thereby, turning off
the downstream signaling cascades responsible for soft tissue sarcoma
tumorigenesis. In October 2016, olaratumab received Food and Drug Administration
(FDA) approval for its use in combination with doxorubicin for treatment of
advanced soft tissue sarcoma. Areas covered: This drug profile takes a
comprehensive look at the clinical studies leading to FDA approval of olaratumab
as well as its safety and efficacy as a front-line treatment option for sarcoma
patients. The literature search was primarily conducted using PubMed. Expert
commentary: The combination of olaratumab plus doxorubicin has provided a new
front-line therapeutic option for soft tissue sarcoma patients. An open-label
phase Ib and randomized phase II trial in patients with advanced soft tissue
sarcoma demonstrated that the addition of olaratumab to doxorubicin prolonged
progression-free survival by 2.5 months and overall survival by 11.8 months when
compared to doxorubicin alone. Of importance, this clinically meaningful
increase in overall survival did not come at the expense of a significantly
greater number of toxicities. A phase III confirmatory trial (ClinicalTrials.gov
Identifier NCT02451943) will be completed in 2020. BACKGROUND AND OBJECTIVES: Olaratumab is a recombit human monoclonal antibody
that binds to platelet-derived growth factor receptor-α (PDGFRα). In a
randomized phase II study, olaratumab plus doxorubicin met its predefined
primary endpoint for progression-free survival and achieved a highly significant
improvement in overall survival versus doxorubicin alone in patients with
advanced or metastatic soft tissue sarcoma (STS). In this study, we characterize
the pharmacokinetics (PKs) of olaratumab in a cancer patient population.
METHODS: Olaratumab was tested at 15 or 20 mg/kg in four phase II studies (in
patients with nonsmall cell lung cancer, glioblastoma multiforme, STS, and
gastrointestinal stromal tumors) as a single agent or in combination with
chemotherapy. PK sampling was performed to measure olaratumab serum levels. PK
data were analyzed by nonlinear mixed-effect modeling techniques using NONMEM®.
RESULTS: The PKs of olaratumab were best described by a two-compartment PK model
with linear clearance (CL). Patient body weight was found to have a significant
effect on both CL and central volume of distribution (V 1), whereas tumor size
significantly affected CL. A small subset of patients developed
treatment-emergent anti-drug antibodies (TE-ADAs); however, TE-ADAs did not have
any effect on CL or PK time course of olaratumab. There was no difference in the
PKs of olaratumab between patients who received olaratumab as a single agent or
in combination with chemotherapy.
CONCLUSION: The PKs of olaratumab were best described by a model with linear
disposition. Patient body weight and tumor size were found to be significant
covariates. The PKs of olaratumab were not affected by immunogenicity or
chemotherapeutic agents. Platelet-derived growth factor receptor α (PDGFRα), a tyrosine kinase receptor,
is up-regulated in hepatic stellate cells (HSCs) during chronic liver injury.
HSCs mediate hepatic fibrosis through their activation from a quiescent state
partially in response to profibrotic growth factors. HSC activation entails
enhanced expression of profibrotic genes, increase in proliferation, and
increase in motility, which facilitates migration within the hepatic lobule. We
show colocalization of PDGFRα in murine carbon tetrachloride, bile duct
ligation, and 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine models of chronic
liver injury, and investigate the role of PDGFRα on proliferation, profibrotic
gene expression, and migration in primary human HSCs (HHSteCs) using the
PDGFRα-specific inhibitory monoclonal antibody olaratumab. Although lacking any
effects on HHSteC transdifferentiation assessed by gene expression of ACTA2,
TGFB1, COL1A1, SYP1, and FN1, olaratumab specifically reduced HHSteC
proliferation (AlamarBlue assay) and cell migration (transwell migration
assays). Using phospho-specific antibodies, we show that olaratumab attenuates
PDGFRα activation in response to PDGF-BB, and reduced phosphorylation of
extracellular signal-regulated kinase 1 and 2, Elk-1, p38, Akt, focal adhesion
kinase, mechanistic target of rapamycin, C10 regulator of kinase II, and C10
regulator of kinase-like, suggesting that PDGFRα contributes to mitogenesis and
actin reorganization through diverse downstream effectors. Our findings support
a distinct contribution of PDGFRα signaling to HSC proliferation and migration
and provide evidence that inhibition of PDGFRα signaling could alter the
pathogenesis of hepatic fibrosis. The outcome for patients with unresectable/metastatic soft tissue sarcoma
remains poor with few treatment options. In the first line setting, a number of
randomized trials have shown no difference in overall survival between
combination anthracycline schedules and single agent doxorubicin. A Phase
Ib/randomized Phase II trial of doxorubicin with or without the monoclonal
antibody to PDGFR-α, olaratumab, demonstrated a significant difference in median
overall survival in favor of the olaratumab arm. The results of this trial led
to approval of olaratumab in combination with doxorubicin in adult
anthracycline-naive unresectable soft tissue sarcoma. In this review, we
describe some of the preclinical and early clinical data of olaratumab in
sarcomas, the Phase Ib/II trial and ongoing trials with olaratumab in sarcomas. OBJECTIVE: To review and summarize data on olaratumab, which was approved by the
US Food and Drug Administration (FDA) in October 2016, in combination with
doxorubicin, for the treatment of advanced soft tissue sarcoma.
DATA SOURCES: A literature search using PubMed was conducted using the search
terms olaratumab, IMC-3G3, and advanced soft tissue sarcoma from January 2005 to
June 2017.
STUDY SELECTION AND DATA EXTRACTION: The literature search was confined to human
studies published in English. Trials of olaratumab for advanced soft tissue
sarcomas were prioritized.
DATA SYNTHESIS: Olaratumab is a human antiplatelet-derived growth factor
receptor α monoclonal antibody. Its accelerated FDA approval was based on a
phase II randomized trial of olaratumab plus doxorubicin (n = 66) versus
doxorubicin monotherapy (n = 67) in patients with advanced soft tissue sarcoma.
Olaratumab 15 mg/kg was administered intravenously (IV) on days 1 and 8 in
combination with doxorubicin 75 mg/m2 IV on day 1 every 21 days for a total of 8
cycles compared to doxorubicin 75 mg/m2 IV monotherapy. The response rate was
18.2% with combination therapy versus 11.9% with monotherapy and median
progression-free survival of 6.6 and 4.1 months, respectively. Additionally,
overall survival was increased by 11.8 months in the olaratumab arm (26.5 months
vs 14.7 months). Clinically relevant adverse effects in the olaratumab +
doxorubicin arm included neutropenia (58%), mucositis (53%), nausea (73%),
vomiting (45%), and diarrhea (34%).
CONCLUSION: Olaratumab, in combination with doxorubicin, represents a novel
treatment strategy for advanced soft tissue sarcoma and provides a significant
survival advantage for this rare disease state with limited treatment options. BACKGROUND: In non-small cell lung cancer (NSCLC), platelet-derived growth
factor receptor (PDGFR) mediates angiogenesis, tissue invasion, and tumor
interstitial pressure. Olaratumab (IMC-3G3) is a fully human anti-PDGFRα
monoclonal antibody. This Phase II study assessed safety and efficacy of
olaratumab+paclitaxel/carboplatin (P/C) versus P/C alone for previously
untreated advanced NSCLC.
MATERIALS AND METHODS: Patients received up to six 21-day cycles of P 200mg/m2
and C AUC 6 (day 1)±olaratumab 15mg/kg (days 1 and 8). Primary endpoint was PFS.
Olaratumab was continued in the olaratumab+P/C arm until disease progression.
RESULTS: 131 patients were: 67 with olaratumab+P/C and 64 with P/C; 74% had
nonsquamous NSCLC. Median PFS was similar between olaratumab+P/C and P/C (4.4
months each) (HR 1.29; 95% CI [0.86-1.93]; p=0.21). Median OS was similar
between olaratumab+P/C (11.8 months) and P/C (11.5 months) (HR 1.04; 95% CI
[0.68-1.57]; p=0.87). Both arms had similar toxicity profiles. All evaluable
cases were PDGFR-negative by immunohistochemistry. Tumor stroma PDGFR expression
was evaluable in 23/131 patients, of which 78% were positive.
CONCLUSIONS: The addition of olaratumab to P/C did not result in significant
prolongation of PFS or OS in advanced NSCLC. Olaratumab studies in other patient
populations, including soft tissue sarcoma (NCT02783599), pancreatic cancer
(NCT03086369), and pediatric maligcies (NCT02677116) are underway. Author information:
(1)Medical Oncology Department, Campus Bio-Medico, University of Rome, Rome,
Italy.
(2)Department of Surgical, Oncological and Oral Sciences, Section of Medical
Oncology, Palermo University Hospital, Palermo, Italy.
(3)Division of Medical Oncology, Candiolo Cancer Institue-FPO, IRCCS, Candiolo,
Italy.
(4)Department of Surgical, Oncological and Oral Sciences, Section of Medical
Oncology, Palermo University Hospital, Palermo, Italy. Electronic address:
[email protected].
(5)Candiolo Cancer Institute-IRCCS, Laboratory of Medical Oncology, Experimental
Cell Therapy, Candiolo, Turin, Italy. Soft-tissue sarcoma (STS) is a heterogeneous group of tumors that arise from
mesenchymal tissue. The prognosis of metastatic STS is poor with a life
expectancy of 12-18 months. The mainstay of treatment is chemotherapy with an
anthracycline. The addition of other chemotherapeutic agents to an anthracycline
has been studied with limited success in improving outcomes for STS patients.
Olaratumab is a fully human IgG1 monoclonal antibody that binds to
platelet-derived growth factor receptor α (PDGFR-α) preventing binding of its
ligands and receptor activation. This drug recently received the US Food and
Drug Administration's accelerated approval for the treatment of advanced STS
when combined with doxorubicin. This approval was based upon an improvement in
overall survival of patients receiving the combination of doxorubicin and
olaratumab compared to those receiving doxo-rubicin alone. In this review, we
have analyzed the available literature on the development of olaratumab, its
clinical utility, and its place in therapy. Based on early-phase clinical
trials, olaratumab appears to be a promising agent for the treatment of STS. Recent randomised phase II trial data have indicated that the addition of
olaratumab, a novel monoclonal antibody against platelet-derived growth factor
receptor alpha (PDGFRα), to doxorubicin confers an unprecedented improvement in
overall survival to patients with anthracycline-naïve advanced soft tissue
sarcoma. However, this result was disproportionate with progression-free
survival and response rate, and consequently there are uswered questions
regarding the precise mechanism of action of olaratumab. While preclinical data
show that olaratumab specifically inhibits PDGFRα-mediated oncogenic signalling
with attendant anti-tumour effects, a lack of correlation between
pharmacodynamics markers of PDGFRα inhibition and clinical benefit from
olaratumab suggest other mechanisms beyond modulation of downstream PDGFRα
molecular pathways. Proposed mechanisms of olaratumab activity include
engagement of anti-tumour immune responses and alterations of the tumour stroma,
but these require further evaluation. Meanwhile, the drug-specific contribution
of cytotoxic agents to olaratumab-containing combinations has yet to be
characterised. Ongoing and future preclinical and translational studies, coupled
with the anticipated results of a phase III trial that has completed enrolment,
should provide greater insight into the efficacy and mode of action of
olaratumab in soft tissue sarcomas. Lartruvo® (olaratumab) is a fully human immunoglobulin G subclass 1 (IgG1)
monoclonal antibody that inhibits platelet-derived growth factor receptor alpha
(PDGFRα). The antitumor activity of olaratumab has been tested in vitro and in
vivo, and inhibition of tumor growth has been observed in cancer cell lines,
including glioblastoma and leiomyosarcoma cells. It represents the
first-in-class antibody to be approved by regulatory authorities for the
treatment of advanced soft-tissue sarcomas (STSs) in combination with
doxorubicin, based on the results of the Phase Ib/II trial by Tap et al. The
median progression-free survival (PFS), which was the primary end point of the
study, was improved for patients treated with olaratumab plus doxorubicin
compared to those treated with doxorubicin monotherapy (6.6 vs 4.1 months,
respectively; HR 0.672, 95% CI 0.442-1.021, p=0.0615). Moreover, final analysis
of overall survival (OS) showed a median OS of 26.5 months with olaratumab plus
doxorubicin vs 14.7 months with doxorubicin, with a gain of 11.8 months (HR
0.46, 95% CI 0.30-0.71, p=0.0003). In October 2016, olaratumab was admitted in
the Accelerated Approval Program by the US Food and Drug Administration (FDA)
for use in combination with doxorubicin for the treatment of adult patients with
STSs. In November 2016, the European Medicines Agency (EMA) granted conditional
approval for olaratumab in the same indication under its Accelerated Assessment
Program. A double-blind, placebo-controlled, randomized Phase III study
(ANNOUNCE trial, NCT02451943) is being performed in order to confirm the
survival advantage of olaratumab and to provide definitive drug confirmation by
regulators. The study is ongoing, but enrollment is closed. The purpose of this
review was to evaluate the rationale of olaratumab in the treatment of advanced
STSs and its emerging role in clinical practice. Olaratumab, a monoclonal antibody targeting human platelet-derived growth factor
receptor α, plus doxorubicin significantly improved overall survival in patients
with advanced soft-tissue sarcoma (STS) in a prior phase 1b/2 randomized trial.
Subsequent exposure-response analysis suggested that higher olaratumab exposures
earlier might improve outcomes in patients at risk of early disease progression.
This phase 1 study (3 treatment cohorts; minimum 6 patients each) investigated
the safety, pharmacokinetics and antitumor activity of olaratumab plus
doxorubicin in Japanese patients with STS. Patients received olaratumab 15 mg/kg
on Days 1 and 8 during each 21-day cycle until disease progression. Patients in
Cohort 3 received a 20 mg/kg loading dose of olaratumab in Cycle 1. Doxorubicin
was administered for up to 6 cycles. Patients in Cohort 1 received doxorubicin
25 mg/m2 on Days 1, 2 and 3. Patients in Cohorts 2 and 3 received doxorubicin
75 mg/m2 on Day 1. One patient in Cohort 2 experienced a dose-limiting toxicity
of Grade 3 febrile neutropenia. Most treatment-emergent adverse events were of
mild and moderate severity, and were known doxorubicin toxicities. Olaratumab
serum concentrations in Cohort 3 reached a steady-state exceeding the target
level in Cycle 1. Partial response was confirmed in 4 patients (2 each in
Cohorts 2 and 3). Olaratumab plus doxorubicin had an acceptable safety profile
in patients with STS. A loading dose of olaratumab 20 mg/kg was effective for
achieving minimum serum concentrations above the target trough level in Cycle 1. |
What is PANDAS disease? | PANDAS stands for (pediatric autoimmune neuropsychiatric disorders associated with streptococcal infection) and has been suggested to be a result of a disordered immune response following an infection causing neuropsychiatric symptoms. | Streptococcal infection in children is usually benign and self-limited. In a
small percentage of children, prominent neurologic and/or psychiatric sequelae
can occur. Sydenham chorea is the best defined and best recognized. PANDAS
(pediatric autoimmune neuropsychiatric disorders associated with streptococcal
infection) is a well-defined syndrome in which tics (motor and/or vocal) and/or
obsessive-compulsive disorder consistently exacerbate in temporal correlation to
a group A beta-hemolytic streptococcal infection. PANDAS constitutes a subset of
children with tics, Tourette syndrome, and obsessive-compulsive disorder. In
addition to strictly defined PANDAS, we and others have recognized several
PANDAS variants, including adult-onset variant, a dystonic variant, a myoclonic
variant, and a "chronic" PANDAS variant. The nosology and classification of
these entities are rapidly evolving. The recognition that some pediatric
neurobehavioral syndromes have infectious and/or immunologic triggers points to
important new avenues of disease treatment. In this review, we summarize this
complex and rapidly evolving area of clinical research. PANDAS Syndrome (Paediatric Autoimmune Neuropsychiatric Disorders Associated
with Streptococcus) is a rare disease described in 1998. In this disease, there
is a relationship between group A beta haemolytic streptococcal tonsil
infections and the exacerbation of neuropsychiatric disorders. A case report of
a 9-year-old child with PANDAS syndrome is presented. This child has had no
further symptoms after tonsillectomy. The understanding about PANDAS syndrome
and tonsillectomy is reviewed. OBJECTIVES: A commonality across a number of pediatric neuropsychiatric
disorders is a higher than typical rate of familial - and especially maternal -
autoimmune disease. Of recent interest, a subtype of obsessive-compulsive
disorder (OCD) and tic disorders known collectively as Pediatric Autoimmune
Neuropsychiatric Disorders Associated with Streptococcus (PANDAS) is believed to
be secondary to central nervous system (CNS) autoimmunity that occurs in
relation to group A streptococcal infection. Thus, we hypothesized that a sample
of children with OCD and/or tics would have an increased maternal risk for an
autoimmune response relative to population norms. We also expected maternal
prevalence of various autoimmune diseases to be higher among those participants
that met the putative criteria for PANDAS.
METHODS: We examined, via structured interview, the medical history of the
biological mothers of 107 children with OCD and/or tics.
RESULTS: Autoimmune disorders were reported in 17.8% of study mothers, which is
significantly greater than the general prevalence among women in the United
States (approximately 5%). Further, study mothers were more likely to report
having an autoimmune disease if their children were considered "likely PANDAS"
cases versus "unlikely PANDAS" cases.
CONCLUSIONS: The results offer preliminary support for hypothesized links
between maternal autoimmune disease and both OCD/tics and PANDAS in youth.
Further research is necessary to clarify these general associations; links to
specific autoimmune disease; and relevance of autoimmune disease in other family
members (e.g., fathers). OBJECTIVES: Pediatric Autoimmune Neuropsychiatric Disorders Associated with
Streptococcal Infections (PANDAS) is a newly defined disease in neuropsychiatry
and occurs with an autoimmune mechanism after Group A Beta Hemolytic
Streptococcus (GABHS) infection. Tumor necrosis factor (TNF), encoded by TNF-α
gene has an important role in the apoptotic mechanisms of autoimmune diseases.
Recently, TNF-α polymorphisms and autoimmune/psychiatric disorders have been
reported to be related. In this regard, we focused on to investigate a possible
relation between the TNF-α gene promoter region-308 G/A and - 850 C/T
polymorphisms and PANDAS.
MATERIALS AND METHODS: In this study, ages of PANDAS patient and control groups
were ranging from 4 years to 12-year-old. Patient group includes childhood onset
PANDAS patients (n = 42) and control group includes healthy children (n = 58).
Diagnoses have been carried out according to Diagnostic and Statistical Manual
of Mental Disorder (DSM-IV) criteria with Affective Disorders and
Schizophrenia-Present and Lifetime (KSAD-S-PL) and Children Yale-Brown Obsessive
Compulsive Scale Moreover, PANDAS criteria established by the American National
Psychiatry Institute have been employed for diagnoses. For identifying
polymorphisms; Polymerase Chain Reaction, Restriction Fragment Length
Polymorphism and Polyacrylamid Gel Electrophoresis were used.
RESULTS AND DISCUSSION: For -308 polymorphism, 37 of 42 PANDAS patients' results
and for -850 C/T polymorphism, 38 of 42 PANDAS patients' results were obtained.
According to our statistical analysis there is a positive relationship between
PANDAS patients for -308 G/A polymorphism but not for -850 C/T polymorphism.
There is no positive relationship between -308 G/A polymorphism and
antistrep-tolysin O (ASO) titers and no relationship between -850 C/T
polymorphism and ASO titers. We found, however, positive relationship between
genders of patients (boys) and the disease. According to our results, we propose
that the AA polymorphism of -308 G/A polymorphism can be used as a molecular
indicator for PANDAS. OBJECTIVES: 'Pediatric Autoimmune Neuropsychiatric Disorders Associated with
Streptococcal Infections' (PANDAS) identified a unique subgroup of patients with
abrupt onset of obsessive compulsive disorder (OCD) symptoms clinically related
to Streptococcus infection and accompanied by neuropsychological and motor
symptoms. After almost 20 years, PANDAS has not been accepted as distinct
disorder and new criteria for paediatric acute-onset neuropsychiatric syndrome
(PANS) have been replaced it, highlighting the fact that several agents rather
than only Streptococcus might be involved.
METHODS: Extensive review of the PANDAS/PANS literature was performed on PubMed.
RESULTS: Although antibiotics have been reported to be effective for acute and
prophylactic phases in several uncontrolled studies and non-steroidal
anti-inflammatory drugs (NSAID) are used during exacerbations, clinical
multicenter trials are still missing. Selective serotonin reuptake inhibitors
(SSRIs) and cognitive behavioural therapy (CBT) are still the first line of
recommendation for acute onset OCD spectrum. Immunological therapies should be
restricted to a few cases.
CONCLUSIONS: While PANDAS has found no confirmation as a distinct syndrome, and
it is not presented in DSM-5, patients with acute onset OCD spectrum,
neurocognitive and motor symptoms should be evaluated for inflammatory,
infective, immunological and metabolic abnormalities with a comprehensive
diagnostic algorithm. BACKGROUND: Pediatric autoimmune neuropsychiatric disorders associated with
streptococcal infections (PANDAS) are immune-mediated diseases characterized by
obsessive-compulsive symptoms and/or tics triggered by group A Streptococcus
infections. Despite the well-known action of 25-hydroxyvitamin D [25(OH)D] on
different conditions driven by systemic inflammation, there are no data about
the 25(OH)D status in patients with PANDAS.
AIMS: To evaluate plasma 25(OH)D levels in a large cohort of children and
adolescents with PANDAS and comparing the results with healthy controls.
METHODS: We have evaluated plasma 25(OH)D levels in 179 Italian patients with
PANDAS (49 females, 130 males, mean age at diagnosis: 101.4 ± 30.1 months) and
in an age-, gender-, and body mass index-matched control group of 224 healthy
subjects.
RESULTS: Patients with PANDAS have shown more frequently reduced 25(OH)D levels
(<30 ng/mL) in comparison with controls (94.6% vs. 82.5%, p = 0.0007). Patients
with PANDAS had also lower levels of 25(OH)D than controls (20.4 ± 6.9 ng/mL vs.
24.8 ± 7.3 ng/mL, p < 0.0001). This difference was observed during both winter
(13.7 ± 3.25 ng/mL vs. 21.4 ± 5.9 ng/mL, p < 0.0001) and summer
(21.8 ± 6.5 ng/mL vs. 32.5 ± 8.7 ng/mL, p < 0.0001). Notably, serum 25(OH)D
levels correlated with both number of streptococcal (strep) infections before
diagnosis of PANDAS (p < 0.005) and with infection recurrence (p < 0.005).
CONCLUSIONS: PANDAS patients have reduced 25(OH)D levels, which appear related
to streptococcal infections and the probability of recurrence. Further long-term
studies with higher number of patients are needed to investigate and confirm
this relationship. Little is known about the natural history of children with pediatric autoimmune
neuropsychiatric disorder associated with streptococcal infections (PANDAS).
This study prospectively followed 33 children with PANDAS for up to 4.8 years
(mean 3.3 ± 0.7 years) after enrollment in a 24-week randomized, double-blind,
placebo-controlled trial of intravenous immunoglobulin (IVIG) (N = 35). Fourteen
of eighteen children randomized to placebo received open label IVIG 6 weeks
after the blinded infusion, so follow-up results reported below largely reflect
outcomes in a population of children who received at least one dose of IVIG.
Telephone interviews with the parents of participants found that at the time of
phone follow-up, 29 (88%) were not experiencing clinically significant
obsessive-compulsive symptoms. During the interim period (6-57 months after
entering the clinical trial), 24 (72%) had experienced at least one exacerbation
of PANDAS symptoms, with a median of one exacerbation per child (range 1-12;
interquartile range 0-3). A variety of treatment modalities, including
antibiotics, IVIG, psychiatric medications, cognitive behavioral therapy, and
others, were used to treat these exacerbations, and were often used in
combination. The outcomes of this cohort are better than those previously
reported for childhood-onset OCD, which may support conceptualization of PANDAS
as a subacute illness similar to Sydenham chorea. However, some children
developed a chronic course of illness, highlighting the need for research that
identifies specific symptoms or biomarkers that can be used to predict the
longitudinal course of symptoms in PANDAS. BACKGROUND: The pediatric autoimmune neuropsychiatric disorders associated with
streptococcal infection (PANDAS) hypothesis suggests an association between
group A beta-hemolytic streptococcus (GABHS) infections and subsequent onset or
exacerbation of neuropsychiatric symptoms, such as obsessive-compulsive disorder
or tic disorders.
METHODS: We performed a systematic review and meta-analysis including
longitudinal, prospective studies on exacerbations of neuropsychiatric symptoms
associated with GABHS infections in children with PANDAS. We searched PubMed and
EMBASE through August 14, 2017. Two independent reviewers extracted data and we
used random-effects analysis to calculate rate ratios (RR).
RESULTS: Three studies were included with a total of 82 PANDAS cases and 127
control children with obsessive-compulsive disorder or chronic tic disorder.
PANDAS cases had a nonsignificantly increased RR of 2.33 [95% confidence
interval [CI]: 0.63-8.70, P = 0.21, I = 28.3%] for exacerbations of
neuropsychiatric symptoms in temporal proximity to a GABHS infection and no
increased risk of GABHS infections (RR = 0.99, 95% CI: 0.56-1.73, P = 0.97, I =
45%) compared with the control children. However, PANDAS cases had an increased
risk of neuropsychiatric exacerbations in general with a RR of 1.54 (95% CI:
1.12-2.11, P = 0.008, I = 0%) compared with the control children. The studies
had methodologic heterogeneity, high risk of selection bias and differed
concerning case definition and infection measures.
CONCLUSIONS: Our findings did not show significant evidence concerning higher
rates of temporally associated GABHS infections and exacerbations of
neuropsychiatric symptoms in children with PANDAS. The included studies were
small and limited by low GABHS rates and exacerbations. Future studies with
large population sizes and routine evaluations are needed to thoroughly examine
the PANDAS hypothesis. |
Are phagosomal proteins ubiquitinated? | Yes,
Phagosomal proteins are ubiquitylated, and ubiquitylation was found to be required for formation of acidic multivesicular structures. | Protein ubiquitination is critical for regulation of numerous eukaryotic
cellular processes such as protein homeostasis, cell cycle progression, immune
response, DNA repair, and vesicular trafficking. Ubiquitination often leads to
the alteration of protein stability, subcellular localization, or interaction
with other proteins. Given the importance of ubiquitination in the regulation of
host immunity, it is not surprising that many infectious agents have evolved
strategies to interfere with the ubiquitination network with sophisticated
mechanisms such as functional mimicry. The facultative intracellular pathogen
Legionella pneumophila is the causative agent of Legionnaires' disease. L.
pneumophila is phagocytosed by macrophages and is able to replicate within a
niche called Legionella-containing vacuole (LCV). The biogenesis of LCV is
dependent upon the Dot/Icm type IV secretion system which delivers more than 330
effector proteins into host cytosol. The optimal intracellular replication of L.
pneumophila requires the host ubiquitin-proteasome system. Furthermore,
membranes of the bacterial phagosome are enriched with ubiquitinated proteins in
a way that requires its Dot/Icm type IV secretion system, suggesting the
involvement of effectors in the manipulation of the host ubiquitination
machinery. Here we summarize recent advances in our understanding of mechanisms
exploited by L. pneumophila effector proteins to hijack the host ubiquitination
pathway. |
A herd immunity of what percentage of the population is required to prevent sporadic outbreaks? | A herd immunity of 95% of the population is required to prevent sporadic outbreaks. | INTRODUCTION: The measles virus is a major human pathogen responsible for
approximately 150,000 deaths annually. The disease is vaccine preventable and
eradication of the virus is considered feasible, in principle. However, a herd
immunity exceeding 95% is required to prevent sporadic viral outbreaks in a
population. Declining disease prevalence, combined with public anxiety over the
vaccination's safety, has led to increased vaccine refusal, especially in
Europe. This has led to the resurgence of measles in some areas.
AREAS COVERED: This article discusses whether synergizing effective measles
therapeutics with the measles vaccination could contribute to finally
eradicating measles. The authors identify key elements in a desirable drug
profile and review current disease management strategies and the state of
experimental inhibitor candidates. The authors also evaluate the risk associated
with viral escape from inhibition, and consider the potential of measles
therapeutics in the management of persistent central nervous system (CNS) viral
infection. Finally, the authors contemplate the possible impact of therapeutics
in controlling the threat imposed by closely related zoonotic pathogens of the
same genus as measles.
EXPERT OPINION: Efficacious therapeutics used for post-exposure prophylaxis of
high-risk social contacts of confirmed index cases may aid measles eradication
by closing herd immunity gaps; this is due to vaccine refusal or failure in
populations with overall good vaccination coverage. The envisioned primarily
prophylactic application of measles therapeutics to a predomitly pediatric
and/or adolescent population, dictates the drug profile. It also has to be safe
and efficacious, orally available, shelf-stable at ambient temperature and
amenable to cost-effective manufacturing. |
Does tremelimumab improve survival of mesothelioma patients? | No. Tremelimumab did not significantly prolong overall survival compared with placebo in patients with previously treated malignant mesothelioma. | Immunotherapy is an emerging therapeutic strategy with a promising clinical
outcome in some solid tumors, particularly metastatic melanoma. One approach to
immunotherapy is immune checkpoint inhibitors, such as blockage of CTLA-4 and
PD-1/PD-L1. This special report aims to describe the state of clinical trials of
tremelimumab in patients with unresectable maligt mesothelioma (MM) in
particular with regard to the clinical efficacy, safety and tolerability.
Criticism and perspective of this treatment are also discussed. Biological and
clinical considerations rule out the use of tremelimumab as single agent for MM
and, more generally, the use of immune checkpoint inhibitors for MM is still
largely questionable and not supported by evidences. BACKGROUND: New therapeutic strategies for maligt mesothelioma are urgently
needed. In the DETERMINE study, we investigated the effects of the
cytotoxic-T-lymphocyte-associated antigen 4 (CTLA-4) monoclonal antibody
tremelimumab in patients with previously treated advanced maligt
mesothelioma.
METHODS: DETERMINE was a double-blind, placebo-controlled, phase 2b trial done
at 105 study centres across 19 countries in patients with unresectable pleural
or peritoneal maligt mesothelioma who had progressed after one or two
previous systemic treatments for advanced disease. Eligible patients were aged
18 years or older with Eastern Cooperative Oncology Group performance status of
0 or 1 and measurable disease as defined in the modified Response Evaluation
Criteria In Solid Tumors (RECIST) version 1.0 for pleural mesothelioma or RECIST
version 1.1 for peritoneal mesothelioma. Patients were randomly assigned (2:1)
in blocks of three, stratified by European Organisation for Research and
Treatment of Cancer status (low risk vs high risk), line of therapy (second line
vs third line), and anatomic site (pleural vs peritoneal), by use of an
interactive voice or web system, to receive intravenous tremelimumab (10 mg/kg)
or placebo every 4 weeks for 7 doses and every 12 weeks thereafter until a
treatment discontinuation criterion was met. The primary endpoint was overall
survival in the intention-to-treat population. Safety was assessed in all
patients who received at least one dose of study drug. The trial is ongoing but
no longer recruiting participants, and is registered with ClinicalTrials.gov,
number NCT01843374.
FINDINGS: Between May 17, 2013, and Dec 4, 2014, 571 patients were randomly
assigned to receive tremelimumab (n=382) or placebo (n=189), of whom 569
patients received treatment (two patients in the tremelimumab group were
excluded from the safety population because they did not receive treatment). At
the data cutoff date (Jan 24, 2016), 307 (80%) of 382 patients had died in the
tremelimumab group and 154 (81%) of 189 patients had died in the placebo group.
Median overall survival in the intention-to-treat population did not differ
between the treatment groups: 7·7 months (95% CI 6·8-8·9) in the tremelimumab
group and 7·3 months (5·9-8·7) in the placebo group (hazard ratio 0·92 [95% CI
0·76-1·12], p=0·41). Treatment-emergent adverse events of grade 3 or worse
occurred in 246 (65%) of 380 patients in the tremelimumab group and 91 (48%) of
189 patients in the placebo group; the most common were dyspnoea (34 [9%]
patients in the tremelimumab group vs 27 [14%] patients in the placebo group),
diarrhoea (58 [15%] vs one [<1%]), and colitis (26 [7%] vs none). The most
common serious adverse events were diarrhoea (69 [18%] patients in the
tremelimumab group vs one [<1%] patient in the placebo group), dyspnoea (29 [8%]
vs 24 [13%]), and colitis (24 [6%] vs none). Treatment-emergent events leading
to death occurred in 36 (9%) of 380 patients in the tremelimumab group and 12
(6%) of 189 in the placebo group; those leading to the death of more than one
patient were mesothelioma (three [1%] patients in the tremelimumab group vs two
[1%] in the placebo group), dyspnoea (three [1%] vs two [1%]); respiratory
failure (one [<1%] vs three [2%]), myocardial infarction (three [1%] vs none),
lung infection (three [1%] patients vs none), cardiac failure (one [<1%] vs one
[<1%]), and colitis (two [<1%] vs none). Treatment-related adverse events
leading to death occurred in five (1%) patients in the tremelimumab group and
none in the placebo group. The causes of death were lung infection in one
patient, intestinal perforation and small intestinal obstruction in one patient;
colitis in two patients, and neuritis and skin ulcer in one patient.
INTERPRETATION: Tremelimumab did not significantly prolong overall survival
compared with placebo in patients with previously treated maligt
mesothelioma. The safety profile of tremelimumab was consistent with the known
safety profile of CTLA-4 inhibitors. Investigations into whether immunotherapy
combination regimens can provide greater efficacy than monotherapies in
maligt mesothelioma are ongoing.
FUNDING: AstraZeneca. BACKGROUND: Tremelimumab, an anti-CTLA4 monoclonal antibody, initially showed
good activity when used alone in patients with mesothelioma, but did not improve
the overall survival of patients who failed on first-line or second-line
chemotherapy compared with placebo in the DETERMINE study. We aimed to
investigate the efficacy and safety of first-line or second-line tremelimumab
combined with durvalumab, an anti-PD-L1 monoclonal antibody, in patients with
maligt mesothelioma.
METHODS: In this open-label, non-randomised, phase 2 trial, patients with
unresectable pleural or peritoneal mesothelioma received intravenous
tremelimumab (1 mg/kg bodyweight) and durvalumab (20 mg/kg bodyweight) every 4
weeks for four doses, followed by maintece intravenous durvalumab at the same
dose and schedule for nine doses. The primary endpoint was the proportion of
patients with an immune-related objective response according to the
immune-related modified Response Evaluation Criteria in Solid Tumors (RECIST;
for pleural mesothelioma) or immune-related RECIST version 1.1 (for peritoneal
mesothelioma). The primary analysis was done by intention to treat, whereas the
safety analysis included patients who received at least one dose of study drug.
This trial is registered with the European Clinical Trials Database, number
2015-001995-23, and ClinicalTrials.gov, number NCT02588131, and is ongoing but
no longer recruiting patients.
FINDINGS: From Oct 30, 2015, to Oct 12, 2016, 40 patients with mesothelioma were
enrolled and received at least one dose each of tremelimumab and durvalumab.
Patients were followed-up for a median of 19·2 months (IQR 13·8-20·5). 11 (28%)
of 40 patients had an immune-related objective response (all partial responses;
confirmed in ten patients), with a median response duration of 16·1 months (IQR
11·5-20·5). 26 (65%) patients had immune-related disease control and 25 (63%)
had disease control. Median immune-related progression-free survival was 8·0
months (95% CI 6·7-9·3), median progression-free survival was 5·7 months
(1·7-9·7), and median overall survival was 16·6 months (13·1-20·1). Baseline
tumour PD-L1 expression did not correlate with the proportion of patients who
had an immune-related objective response or immune-related disease control, with
immune-related progression-free survival, or with overall survival. 30 (75%)
patients experienced treatment-related adverse events of any grade, of whom
seven (18%) had grade 3-4 treatment-related adverse events. Treatment-related
toxicity was generally manageable and reversible with protocol guidelines.
INTERPRETATION: The combination of tremelimumab and durvalumab appeared active,
with a good safety profile in patients with mesothelioma, warranting further
exploration.
FUNDING: Network Italiano per la Bioterapia dei Tumori Foundation, Associazione
Italiana per la Ricerca sul Cancro, AstraZeneca, and Istituto Toscano Tumori. |
Can enasidenib be used for the treatment of acute myeloid leukemia? | Yes, enasidenib has been approved for the treatment of adults with relapsed and refracctory acture myelogenous leukemia with an IDH2 mutation. | In August 2017, the United States Federal Drug Administration (FDA) approved
enasidenib (Idhifa, Celgene/Agios) for adults with relapsed and refractory acute
myelogenous leukemia (AML) with an IDH2 mutation. Enasidenib targets cells with
mutant copies of isocitrate dehydrogenase-2 (IDH2), inhibiting the
oncometabolite 2-hydroxyglutarte (2-HG) formed by the mutant IDH2. Areas
covered: We review the studies leading to enasidenib's approval, as well as
common side effects and safety issues experienced during the clinical trials.
There is a focus on the diagnosis and treatment of these side effects including
differentiation syndrome. Expert commentary: We are experiencing a revolution in
the understanding of the mechanism of AML. A majority of the effort has been
concentrated on targeting gene mutations or pathway activations with precision
therapeutics. Enasidenib is beneficial in a patient population that previously
had limited treatment options. However, given the fact that enasidenib is a
highly specific inhibitor of an early stable mutation, it is questionable
whether a strategy of targeting a single mutation or pathway in relapsed AML
will allow for better than the 20% complete remission (CR) rate observed with
this therapy. The proper role for single mutation targeting in AML needs to be
carefully considered. |
What membrane proteins constitute TAM family of receptor tyrosine kinases (RTKs)? | Tyro3, Axl, and Mer are integral membrane proteins that constitute TAM family of receptor tyrosine kinases (RTKs). | Gas6 (growth arrest-specific gene 6) is the last addition to the family of
plasma vitamin K-dependent proteins. Gas6 was cloned and characterized in 1993
and found to be similar to the plasma anticoagulant protein S. Soon after it was
recognized as a growth factor-like molecule, as it interacted with receptor
tyrosine kinases (RTKs) of the TAM family; Tyro3, Axl, and MerTK. Since then,
the role of Gas6, protein S, and the TAM receptors has been found to be
important in inflammation, hemostasis, and cancer, making this system an
interesting target in biomedicine. Gas6 employs a unique mechanism of action,
interacting through its vitamin K-dependent Gla module with
phosphatidylserine-containing membranes and through its carboxy-terminal LG
domains with the TAM membrane receptors. The fact that these proteins are
affected by anti-vitamin K therapy is discussed in detail. Tyro-3, Axl, and Mer constitute the TAM family of receptor tyrosine kinases
(RTKs) characterized by a conserved sequence within the kinase domain and
adhesion molecule-like extracellular domains. This small family of RTKs
regulates an intriguing mix of processes, including cell proliferation/survival,
cell adhesion and migration, blood clot stabilization, and regulation of
inflammatory cytokine release. Genetic or experimental alteration of TAM
receptor function can contribute to a number of disease states, including
coagulopathy, autoimmune disease, retinitis pigmentosa, and cancer. In this
chapter, we first provide a comprehensive review of the structure, regulation,
biologic functions, and downstream signaling pathways of these receptors. In
addition, we discuss recent evidence which suggests a role for TAM receptors in
oncogenic mechanisms as family members are overexpressed in a spectrum of human
cancers and have prognostic significance in some. Possible strategies for
targeted inhibition of the TAM family in the treatment of human cancer are
described. Further research will be necessary to evaluate the full clinical
implications of TAM family expression and activation in cancer. The TAM subfamily of Receptor Tyrosine Kinases (RTKs) contains three human
proteins of therapeutical interest, Axl, Mer, and Tyro3. Our goal was to design
a type II inhibitor specific for this family, i.e. able to interact with the
allosteric pocket and with the hinge region of the kinase. We report the
synthesis of several series of purine analogues of BMS-777607. The structural
diversity of the designed inhibitors was expected to modify the interactions
formed in the binding site and consequently to modulate their selectivity
profiles. The most potent inhibitor 6g exhibits Kds of 39, 42, 65 and 200 nM
against Axl, Mer, Met and Tyro3 respectively. Analysis of the affinity of 6g for
active and inactive forms of Abl1, an RTK protein that does not belong to the
TAM subfamily, together with the binding modes of 6g predicted by docking
studies, indicates that 6g displays some selectivity for the TAM family and may
act as a type II inhibitor. Receptor tyrosine kinases (RTKs) are cell surface proteins that tightly regulate
a variety of downstream intra-cellular processes; ligand-receptor interactions
result in cascades of signaling events leading to growth, proliferation,
differentiation and migration. There are 58 described RTKs, which are further
categorized into 20 different RTK families. When dysregulated or overexpressed,
these RTKs are implicated in disordered growth, development, and oncogenesis.
The TAM family of RTKs, consisting of Tyro3, Axl, and MerTK, is prominently
expressed during the development and function of the central nervous system
(CNS). Aberrant expression and dysregulated activation of TAM family members has
been demonstrated in a variety of CNS-related disorders and diseases, including
the most common but least treatable brain cancer in children and adults:
glioblastoma multiforme. The TYRO3, AXL (also known as UFO) and MERTK (TAM) family of receptor tyrosine
kinases (RTKs) are aberrantly expressed in multiple haematological and
epithelial maligcies. Rather than functioning as oncogenic drivers, their
induction in tumour cells predominately promotes survival, chemoresistance and
motility. The unique mode of maximal activation of this RTK family requires an
extracellular lipid–protein complex. For example, the protein ligand, growth
arrest-specific protein 6 (GAS6), binds to phosphatidylserine (PtdSer) that is
externalized on apoptotic cell membranes, which activates MERTK on macrophages.
This triggers engulfment of apoptotic material and subsequent anti-inflammatory
macrophage polarization. In tumours, autocrine and paracrine ligands and
apoptotic cells are abundant, which provide a survival signal to the tumour cell
and favour an anti-inflammatory, immunosuppressive microenvironment. Thus, TAM
kinase inhibition could stimulate antitumour immunity, reduce tumour cell
survival, enhance chemosensitivity and diminish metastatic potential. Nature repeatedly repurposes, in that molecules that serve as metabolites,
energy depots, or polymer subunits are at the same time used to deliver signals
within and between cells. The preeminent example of this repurposing is ATP,
which functions as a building block for nucleic acids, an energy source for
enzymatic reactions, a phosphate donor to regulate intracellular signaling, and
a neurotransmitter to control the activity of neurons. A series of recent
studies now consolidates the view that phosphatidylserine (PtdSer), a common
phospholipid constituent of membrane bilayers, is similarly repurposed for use
as a signal between cells and that the ligands and receptors of the
Tyro3/Axl/Mer (TAM) family of receptor tyrosine kinases (RTKs) are prominent
transducers of this signal. Receptor tyrosine kinases (RTKs) have been demonstrated to signal via regulated
intramembrane proteolysis, in which ectodomain shedding and subsequent
intramembrane cleavage by gamma-secretase leads to release of a soluble
intracellular receptor fragment with functional activity. For most RTKs,
however, it is unknown whether they can exploit this new signaling mechanism.
Here we used a system-wide screen to address the frequency of susceptibility to
gamma-secretase cleavage among human RTKs. The screen covering 45 of the 55
human RTKs identified 12 new as well as all nine previously published
gamma-secretase substrates. We biochemically validated the screen by
demonstrating that the release of a soluble intracellular fragment from
endogenous AXL was dependent on the sheddase disintegrin and metalloprotease 10
(ADAM10) and the gamma-secretase component presenilin-1. Functional analysis of
the cleavable RTKs indicated that proliferation promoted by overexpression of
the TAM family members AXL or TYRO3 depends on gamma-secretase cleavage. Taken
together, these data indicate that gamma-secretase-mediated cleavage provides an
additional signaling mechanism for numerous human RTKs. |
What are the effects of the deletion of all three Pcdh clusters (tricluster deletion) in mice? | Multicluster Pcdh diversity is required for mouse olfactory neural circuit assembly. The vertebrate clustered protocadherin (Pcdh) cell surface proteins are encoded by three closely linked gene clusters (Pcdhα, Pcdhβ, and Pcdhγ). Although deletion of individual Pcdh clusters had subtle phenotypic consequences, the loss of all three clusters (tricluster deletion) led to a severe axonal arborization defect and loss of self-avoidance. | The vertebrate clustered protocadherin (Pcdh) cell surface proteins are encoded
by three closely linked gene clusters (Pcdhα, Pcdhβ, and Pcdhγ). Here, we show
that all three gene clusters functionally cooperate to provide individual mouse
olfactory sensory neurons (OSNs) with the cell surface diversity required for
their assembly into distinct glomeruli in the olfactory bulb. Although deletion
of individual Pcdh clusters had subtle phenotypic consequences, the loss of all
three clusters (tricluster deletion) led to a severe axonal arborization defect
and loss of self-avoidance. By contrast, when endogenous Pcdh diversity is
overridden by the expression of a single-tricluster gene repertoire (α and β and
γ), OSN axons fail to converge to form glomeruli, likely owing to
contact-mediated repulsion between axons expressing identical combinations of
Pcdh isoforms. |
What is CPX351? | CPX-351, a novel liposomal formulation which encapsulates cytarabine and daunorubicin in 5:1 molar ratio, has shown promising efficacy, leading to recent US FDA approval for front-line therapy for patients with therapy-related AML and AML with myelodysplasia-related changes based on a large multicenter Phase III clinical trial. | Multiple novel therapeutic agents against acute myeloid leukemia (AML) have been
evaluated in the past several decades without meaningful clinical improvement in
outcomes, especially for AML patients age ≥60, where the overall incidence of
AML is highest. Therapeutic options mainly consist of hypomethylating agents,
ongoing clinical trials and, less commonly, intensive cytotoxic chemotherapy.
CPX-351, a novel liposomal formulation which encapsulates cytarabine and
daunorubicin in 5:1 molar ratio, has shown promising efficacy, leading to recent
US FDA approval for front-line therapy for patients with therapy-related AML and
AML with myelodysplasia-related changes based on a large multicenter Phase III
clinical trial. This review summarizes the clinical development of CPX-351 as
induction therapy. |
Is collagen the most abundant human protein? | Yes, collagen is the most abundant protein family in mammals. | Collagen is a fibrillar protein that conforms the conjunctive and connective
tissues in the human body, essentially skin, joints, and bones. This molecule is
one of the most abundant in many of the living organisms due to its connective
role in biological structures. Due to its abundance, strength and its directly
proportional relation with skin aging, collagen has gained great interest in the
cosmetic industry. It has been established that the collagen fibers are damaged
with the pass of time, losing thickness and strength which has been strongly
related with skin aging phenomena [Colágeno para todo. 60 y más. 2016.
http://www.revista60ymas.es/InterPresent1/groups/revistas/documents/binario/ses330informe.pdf.].
As a solution, the cosmetic industry incorporated collagen as an ingredient of
different treatments to enhance the user youth and well-being, and some common
presentations are creams, nutritional supplement for bone and cartilage
regeneration, vascular and cardiac reconstruction, skin replacement, and
augmentation of soft skin among others [J App Pharm Sci. 2015;5:123-127].
Nowadays, the biomolecule can be obtained by extraction from natural sources
such as plants and animals or by recombit protein production systems
including yeast, bacteria, mammalian cells, insects or plants, or artificial
fibrils that mimic collagen characteristics like the artificial polymer
commercially named as KOD. Because of its increased use, its market size is
valued over USD 6.63 billion by 2025 [Collagen Market By Source (Bovine,
Porcine, Poultry, Marine), Product (Gelatin, Hydrolyzed Collagen), Application
(Food & Beverages, Healthcare, Cosmetics), By Region, And Segment Forecasts,
2014 - 2025. Grand View Research.
http://www.grandviewresearch.com/industry-analysis/collagen-market. Published
2017.]. Nevertheless, there has been little effort on identifying which collagen
types are the most suitable for cosmetic purposes, for which the present review
will try to enlighten in a general scope this unattended matter. Collagen is the most abundant protein family in mammals. Commercial edible
gelatins are often produced from bovine and porcine skin and bone and consist
mainly of partially hydrolyzed collagen type 1. The gelatin industry would
benefit from a sensitive and reliable species detection method to unambiguously
demonstrate species authenticity of their products. PCR and ELISA could in
principle be used for this purpose. However, for gelatin, problems associated
with false-positive and false-negative results, inconsistencies and low
reactivity of commercially available kits have been observed with regard to
ELISA and PCR methods. Therefore we developed a selective bottom-up LC-MS
methodology for quantitative gelatin species determination with a lower limit of
quantification of 0.05%. The present article describes the validation of this
method, which was performed according to Good Laboratory Practice, and the
theoretical justification for bovine and porcine target selection. The validated
method can be used to determine the purity of gelatin batches with regard to
bovine and porcine constituents. |
What micro-RNAs are useful in the diagnosis and prognosis of Heart Failure? | In particular, miR-214, miR-423-5p, appear to be promising for the diagnosis, prognosis and management of HF patients. | MicroRNAs (miRNAs) are a group of newly discovered small RNAs, non-coding, which
represent one of the most exciting areas of modern medical science as they
modulate a huge and complex regulatory network of gene expression. Lines of
evidence have recently suggested that miRNAs play a key role in the pathogenesis
of heart failure. Some miRNAs highly expressed in the heart, such as miR-1,
miR-133 and miR-208, are strongly associated with the development of cardiac
hypertrophy, while the exact role of miR-21 in the cardiovascular system remains
controversial. Serum levels of circulating miRNAs such as miR-423-5p are being
evaluated as potential biomarkers in the diagnosis and prognosis of heart
failure. On the other hand, the manipulation of levels of miRNAs using
techniques such as mimicking the miRNAs (miRmimics) and antagonistic miRNAs
(antagomiRs) is making increasingly evident the enormous potential of miRNAs as
promising therapeutic strategies in heart failure. MicroRNAs (miRNAs) are a class of non-coding small RNAs representing one of the
most exciting areas of modern medical science. miRNAs modulate a large and
complex regulatory network of gene expression of the majority of the
protein-coding genes. Currently, evidences suggest that miRNAs play a crucial
role in the pathogenesis of heart failure. Some miRNAs as miR-1, miR-133 and
miR-208a are highly expressed in the heart and strongly associated with the
development of cardiac hypertrophy. Recent data indicate that these miRNAs as
well as miR-206 change their expression quickly in response to physical
activity. The differential regulation of miRNAs in response to exercise suggests
a potential value of circulating miRNAs (c-miRNAs) as biomarkers of
physiological mediators of the cardiovascular adaptation induced by exercise.
Likewise, serum levels of c-miRNAs such as miR-423-5p have been evaluated as
potential biomarkers in the diagnosis and prognosis of heart failure. On the
other hand, the manipulation of miRNAs levels using techniques such as 'miR
mimics' and 'antagomiRs' is becoming evident the enormous potential of miRNAs as
promising therapeutic strategies in heart failure. Cardiovascular disease (CVD) is the leading cause of death throughout the world.
The increase in new patients every year leads to a demand for the identification
of valid and novel prognostic and diagnostic biomarkers for the prevention and
treatment of cardiovascular diseases. MicroRNAs (miRNAs) are critical endogenous
small noncoding RNAs that negatively modulate gene expression by regulating its
translation. miRNAs are implicated in most physiological processes of the heart
and in the pathological progression of cardiovascular diseases. miR-214 is a
deregulated miRNA in many pathological conditions, and it contributes to the
pathogenesis of multiple human disorders, including cancer and cardiovascular
diseases. miR-214 has dual functions in different cardiac pathological
circumstances. However, it is considered as a promising marker in the prognosis,
diagnosis and treatment of cardiovascular diseases. In this review, we discuss
the role of miR-214 in various cardiac disease conditions, including ischaemic
heart diseases, cardiac hypertrophy, pulmonary arterial hypertension (PAH),
angiogenesis following vascular injury and heart failure. |
What is ivosidenib? | AG-120 (ivosidenib) ia an inhibitor of the IDH1 mutant enzyme that exhibits profound 2-HG lowering in tumor models and the ability to effect differentiation of primary patient AML samples ex vivo. Preliminary data from phase 1 clinical trials enrolling patients with cancers harboring an IDH1 mutation indicate that AG-120 has an acceptable safety profile and clinical activity. | Somatic point mutations at a key arginine residue (R132) within the active site
of the metabolic enzyme isocitrate dehydrogenase 1 (IDH1) confer a novel gain of
function in cancer cells, resulting in the production of d-2-hydroxyglutarate
(2-HG), an oncometabolite. Elevated 2-HG levels are implicated in epigenetic
alterations and impaired cellular differentiation. IDH1 mutations have been
described in an array of hematologic maligcies and solid tumors. Here, we
report the discovery of AG-120 (ivosidenib), an inhibitor of the IDH1 mutant
enzyme that exhibits profound 2-HG lowering in tumor models and the ability to
effect differentiation of primary patient AML samples ex vivo. Preliminary data
from phase 1 clinical trials enrolling patients with cancers harboring an IDH1
mutation indicate that AG-120 has an acceptable safety profile and clinical
activity. |
List proteins interacting with Star-PAP | Phosphorylation regulates the Star-PAP-PIPKIα interaction and directs specificity toward mRNA targets.
Star-PAP directly associated with cleavage and polyadenylation specificity factor (CPSF) 160 and 73 subunits and also the targeted pre-mRNA.
we show that Larp7 interacts with a poly(A) polymerase Star-PAP to maintain Lin28 mRNA stability. | Phosphoinositides are a family of lipid signalling molecules that regulate many
cellular functions in eukaryotes. Phosphatidylinositol-4,5-bisphosphate
(PtdIns4,5P2), the central component in the phosphoinositide signalling
circuitry, is generated primarily by type I phosphatidylinositol 4-phosphate
5-kinases (PIPKIalpha, PIPKIbeta and PIPKIgamma). In addition to functions in
the cytosol, phosphoinositides are present in the nucleus, where they modulate
several functions; however, the mechanism by which they directly regulate
nuclear functions remains unknown. PIPKIs regulate cellular functions through
interactions with protein partners, often PtdIns4,5P2 effectors, that target
PIPKIs to discrete subcellular compartments, resulting in the spatial and
temporal generation of PtdIns4,5P2 required for the regulation of specific
signalling pathways. Therefore, to determine roles for nuclear PtdIns4,5P2 we
set out to identify proteins that interacted with the nuclear PIPK, PIPKIalpha.
Here we show that PIPKIalpha co-localizes at nuclear speckles and interacts with
a newly identified non-canonical poly(A) polymerase, which we have termed
Star-PAP (nuclear speckle targeted PIPKIalpha regulated-poly(A) polymerase) and
that the activity of Star-PAP can be specifically regulated by PtdIns4,5P2.
Star-PAP and PIPKIalpha function together in a complex to control the expression
of select mRNAs, including the transcript encoding the key cytoprotective enzyme
haem oxygenase-1 (refs 8, 9) and other oxidative stress response genes by
regulating the 3'-end formation of their mRNAs. Taken together, the data
demonstrate a model by which phosphoinositide signalling works in tandem with
complement pathways to regulate the activity of Star-PAP and the subsequent
biosynthesis of its target mRNA. The results reveal a mechanism for the
integration of nuclear phosphoinositide signals and a method for regulating gene
expression. Star-PAP is a nuclear non-canonical poly(A) polymerase (PAP) that shows
specificity toward mRNA targets. Star-PAP activity is stimulated by lipid
messenger phosphatidyl inositol 4,5 bisphoshate (PI4,5P2) and is regulated by
the associated Type I phosphatidylinositol-4-phosphate 5-kinase that synthesizes
PI4,5P2 as well as protein kinases. These associated kinases act as coactivators
of Star-PAP that regulates its activity and specificity toward mRNAs, yet the
mechanism of control of these interactions are not defined. We identified a
phosphorylated residue (serine 6, S6) on Star-PAP in the zinc finger region, the
domain required for PIPKIα interaction. We show that S6 is phosphorylated by
CKIα within the nucleus which is required for Star-PAP nuclear retention and
interaction with PIPKIα. Unlike the CKIα mediated phosphorylation at the
catalytic domain, Star-PAP S6 phosphorylation is insensitive to oxidative stress
suggesting a signal mediated regulation of CKIα activity. S6 phosphorylation
together with coactivator PIPKIα controlled select subset of Star-PAP target
messages by regulating Star-PAP-mRNA association. Our results establish a novel
role for phosphorylation in determining Star-PAP target mRNA specificity and
regulation of 3'-end processing. |
Describe symptoms of the Visual snow syndrome. | Visual snow (VS) is a constant visual disturbance described as flickering dots occupying the entire visual field. Recently, it was characterized as the defining feature of a VS syndrome (VSS), which includes palinopsia, photophobia, photopsias, entoptic phenomena, nyctalopia, and tinnitus. | Visual snow is a symptom described as the continuous perception of tiny
flickering dots in the entire field of vision, similar to static of an analog
television. Visual snow syndrome is a cluster of symptoms found highly prevalent
in patients that present with visual snow. While most of these symptoms appear
to be visual in nature, approximately 63% of patients studied also report
continuous bilateral tinnitus. The high correlation of visual-snow-syndrome
patients presenting with tinnitus suggests that they may share a common
underlying pathophysiology. PURPOSE OF REVIEW: We provide an overview of the neurological condition known as
visual snow syndrome. Patients affected by this chronic disorder suffer with a
pan-field visual disturbance described as tiny flickering dots, which resemble
the static noise of an untuned television.
RECENT FINDINGS: The term 'visual snow' has only appeared in the medical
literature very recently. The clinical features of the syndrome have now been
reasonably described and the pathophysiology has begun to be explored. This
review focuses on what is currently known about visual snow.
SUMMARY: Recent evidence suggests visual snow is a complex neurological syndrome
characterized by debilitating visual symptoms. It is becoming better understood
as it is systematically studied. Perhaps the most important unmet need for the
condition is a sufficient understanding of it to generate and test hypotheses
about treatment. PURPOSE OF REVIEW: In this article, we review illustrative case descriptions of
both primary and secondary visual snow from our clinic. We discuss recently
proposed criteria for visual snow syndrome and offer a slight modification of
these criteria. We also discuss the theories on the pathophysiological
mechanisms of visual snow, as well as the current approach to treatment.
RECENT FINDINGS: Visual snow is a condition where patients see constant,
innumerable flickering dots throughout the visual field, similar to "TV static."
Though visual snow was originally described in 1995, there were still fewer than
10 cases in the literature prior to 2014. In the last 4 years, this has grown to
approximately 200 cases and there has been a concentrated effort to better
understand and characterize this condition. It has become apparent that patients
who see visual snow frequently have additional visual and non-visual symptoms,
and the consistency of these symptoms has led to proposed criteria for visual
snow syndrome. When seeing a patient with visual snow, it is important to rule
out a possible underlying secondary etiology. Patients with visual snow syndrome
frequently have comorbid migraine, but visual snow appears to be a separate
entity from persistent migraine aura. The pathophysiology of this syndrome is
not clear, but recent neurophysiologic and neuroimaging studies have helped
advance our understanding. BACKGROUND: Visual snow (VS) is a constant visual disturbance described as
flickering dots occupying the entire visual field. Recently, it was
characterized as the defining feature of a VS syndrome (VSS), which includes
palinopsia, photophobia, photopsias, entoptic phenomena, nyctalopia, and
tinnitus. Sixty percent of patients with VSS also experience migraine, with or
without aura. This entity often is considered psychogenic in nature, to the
detriment of the patient's best interests, but the high frequency of similar
visual symptoms argues for an organic deficit. The purpose of this review is to
clarify VSS as a true entity and elaborate the nature of individual symptoms and
their relationship to each other.
EVIDENCE ACQUISITION: The literature was reviewed with specific regard to the
clinical presentation and psychophysical, neurophysiological, and functional
imaging studies in patients with defined visual disturbances that comprise VSS.
RESULTS: Consideration of the individual symptoms suggests that multiple factors
are potentially involved in the development of VSS, including subcortical
network malfunction and cortical hyperexcitation. Although there is substantial
overlap between VSS and migraine syndromes in terms of co-occurring symptoms,
both neurophysiological and neuroimaging studies provide substantial evidence of
separate abnormalities of processing, supporting these as separate syndromes.
CONCLUSIONS: VSS is likely associated with either hyperactive visual cortices
or, alternatively, impaired processing of simultaneous afferent information
projecting to cortex. VSS likely results from widespread disturbance of sensory
processing resulting in sensory misperception. There may be a number of
syndromes associated with impaired sensory processing resulting in sensory
misperception, including migraine, persistent perceptual postural dizziness, and
tinnitus, which overlap with VSS. Elucidation of abnormality in one defined
syndrome may provide a path forward for investigating all. |
What is the role of the Leucosporidium ice-binding protein | Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein (LeIBP) with a molecular mass of ∼25 kDa, which can lower the freezing point below the melting point once it binds to ice. ce-binding proteins (IBPs) inhibit ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments. | Arctic yeast Leucosporidium sp. produces a glycosylated ice-binding protein
(LeIBP) with a molecular mass of ∼25 kDa, which can lower the freezing point
below the melting point once it binds to ice. LeIBP is a member of a large class
of ice-binding proteins, the structures of which are unknown. Here, we report
the crystal structures of non-glycosylated LeIBP and glycosylated LeIBP at 1.57-
and 2.43-Å resolution, respectively. Structural analysis of the LeIBPs revealed
a dimeric right-handed β-helix fold, which is composed of three parts: a large
coiled structural domain, a long helix region (residues 96-115 form a long
α-helix that packs along one face of the β-helix), and a C-terminal hydrophobic
loop region ((243)PFVPAPEVV(251)). Unexpectedly, the C-terminal hydrophobic loop
region has an extended conformation pointing away from the body of the coiled
structural domain and forms intertwined dimer interactions. In addition,
structural analysis of glycosylated LeIBP with sugar moieties attached to
Asn(185) provides a basis for interpreting previous biochemical analyses as well
as the increased stability and secretion of glycosylated LeIBP. We also
determined that the aligned Thr/Ser/Ala residues are critical for ice binding
within the B face of LeIBP using site-directed mutagenesis. Although LeIBP has a
common β-helical fold similar to that of canonical hyperactive antifreeze
proteins, the ice-binding site is more complex and does not have a simple
ice-binding motif. In conclusion, we could identify the ice-binding site of
LeIBP and discuss differences in the ice-binding modes compared with other known
antifreeze proteins and ice-binding proteins. Ice-binding proteins (IBPs) can bind to the ice crystal and inhibit its growth.
Because this property of IBPs can increase the freeze-thaw survival of cells,
IBPs have attracted the attention from industries for their potential use in
biotechnological applications. However, their use was largely hampered by the
lack of the large-scale recombit production system. In this study, the
codon-optimized IBP from Leucosporidium sp. (LeIBP) was constructed and
subjected to high-level expression in methylotrophic Pichia pastoris system. In
a laboratory-scale fermentation (7 L), the optimal induction temperature and pH
were determined to be 25 °C and 6.0, respectively. Further, employing glycerol
fed-batch phase prior to methanol induction phase enhanced the production of
recombit LelBP (rLeIBP) by ∼100 mg/l. The total amount of secreted proteins
at these conditions (25 °C, pH 6.0, and glycerol fed-batch phase) was ∼443 mg/l,
60 % of which was rLeIBP, yielding ∼272 mg/l. In the pilot-scale fermentation
(700 L) under the same conditions, the yield of rLeIBP was 300 mg/l. To our best
knowledge, this result reports the highest production yield of the recombit
IBP. More importantly, the rLeIBP secreted into culture media was stable and
active for 6 days of fermentation. The thermal hysteresis (TH) activity of
rLeIBP was about 0.42 °C, which is almost the same to those reported previously.
The availability of large quantities of rLeIBP may accelerate further
application studies. Ice-binding proteins (IBPs) inhibit ice growth through direct interaction with
ice crystals to permit the survival of polar organisms in extremely cold
environments. FfIBP is an ice-binding protein encoded by the Antarctic bacterium
Flavobacterium frigoris PS1. The X-ray crystal structure of FfIBP was determined
to 2.1 Å resolution to gain insight into its ice-binding mechanism. The refined
structure of FfIBP shows an intramolecular disulfide bond, and analytical
ultracentrifugation and analytical size-exclusion chromatography show that it
behaves as a monomer in solution. Sequence alignments and structural comparisons
of IBPs allowed two groups of IBPs to be defined, depending on sequence
differences between the α2 and α4 loop regions and the presence of the disulfide
bond. Although FfIBP closely resembles Leucosporidium (recently re-classified as
Glaciozyma) IBP (LeIBP) in its amino-acid sequence, the thermal hysteresis (TH)
activity of FfIBP appears to be tenfold higher than that of LeIBP. A comparison
of the FfIBP and LeIBP structures reveals that FfIBP has different ice-binding
residues as well as a greater surface area in the ice-binding site. Notably, the
ice-binding site of FfIBP is composed of a T-A/G-X-T/N motif, which is similar
to the ice-binding residues of hyperactive antifreeze proteins. Thus, it is
proposed that the difference in TH activity between FfIBP and LeIBP may arise
from the amino-acid composition of the ice-binding site, which correlates with
differences in affinity and surface complementarity to the ice crystal. In
conclusion, this study provides a molecular basis for understanding the
antifreeze mechanism of FfIBP and provides new insights into the reasons for the
higher TH activity of FfIBP compared with LeIBP. Ice binding proteins (IBPs) have been attracting significant interest on account
of their characteristic of inhibiting ice growth and recrystallization. Owing to
their unique characteristics, IBPs have been studied for applications in food,
pharmaceuticals, and medicine, as well as from a general scientific point of
view. In this study, we have used differential scanning calorimetry (DSC) and
Raman spectroscopy as tools to understand the ice binding activity of the
Arctic-yeast-originating extracellular ice binding glycoprotein (LeIBP) isolated
from Leucosporidium sp. AY30. From the DSC results, an increase in the specific
heat capacity was confirmed for 1 mg/mL LeIBP, which suggested that additional
heat flow was required for the change in temperature. In addition, the
temperature corresponding to the phase change of the solution was measured, and
Raman spectroscopy was carried out on the frozen and molten phases,
respectively. From the results of Raman analysis, we confirmed that the helical
vibrations related to the ice binding sites on LeIBP were dramatically
suppressed when the LeIBP solution was frozen. Furthermore, principal component
analysis (PCA) of the Raman spectra yielded the contrast factor between the
freezing and melting states. Both DSC and Raman spectroscopy are widely used to
study the ice binding activity and the structural changes associated with
molecular vibrations in cryobiology. |
Is the enzyme ERAP2 associated with the disease birdshot chorioretinopathy? | Yes,
BSCR is also associated with endoplasmic reticulum aminopeptidase 2 (ERAP2), an enzyme involved in processing HLA class I ligands. | Author information:
(1)Department of Ophthalmology, Department of Clinical Chemistry and Hematology.
(2)Department of Medical Genetics.
(3)Program in Medical and Population Genetics, Broad Institute of Harvard and
MIT, Cambridge, MA, USA, Center for Human Genetic Research, Massachusetts
General Hospital, Harvard Medical School, Boston, MA, USA.
(4)The Rotterdam Eye Hospital, Rotterdam, The Netherlands.
(5)Department of Ophthalmology.
(6)Department of Ophthalmology and Department of Human Genetics, Radboud
University Nijmegen Medical Centre, Nijmegen, the Netherlands.
(7)Department of Ophthalmology and.
(8)Unidad de Uveitis. Servicio de Oftalmología, Hospital Universitario de León,
León, Spain.
(9)Instituto de Parasitología y Biomedicina López-Neyra, IPBLN, CSIC, Granada,
Spain.
(10)Institut Clinic d'Oftalmologia (ICOF), Hospital Clinic de Barcelona,
Barcelona, Spain.
(11)Moorfields Eye Hospital NHS Foundation Trust, London, UK.
(12)Department of Psychiatry, Rudolph Magnus Institute of Neuroscience.
(13)Department of Psychiatry, Rudolph Magnus Institute of Neuroscience, Center
for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior,
Department of Human Genetics, David Geffen School of Medicine, University of
California Los Angeles, Los Angeles, CA, USA and.
(14)Department of Ophthalmology, Erasmus University Medical Center, Rotterdam,
The Netherlands.
(15)Department of Medical Genetics, Department of Epidemiology, University
Medical Center Utrecht, Utrecht, The Netherlands.
(16)Department of Clinical Chemistry and Hematology.
(17)Department of Medical Genetics, [email protected]. Virtually all patients of the rare inflammatory eye disease birdshot
chorioretinopathy (BSCR) carry the HLA-A*29:02 allele. BSCR is also associated
with endoplasmic reticulum aminopeptidase 2 (ERAP2), an enzyme involved in
processing HLA class I ligands, thus implicating the A*29:02 peptidome in this
disease. To investigate the relationship between both risk factors we employed
label-free quantitative mass spectrometry to characterize the effects of ERAP2
on the A*29:02-bound peptidome. An ERAP2-negative cell line was transduced with
lentiviral constructs containing GFP-ERAP2 or GFP alone, and the A*29:02
peptidomes from both transduced cells were compared. A similar analysis was
performed with two additional A*29:02-positive, ERAP1-concordant, cell lines
expressing or not ERAP2. In both comparisons the presence of ERAP2 affected the
following features of the A*29:02 peptidome: 1) Length, with increased amounts
of peptides >9-mers, and 2) N-terminal residues, with less ERAP2-susceptible and
more hydrophobic ones. The paradoxical effects on peptide length suggest that
unproductive binding to ERAP2 might protect some peptides from ERAP1
over-trimming. The influence on N-terminal residues can be explained by a direct
effect of ERAP2 on trimming, without ruling out and improved processing in
concert with ERAP1. The alterations in the A*29:02 peptidome suggest that the
association of ERAP2 with BSCR is through its effects on peptide processing.
These differ from those on the ankylosing spondylitis-associated HLA-B*27. Thus,
ERAP2 alters the peptidome of distinct HLA molecules as a function of their
specific binding preferences, influencing different pathological outcomes in an
allele-dependent way. |
As of September 2018, what machine learning algorithm is used to for cardiac arrhythmia detection from a short single-lead ECG recorded by a wearable device? | Support Vector machines( SVM) can be used for cardiac arrhythmia detection in from an ECG recorded by a wearable device. | OBJECTIVE: Use of wearable ECG devices for arrhythmia screening is limited due
to poor signal quality, small number of leads and short records, leading to
incorrect recognition of pathological events. This paper introduces a novel
approach to classification (normal/'N', atrial fibrillation/'A', other/'O', and
noisy/'P') of short single-lead ECGs recorded by wearable devices.
APPROACH: Various rhythm and morphology features are derived from the separate
beats ('local' features) as well as the entire ECGs ('global' features) to
represent short-term events and general trends respectively. Various types of
atrial and ventricular activity, heart beats and, finally, ECG records are then
recognised by a multi-level approach combining a support vector machine (SVM),
decision tree and threshold-based rules.
MAIN RESULTS: The proposed features are suitable for the recognition of 'A'. The
method is robust due to the noise estimation involved. A combination of radial
and linear SVMs ensures both high predictive performance and effective
generalisation. Cost-sensitive learning, genetic algorithm feature selection and
thresholding improve overall performance. The generalisation ability and
reliability of this approach are high, as verified by cross-validation on a
training set and by blind testing, with only a slight decrease of overall
F1-measure, from 0.84 on training to 0.81 on the tested dataset. 'O' recognition
seems to be the most difficult (test F1-measures: 0.90/'N', 0.81/'A' and
0.72/'O') due to high inter-patient variability and similarity with 'N'.
SIGNIFICANCE: These study results contribute to multidisciplinary areas,
focusing on creation of robust and reliable cardiac monitoring systems in order
to improve diagnosis, reduce unnecessary time-consuming expert ECG scoring and,
consequently, ensure timely and effective treatment. |
Does Panitumumab prolong survival of biliary tract cancer patients? | No. Panitumumab in combination with chemotherapy does not improve survival of biliary cancer patients. | BACKGROUND: Biliary tract cancer (BTC) is a rare and lethal disease with few
therapeutic options. Preclinical data suggest that the epidermal growth factor
receptor (EGFR) pathway could be involved in its progression.
METHODS: This open-label, randomized phase 2 trial recruited chemotherapy-naive
patients with advanced BTC displaying a wild-type (WT) KRAS status. Patients
were randomized to gemcitabine (1000 mg/m(2) ) and oxaliplatin (100 mg/m(2) )
with (arm A) or without (arm B) panitumumab (6 mg/kg) for up to 12 cycles. The
primary endpoint was progression-free survival (PFS) analyzed in an
intention-to-treat fashion.
RESULTS: Eighty-nine patients (45 in arm A and 44 in arm B) were enrolled
between June 2010 and September 2013. After a median follow-up of 10.1 months,
the median PFS was 5.3 months (95% confidence interval, 3.3-7.2 months) in arm A
and 4.4 months (95% confidence interval, 2.6-6.2 months) in arm B (P = .27). No
survival differences were observed: the median overall survival was 9.9 months
in arm A and 10.2 months in arm B (P = .42). In a subgroup analysis, no
differences in PFS according to the site of the primary tumor were observed;
patients with intrahepatic cholangiocarcinoma treated with panitumumab may have
had a survival benefit in comparison with the control group (15.1 vs 11.8
months, P = .13). As for safety, skin toxicity was the main adverse event in arm
A (80% of the patients). A higher incidence of diarrhea (55.5% vs 31.8%),
mucositis (22.2% vs 13.6%), and constipation (24.4% vs 15.9%) was seen in arm A.
CONCLUSIONS: These results confirm the marginal role of anti-EGFR therapy even
for WT KRAS-selected BTC. Author information:
(1)Department of Gastroenterology, Hepatology and Endocrinology, Hannover
Medical School, Hannover, Germany. Electronic address:
[email protected].
(2)Department of Medical Oncology, West German Cancer Center, University
Hospital Essen, Essen, Germany.
(3)Department of Internal Medicine I, University Hospital Tübingen, Tübingen,
Germany.
(4)Department of Medical Oncology and Hematology, University Cancer Center
Hamburg, University Hamburg-Eppendorf, Hamburg, Germany.
(5)Department of Hematology and Oncology, University Hospital Charité, Berlin,
Germany.
(6)National Center for Tumor Diseases, University of Heidelberg, Heidelberg,
Germany.
(7)Department of Gastroenterology, Johannes-Gutenberg University, Mainz,
Germany.
(8)Institute of Pathology, University Hospital and National Center for Tumor
Diseases Heidelberg, Germany; Institute of Pathology, Technical University
Munich, Munich, Germany.
(9)Institute of Pathology, University Hospital and National Center for Tumor
Diseases Heidelberg, Germany.
(10)Interdisziplinären Tumorzentrum Mannheim, Mannheim, Germany.
(11)Department of Internal Medicine, University Hospital Regensburg, Germany,
Regensburg, Germany.
(12)2nd Department of Internal Medicine, Technical University, Munich, Germany.
(13)Department of Gastroenterology, Philipps-University Marburg, Marburg,
Germany.
(14)Department of Gastroenterology and Hepatology, University of Cologne,
Cologne, Germany.
(15)Department of Medicine II, University Hospital Freiburg, Freiburg, Germany.
(16)Department of Gastroenterology and Oncology, Klinikum Esslingen, Esslingen,
Germany.
(17)Department of Hematology, Oncology and Palliative Care, Klinikum Magdeburg,
Magdeburg, Germany.
(18)Lindenallee 53b, 59174 Kamen, Germany.
(19)Gottfried Wilhelm Leibniz University Hannover, Center for Health Economics
Research Hannover, Germany.
(20)Institute of Pathology, University Hospital and National Center for Tumor
Diseases Heidelberg, Germany; Institute of Pathology, Technical University
Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner Site Munich,
Germany.
(21)Cancer Center Reutlingen, Reutlingen, Germany. Biliary tract cancer, carcinoma of the extrahepatic bile ducts, carcinoma of the
gall bladder, ampullary carcinoma and intrahepatic cholangiocarcinoma are often
identified at an advanced stage and have poor prognoses. Although effective
chemotherapy regimens are needed, their development remains unsatisfactory. From
the results of a phase III clinical trial (ABC-02 trial), gemcitabine plus
cisplatin is the standard first-line chemotherapeutic regimen for advanced
biliary tract cancer. A phase III trial of gemcitabine plus cisplatin vs.
gemcitabine plus S-1 therapy (FUGA-BT) demonstrated the non-inferiority of
gemcitabine plus S-1 to gemcitabine plus cisplatin. A phase III trial of
gemcitabine plus cisplatin vs. gemcitabine plus cisplatin plus S-1 (MITSUBA) was
conducted, and the report on the results of the final analysis is being awaited.
A standard second-line chemotherapeutic regimen has not yet been established.
Fluoropyrimidines are frequently used in clinical practice. Despite many
clinical trials being conducted with molecular targeted agents including
erlotinib, cetuximab, panitumumab, bevacizumab, sorafenib, cediranib, trametinib
and vandetanib, no agent has shown to be effective for advanced biliary tract
cancer. Next-generation sequencing shows great promise by allowing rapid
mutational analysis of multiple genes in human cancers, and attractive driver
genetic alterations have been reported in biliary tract cancer. FGFR2 fusion
gene, mutations of IDH1/2, BRAF, BRCA1/2, ATM, PIK3CA and overexpression of
c-MET and HER2/neu are reported relatively frequently and are interesting
targets. Therefore, future development in precision medicine utilizing
next-generation sequencing is expected. Although the efficacy of immune
checkpoint inhibitors, such as anti-PD-1, anti-PD-L1 and anti-CTLA4 antibodies,
remains unknown at present, basic data and results of ongoing clinical trials
are anticipated. |
Which microRNA is the mediator of the obesity phenotype of patients carrying 1p21.3 microdeletions? | MIR137 is the mediator of the obesity phenotype of patients carrying 1p21.3 microdeletions. | BACKGROUND: Deletions in the long arm of chromosome 1 have been described in
patients with a phenotype consisting primarily of obesity, intellectual
disability and autism-spectrum disorder. The minimal region of overlap comprises
two genes: DPYD and MIR137.
CASE PRESENTATION: We describe a 10-year-old boy with syndromic obesity who
carries a novel 1p21.3 deletion overlapping the critical region with the MIR137
gene only.
CONCLUSIONS: This study suggests that MIR137 is the mediator of the obesity
phenotype of patients carrying 1p21.3 microdeletions. |
What is the aim of the METABRIC project? | The METABRIC [Molecular Taxonomy of Breast Cancer International Consortium] cohort aims at the integration of genomic and transcriptomic profiles of 2000 breast tumours. | BACKGROUND: In molecular profiling studies of cancer patients, experimental and
clinical data are combined in order to understand the clinical heterogeneity of
the disease: clinical information for each subject needs to be linked to tumour
samples, macromolecules extracted, and experimental results. This may involve
the integration of clinical data sets from several different sources: these data
sets may employ different data definitions and some may be incomplete.
METHODS: In this work we employ semantic web techniques developed within the
CancerGrid project, in particular the use of metadata elements and logic-based
inference to annotate heterogeneous clinical information, integrate and query
it.
RESULTS: We show how this integration can be achieved automatically, following
the declaration of appropriate metadata elements for each clinical data set; we
demonstrate the practicality of this approach through application to
experimental results and clinical data from five hospitals in the UK and Canada,
undertaken as part of the METABRIC project (Molecular Taxonomy of Breast Cancer
International Consortium).
CONCLUSION: We describe a metadata approach for managing similarities and
differences in clinical datasets in a standardized way that uses Common Data
Elements (CDEs). We apply and evaluate the approach by integrating the five
different clinical datasets of METABRIC. Large research consortia such as the Molecular Taxonomy of Breast Cancer
International Consortium (METABRIC), The Cancer Genome Atlas and International
Cancer Genomics Consortium are systematically interrogating large sets of tumor
samples through integrated analysis of genome-wide DNA copy number and promoter
methylation, transcriptome-wide RNA expression, protein expression and
exome-wide sequencing. A recent METABRIC study explored the effects of
cis-acting and trans-acting factors of gene expression regulation in breast
cancer. By making their data sets publicly available, these large consortia are
inviting new types of analysis that have the potential to drive breast cancer
research into previously unexplored avenues. BACKGROUND: The prediction of breast cancer intrinsic subtypes has been
introduced as a valuable strategy to determine patient diagnosis and prognosis,
and therapy response. The PAM50 method, based on the expression levels of 50
genes, uses a single sample predictor model to assign subtype labels to samples.
Intrinsic errors reported within this assay demonstrate the challenge of
identifying and understanding the breast cancer groups. In this study, we aim
to: a) identify novel biomarkers for subtype individuation by exploring the
competence of a newly proposed method named CM1 score, and b) apply an ensemble
learning, as opposed to the use of a single classifier, for sample subtype
assignment. The overarching objective is to improve class prediction.
METHODS AND FINDINGS: The microarray transcriptome data sets used in this study
are: the METABRIC breast cancer data recorded for over 2000 patients, and the
public integrated source from ROCK database with 1570 samples. We first computed
the CM1 score to identify the probes with highly discriminative patterns of
expression across samples of each intrinsic subtype. We further assessed the
ability of 42 selected probes on assigning correct subtype labels using 24
different classifiers from the Weka software suite. For comparison, the same
method was applied on the list of 50 genes from the PAM50 method.
CONCLUSIONS: The CM1 score portrayed 30 novel biomarkers for predicting breast
cancer subtypes, with the confirmation of the role of 12 well-established genes.
Intrinsic subtypes assigned using the CM1 list and the ensemble of classifiers
are more consistent and homogeneous than the original PAM50 labels. The new
subtypes show accurate distributions of current clinical markers ER, PR and
HER2, and survival curves in the METABRIC and ROCK data sets. Remarkably, the
paradoxical attribution of the original labels reinforces the limitations of
employing a single sample classifiers to predict breast cancer intrinsic
subtypes. Author information:
(1)Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology
Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of
Medicine, Nashville, Tennessee.
(2)Centre for Cancer Genetic Epidemiology, Department of Public Health and
Primary Care, University of Cambridge, Cambridge, United Kingdom.
(3)Centre for Cancer Genetic Epidemiology, Department of Oncology, University of
Cambridge, Cambridge, United Kingdom.
(4)Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Victoria,
Australia. Centre for Epidemiology and Biostatistics, School of Population and
Global health, The University of Melbourne, Melbourne, Victoria, Australia.
(5)Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane,
Australia.
(6)Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto,
Canada. Department of Molecular Genetics, University of Toronto, Toronto,
Canada.
(7)Department of Epidemiology, University of California Irvine, Irvine,
California.
(8)Division of Clinical Epidemiology and Aging Research, German Cancer Research
Center, Heidelberg, Germany.
(9)Department of Gynaecology and Obstetrics, University Hospital Erlangen,
Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany.
(10)Human Cancer Genetics Program, Spanish National Cancer Research Centre,
Madrid, Spain. Centro de Investigación en Red de Enfermedades Raras, Valencia,
Spain.
(11)Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology
Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of
Medicine, Nashville, Tennessee. International Epidemiology Institute, Rockville,
Maryland.
(12)Department of Radiation Oncology, Hannover Medical School, Hannover,
Germany.
(13)Copenhagen General Population Study, Herlev Hospital, Herlev, Denmark.
Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University
Hospital, Herlev, Denmark. Faculty of Health and Medical Sciences, University of
Copenhagen, Copenhagen, Denmark.
(14)Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart,
Germany. University of Tübingen, Tübingen, Germany. German Cancer Consortium,
German Cancer Research Center, Heidelberg, Germany.
(15)Division of Clinical Epidemiology and Aging Research, German Cancer Research
Center, Heidelberg, Germany. German Cancer Consortium, German Cancer Research
Center, Heidelberg, Germany. Division of Preventive Oncology, German Cancer
Research Center (DKFZ), Heidelberg, Germany.
(16)Division of Cancer Epidemiology and Genetics, National Cancer Institute,
Rockville, Maryland.
(17)Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam,
the Netherlands.
(18)Institute for Prevention and Occupational Medicine of the German Social
Accident Insurance, Bochum, Germany.
(19)Division of Molecular Genetic Epidemiology, German Cancer Research Center,
Heidelberg, Germany. Molecular Epidemiology Group, German Cancer Research
Center, Heidelberg, Germany.
(20)Division of Cancer Epidemiology, German Cancer Research Center, Heidelberg,
Germany.
(21)Department of Biomedical Sciences, Seoul National University College of
Medicine, Seoul, Korea. Cancer Research Institute, Seoul National University
College of Medicine, Seoul, Korea.
(22)Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester,
Minnesota.
(23)Sheffield Cancer Research Centre, Department of Oncology, University of
Sheffield, Sheffield, United Kingdom.
(24)Academic Unit of Pathology, Department of Neuroscience, University of
Sheffield, Sheffield, United Kingdom.
(25)Department of Medical Epidemiology and Biostatistics, Karolinska Institutet,
Stockholm, Sweden.
(26)Department of Pathology, Leiden University Medical Center, Leiden, the
Netherlands. Department of Human Genetics, Leiden University Medical Center,
Leiden, the Netherlands.
(27)Centre Hospitalier Universitaire de Québec Research Center, Laval
University, Québec, Canada.
(28)Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.
(29)Department of Gynaecology and Obstetrics, University Hospital Erlangen,
Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany. David
Geffen School of Medicine, Department of Medicine, Division of Hematology and
Oncology, University of California at Los Angeles, Los Angeles, California.
(30)Division of Cancer Studies, Breakthrough Breast Cancer Research Centre,
Institute of Cancer Research, London, United Kingdom.
(31)Department of Breast Surgery, Herlev Hospital, Copenhagen University
Hospital, Herlev, Denmark.
(32)Molecular Diagnostics Laboratory, IRRP, National Centre for Scientific
Research "Demokritos", Athens, Greece.
(33)International Agency for Research on Cancer, Lyon, France.
(34)Division of Cancer Studies, Breakthrough Breast Cancer Research Centre,
Institute of Cancer Research, London, United Kingdom. Division of Genetics and
Epidemiology, Institute of Cancer Research, London, United Kingdom.
(35)Department of Surgery, Oulu University Hospital and University of Oulu,
Oulu, Finland.
(36)Environmental Epidemiology of Cancer, Center for Research in Epidemiology
and Population Health, INSERM, Villejuif, France. University Paris-Sud,
Villejuif, France.
(37)Department of Preventive Medicine, Keck School of Medicine, University of
Southern California, Los Angeles, California.
(38)Molecular Genetics of Breast Cancer, German Cancer Research Center,
Heidelberg, Germany.
(39)Saw Swee Hock School of Public Health, National University of Singapore,
Singapore, Singapore. Department of Surgery, National University Health System,
Singapore.
(40)Department of Medical Oncology, Erasmus University Medical Center,
Rotterdam, the Netherlands.
(41)Centre for Epidemiology and Biostatistics, School of Population and Global
health, The University of Melbourne, Melbourne, Victoria, Australia.
(42)Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
(43)Division of Epidemiology and Prevention, Aichi Cancer Center Research
Institute, Aichi, Japan.
(44)Department of Genetics and Pathology, Pomeranian Medical University,
Szczecin, Poland.
(45)Department of Biomedical Sciences, Seoul National University College of
Medicine, Seoul, Korea. Cancer Research Institute, Seoul National University
College of Medicine, Seoul, Korea. Department of Preventive Medicine, Seoul
National University College of Medicine, Seoul, Korea.
(46)Department of Obstetrics and Gynecology, Helsinki University Central
Hospital, University of Helsinki, Helsinki, Finland.
(47)Prosserman Centre for Health Research, Lunenfeld-Tanenbaum Research
Institute of Mount Sinai Hospital, Toronto, Ontario, Canada. Division of
Epidemiology, Dalla Lana School of Public Health, University of Toronto,
Toronto, Ontario, Canada.
(48)School of Medicine, Institute of Clinical Medicine, Pathology and Forensic
Medicine and Cancer Center of Eastern Finland, University of Eastern Finland,
Kuopio, Finland; Imaging Center, Department of Clinical Pathology, Kuopio
University Hospital, Kuopio, Finland.
(49)Vesalius Research Center, Leuven, Belgium. Laboratory for Translational
Genetics, Department of Oncology, University of Leuven, Leuven, Belgium.
(50)University of Hawaii Cancer Center, Honolulu, Hawaii.
(51)Department of Molecular Medicine and Surgery, Karolinska Institutet,
Stockholm, Sweden.
(52)Division of Health Sciences, Warwick Medical School, Warwick University,
Coventry, United Kingdom.
(53)Unit of Medical Genetics, Department of Preventive and Predictive Medicine,
Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy.
(54)Department of Oncology - Pathology, Karolinska Institutet, Stockholm,
Sweden.
(55)National Center for Tumor Diseases, University of Heidelberg, Heidelberg,
Germany. Department of Obstetrics and Gynecology, University of Heidelberg,
Heidelberg, Germany.
(56)Department of Preventive Medicine, Kyushu University Faculty of Medical
Sciences, Fukuoka, Japan.
(57)Anatomical Pathology, The Alfred Hospital, Melbourne, Victoria, Australia.
(58)Division of Gynaecology and Obstetrics, Technische Universität München,
Munich, Germany.
(59)Unit of Medical Genetics, Department of Preventive and Predictive Medicine,
Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy. Institute of
Population Health, University of Manchester, Manchester, United Kingdom.
(60)Beckman Research Institute of City of Hope, Duarte, California.
(61)Department of Genetics, Institute for Cancer Research, Oslo University
Hospital, Radiumhospitalet, Ullernchausseen, Oslo, Norway. K.G. Jebsen Center
for Breast Cancer Research, Institute for Clinical Medicine, Faculty of
Medicine, University of Oslo, Kirkeveien, Oslo, Norway.
(62)Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
(63)Division of Breast Cancer Research, Institute of Cancer Research, London,
United Kingdom; Cancer Research, Institute of Cancer Research, London, United
Kingdom.
(64)IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.
(65)Department of Pathology, National University Health System, Singapore.
(66)National Cancer Institute, Bangkok, Thailand.
(67)Research Oncology, Guy's Hospital, King's College London, London, United
Kingdom.
(68)Division of Molecular Gyneco-Oncology, Department of Gynaecology and
Obstetrics, University Hospital of Cologne, Cologne, Germany. Center for
Integrated Oncology, University Hospital of Cologne, Cologne, Germany. Center
for Molecular Medicine, University Hospital of Cologne, Cologne, Germany. Center
of Familial Breast and Ovarian Cancer, University Hospital of Cologne, Cologne,
Germany.
(69)School of Public Health, China Medical University, Taichung, Taiwan. Taiwan
Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
(70)Department of Pathology, The University of Melbourne, Melbourne, Victoria,
Australia.
(71)Division of Genetics and Epidemiology and Division of Breast Cancer
Research, Institute of Cancer Research, London, United Kingdom.
(72)Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia.
Breast Cancer Research Unit, Cancer Research Institute, University Malaya
Medical Centre, Kuala Lumpur, Malaysia.
(73)Department of Molecular Virology, Immunology, and Medical Genetics,
Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
(74)Department of Surgical Oncology, Leiden University Medical Center, Leiden,
the Netherlands.
(75)Wellcome Trust Centre for Human Genetics and Oxford Biomedical Research
Centre, University of Oxford, Oxford, United Kingdom.
(76)Department of Clinical Genetics, Erasmus University Medical Center,
Rotterdam, the Netherlands.
(77)Laboratory of Cancer Genetics and Tumor Biology, Department of Clinical
Chemistry, University of Oulu, Oulu, Finland. Laboratory of Cancer Genetics and
Tumor Biology, Northern Finland Laboratory Centre NordLab, Oulu, Finland.
(78)Breast Cancer Research Unit, Cancer Research Institute, University Malaya
Medical Centre, Kuala Lumpur, Malaysia.
(79)Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain.
(80)Shanghai Municipal Center for Disease Control and Prevention, Shanghai, PR
China.
(81)Centre for Cancer Genetic Epidemiology, Department of Public Health and
Primary Care, University of Cambridge, Cambridge, United Kingdom. Centre for
Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge,
Cambridge, United Kingdom.
(82)Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology
Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of
Medicine, Nashville, Tennessee. [email protected]. IHC4 and PAM50 assays have been shown to provide additional prognostic
information for patients with early breast cancer. We evaluated whether
incorporating TP53 mutation analysis can further enhance their prognostic
accuracy. We examined TP53 mutation and the IHC4 score in tumors of 605 patients
diagnosed with stage I-III breast cancer at National Taiwan University Hospital
(the NTUH cohort). We obtained information regarding TP53 mutation and PAM50
subtypes in 699 tumors from the Molecular Taxonomy of Breast Cancer
International Consortium (METABRIC) cohort. We found that TP53 mutation was
significantly associated with high-risk IHC4 group and with luminal B,
HER2-enriched, and basal-like subtypes. Despite the strong associations, TP53
mutation independently predicted shorter relapse-free survival (hazard ratio
[HR] = 1.63, P = 0.007) in the NTUH cohort and shorter breast cancer-specific
survival (HR = 2.35, P = <0.001) in the METABRIC cohort. TP53 mutational
analysis added significant prognostic information in addition to the IHC4 score
(∆ LR-χ(2) = 8.61, P = 0.002) in the NTUH cohort and the PAM50 subtypes (∆
LR-χ(2) = 18.9, P = <0.001) in the METABRIC cohort. We conclude that
incorporating TP53 mutation analysis can enhance the prognostic accuracy of the
IHC4 and PAM50 assays. BACKGROUND: Multi-gene lists and single sample predictor models have been
currently used to reduce the multidimensional complexity of breast cancers, and
to identify intrinsic subtypes. The perceived inability of some models to deal
with the challenges of processing high-dimensional data, however, limits the
accurate characterisation of these subtypes. Towards the development of robust
strategies, we designed an iterative approach to consistently discriminate
intrinsic subtypes and improve class prediction in the METABRIC dataset.
FINDINGS: In this study, we employed the CM1 score to identify the most
discriminative probes for each group, and an ensemble learning technique to
assess the ability of these probes on assigning subtype labels using 24
different classifiers. Our analysis is comprised of an iterative computation of
these methods and statistical measures performed on a set of over 2000 samples.
The refined labels assigned using this iterative approach revealed to be more
consistent and in better agreement with clinicopathological markers and
patients' overall survival than those originally provided by the PAM50 method.
CONCLUSIONS: The assignment of intrinsic subtypes has a significant impact in
translational research for both understanding and managing breast cancer. The
refined labelling, therefore, provides more accurate and reliable information by
improving the source of fundamental science prior to clinical applications in
medicine. A major roadblock in the effective treatment of cancers is their heterogeneity,
whereby multiple molecular landscapes are classified as a single disease. To
explore the contribution of cellular metabolism to cancer heterogeneity, we
analyse the Metabric dataset, a landmark genomic and transcriptomic study of
2,000 individual breast tumours, in the context of the human genome-scale
metabolic network. We create personalized metabolic landscapes for each tumour
by exploring sets of active reactions that satisfy constraints derived from
human biochemistry and maximize congruency with the Metabric transcriptome data.
Classification of the personalized landscapes derived from 997 tumour samples
within the Metabric discovery dataset reveals a novel poor prognosis cluster,
reproducible in the 995-sample validation dataset. We experimentally follow
mechanistic hypotheses resulting from the computational study and establish that
active serotonin production is a major metabolic feature of the poor prognosis
group. These data support the reconsideration of concomitant serotonin-specific
uptake inhibitors treatment during breast cancer chemotherapy. BACKGROUND: Proliferation markers and profiles have been recommended for guiding
the choice of systemic treatments for breast cancer. However, the best molecular
marker or test to use has not yet been identified. We did this study to identify
factors that drive proliferation and its associated features in breast cancer
and assess their association with clinical outcomes and response to
chemotherapy.
METHODS: We applied an artificial neural network-based integrative data mining
approach to data from three cohorts of patients with breast cancer (the
Nottingham discovery cohort (n=171), Uppsala cohort (n=249), and Molecular
Taxonomy of Breast Cancer International Consortium [METABRIC] cohort; n=1980).
We then identified the genes with the most effect on other genes in the
resulting interactome map. Sperm-associated antigen 5 (SPAG5) featured
prominently in our interactome map of proliferation and we chose to take it
forward in our analysis on the basis of its fundamental role in the function and
dynamic regulation of mitotic spindles, mitotic progression, and chromosome
segregation fidelity. We investigated the clinicopathological relevance of SPAG5
gene copy number aberrations, mRNA transcript expression, and protein expression
and analysed the associations of SPAG5 copy number aberrations, transcript
expression, and protein expression with breast cancer-specific survival,
disease-free survival, distant relapse-free survival, pathological complete
response, and residual cancer burden in the Nottingham discovery cohort, Uppsala
cohort, METABRIC cohort, a pooled untreated lymph node-negative cohort (n=684),
a multicentre combined cohort (n=5439), the Nottingham historical early stage
breast cancer cohort (Nottingham-HES; n=1650), Nottingham early stage oestrogen
receptor-negative breast cancer adjuvant chemotherapy cohort
(Nottingham-oestrogen receptor-negative-ACT; n=697), the Nottingham
anthracycline neoadjuvant chemotherapy cohort (Nottingham-NeoACT; n=200), the MD
Anderson taxane plus anthracycline-based neoadjuvant chemotherapy cohort (MD
Anderson-NeoACT; n=508), and the multicentre phase 2 neoadjuvant clinical trial
cohort (phase 2 NeoACT; NCT00455533; n=253).
FINDINGS: In the METABRIC cohort, we detected SPAG5 gene gain or amplification
at the Ch17q11.2 locus in 206 (10%) of 1980 patients overall, 46 (19%) of 237
patients with a PAM50-HER2 phenotype, and 87 (18%) of 488 patients with
PAM50-LumB phenotype. Copy number aberration leading to SPAG5 gain or
amplification and high SPAG5 transcript and SPAG5 protein concentrations were
associated with shorter overall breast cancer-specific survival (METABRIC cohort
[copy number aberration]: hazard ratio [HR] 1·50, 95% CI 1·18-1·92, p=0·00010;
METABRIC cohort [transcript]: 1·68, 1·40-2·01, p<0·0001; and
Nottingham-HES-breast cancer cohort [protein]: 1·68, 1·32-2·12, p<0·0001). In
multivariable analysis, high SPAG5 transcript and SPAG5 protein expression were
associated with reduced breast cancer-specific survival at 10 years compared
with lower concentrations (Uppsala: HR 1·62, 95% CI 1·03-2·53, p=0·036;
METABRIC: 1·27, 1·02-1·58, p=0·034; untreated lymph node-negative cohort: 2·34,
1·24-4·42, p=0·0090; and Nottingham-HES: 1·73, 1·23-2·46, p=0·0020). In patients
with oestrogen receptor-negative breast cancer with high SPAG5 protein
expression, anthracycline-based adjuvant chemotherapy increased breast
cancer-specific survival overall compared with that for patients who did not
receive chemotherapy (Nottingham-oestrogen receptor-negative-ACT cohort: HR
0·37, 95% CI 0·20-0·60, p=0·0010). Multivariable analysis showed high SPAG5
transcript concentrations to be independently associated with longer distant
relapse-free survival after receiving taxane plus anthracycline neoadjuvant
chemotherapy (MD Anderson-NeoACT: HR 0·68, 95% CI 0·48-0·97, p=0·031). In
multivariable analysis, both high SPAG5 transcript and high SPAG5 protein
concentrations were independent predictors for a higher proportion of patients
achieving a pathological complete response after combination cytotoxic
chemotherapy (MD Anderson-NeoACT: OR 1·71, 95% CI, 1·07-2·74, p=0·024;
Nottingham-ACT: 8·75, 2·42-31·62, p=0·0010).
INTERPRETATION: SPAG5 is a novel amplified gene on Ch17q11.2 in breast cancer.
The transcript and protein products of SPAG5 are independent prognostic and
predictive biomarkers that might have clinical utility as biomarkers for
combination cytotoxic chemotherapy sensitivity, especially in oestrogen
receptor-negative breast cancer.
FUNDING: Nottingham Hospitals Charity and the John and Lucille van Geest
Foundation. BACKGROUND: Most patients with early stage triple negative breast cancer (TNBC)
receive adjuvant chemotherapy. Activation of the immune system is associated
with tumor response and may help identify TNBC with favorable outcome.
METHODS: Gene expression data were obtained from the GEO Dataset
GDS2250/GSE3744. Affymetrix CEL files were downloaded and analyzed with
Affymetrix Transcriptome Analysis Console 3.0. Functional genomics was
implemented with David Bioinformatics Resources 6.8. Data contained at Oncomine
were used to identify genes upregulated in basal-like cancer compared to normal
breast tissue. Data contained at cBioportal were used to assess for molecular
alterations. The KMPlotter online tool, METABRIC and GSE25066 datasets were used
to associate gene signatures with clinical outcome.
RESULTS: 1564 upregulated genes were identified as differentially expressed
between normal and basal-like tumors. Of these, 16 genes associated with immune
function were linked with clinical outcome. HLA-C, HLA-F, HLA-G and TIGIT were
associated with both improved relapse-free survival (RFS) and overall survival
(OS). The combination of HLA-F/TIGIT and HLA-C/HLA-F/TIGIT showed the most
favorable outcome (HR for RFS 0.44, p<0.001; HR for OS 0.22, p<0.001; and HR for
RFS 0.46, p<0.001; HR for OS 0.15, p<0.001; respectively). The association of
HLA-C/HLA-F with outcome was confirmed using the METABRIC and GSE25066 datasets.
No copy number alterations of these genes were identified.
CONCLUSION: We describe a gene signature associated with immune function and
favorable outcome in basal-like breast cancer. Incorporation of this signature
in prospective studies may help to stratify risk of early stage TNBC. Genomic aberrations and gene expression-defined subtypes in the large METABRIC
patient cohort have been used to stratify and predict survival. The present
study used normalized gene expression signatures of paclitaxel drug response to
predict outcome for different survival times in METABRIC patients receiving
hormone (HT) and, in some cases, chemotherapy (CT) agents. This machine learning
method, which distinguishes sensitivity vs. resistance in breast cancer cell
lines and validates predictions in patients; was also used to derive gene
signatures of other HT (tamoxifen) and CT agents (methotrexate, epirubicin,
doxorubicin, and 5-fluorouracil) used in METABRIC. Paclitaxel gene signatures
exhibited the best performance, however the other agents also predicted survival
with acceptable accuracies. A support vector machine (SVM) model of paclitaxel
response containing genes ABCB1, ABCB11, ABCC1, ABCC10, BAD, BBC3, BCL2,
BCL2L1, BMF, CYP2C8, CYP3A4, MAP2, MAP4, MAPT, NR1I2, SLCO1B3, TUBB1, TUBB4A,
and TUBB4B was 78.6% accurate in predicting survival of 84 patients treated with
both HT and CT (median survival ≥ 4.4 yr). Accuracy was lower (73.4%) in 304
untreated patients. The performance of other machine learning approaches was
also evaluated at different survival thresholds. Minimum redundancy maximum
relevance feature selection of a paclitaxel-based SVM classifier based on
expression of genes BCL2L1, BBC3, FGF2, FN1, and TWIST1 was 81.1% accurate in
53 CT patients. In addition, a random forest (RF) classifier using a gene
signature ( ABCB1, ABCB11, ABCC1, ABCC10, BAD, BBC3, BCL2, BCL2L1, BMF, CYP2C8,
CYP3A4, MAP2, MAP4, MAPT, NR1I2,SLCO1B3, TUBB1, TUBB4A, and TUBB4B) predicted
>3-year survival with 85.5% accuracy in 420 HT patients. A similar RF gene
signature showed 82.7% accuracy in 504 patients treated with CT and/or HT. These
results suggest that tumor gene expression signatures refined by machine
learning techniques can be useful for predicting survival after drug therapies. The integration of genomic and transcriptomic profiles of 2000 breast tumours
from the METABRIC [Molecular Taxonomy of Breast Cancer International Consortium]
cohort revealed ten subtypes, termed integrative clusters (IntClust/s),
characterised by distinct genomic drivers. Central histopathology (N = 1643)
review was undertaken to explore the relationship between these ten molecular
subtypes and traditional clinicopathological features. IntClust subtypes were
significantly associated with histological type, tumour grade, receptor status,
and lymphocytic infiltration (p < 0.0001). Lymph node status and Nottingham
Prognostic Index [NPI] categories were also significantly associated with
IntClust subtype. IntClust 3 was enriched for tubular and lobular carcinomas,
the latter largely accounting for the association with CDH1 mutations in this
cluster. Mucinous carcinomas were not present in IntClusts 5 or 10, but did not
show an association with any of the remaining IntClusts. In contrast,
medullary-like cancers were associated with IntClust 10 (15/26). Hormone
receptor-positive tumours were scattered across all IntClusts. IntClust 5 was
dominated by HER2 positivity (127/151), including both hormone receptor-positive
(60/72) and hormone receptor-negative tumours (67/77). Triple-negative tumours
comprised the majority of IntClust 10 (132/159) and around a quarter of IntClust
4 (52/217). Whilst the ten IntClust subtypes of breast cancer show
characteristic patterns of association with traditional clinicopathological
variables, no IntClust can be adequately identified by these variables alone.
Hence, the addition of genomic stratification has the potential to enhance the
biological relevance of the current clinical evaluation and facilitate
genome-guided therapeutic strategies. INTRODUCTION: Early stage estrogen receptor (ER)-positive breast cancer may be
treated with chemotherapy in addition to hormone therapy. Currently available
molecular signatures assess the risk of recurrence and the benefit of
chemotherapy; however, these tests may have large intermediate risk groups,
limiting their usefulness.
METHODS: The EarlyR prognostic score was developed using integrative analysis of
microarray data sets and formalin-fixed, paraffin-embedded-based quantitative
real-time PCR assay and validated in Affymetrix data sets and METABRIC cohort
using Cox proportional hazards models and Kaplan-Meier survival analysis.
Concordance index was used to measure the probability of prognostic score
agreement with outcome.
RESULTS: The EarlyR score and categorical risk strata (EarlyR-Low, EarlyR-Int,
EarlyR-High) derived from expression of ESPL1, MKI67, SPAG5, PLK1 and PGR was
prognostic of 8-year distant recurrence-free interval in Affymetrix (categorical
P = 3.5 × 10-14; continuous P = 8.8 × 10-15) and METABRIC (categorical P < 2.2 ×
10-16; continuous P < 10-16) data sets of ER+ breast cancer. Similar results
were observed for the breast cancer-free interval end point. At most 13% of
patients were intermediate risk and at least 66% patients were low risk in both
ER+ cohorts. The EarlyR score was significantly prognostic (distant
recurrence-free interval; P < .001) in both lymph node-negative and lymph
node-positive patients and was independent from clinical factors. EarlyR and
surrogates of current molecular signatures were comparable in prognostic
significance by concordance index.
CONCLUSION: The 5-gene EarlyR score is a robust prognostic assay that identified
significantly fewer patients as intermediate risk and more as low risk than
currently available assays. Further validation of the assay in clinical
trial-derived cohorts is ongoing. Author information:
(1)McDonnell Genome Institute, Washington University School of Medicine, St.
Louis, 63108, MO, USA.
(2)Department of Medicine, Division of Oncology, Washington University School of
Medicine, St. Louis, 63110, MO, USA.
(3)Siteman Cancer Center, Washington University School of Medicine, St. Louis,
63110, MO, USA.
(4)Department of Genetics, Washington University School of Medicine, St. Louis,
63110, MO, USA.
(5)Lester and Sue Smith Breast Center and Dan L. Duncan Cancer Center, Baylor
College of Medicine, Houston, 77030, TX, USA.
(6)Departments of Medicine and Molecular and Cellular Biology, Baylor College of
Medicine, Houston, 77030, TX, USA.
(7)Division of Biostatistics, Washington University School of Medicine, St.
Louis, 63110, MO, USA.
(8)Genetic Pathology Evaluation Centre, University of British Columbia,
Vancouver, V6H 3Z6, Canada.
(9)Institute of Cancer Research, London, SM2 5NG, UK.
(10)Nationwide Children's Hospital and Department of Pediatrics, The Ohio State
University College of Medicine, Columbus, 43205, OH, USA.
(11)McDonnell Genome Institute, Washington University School of Medicine, St.
Louis, 63108, MO, USA. [email protected].
(12)Siteman Cancer Center, Washington University School of Medicine, St. Louis,
63110, MO, USA. [email protected].
(13)Department of Genetics, Washington University School of Medicine, St. Louis,
63110, MO, USA. [email protected].
(14)Nationwide Children's Hospital and Department of Pediatrics, The Ohio State
University College of Medicine, Columbus, 43205, OH, USA.
[email protected].
(15)Lester and Sue Smith Breast Center and Dan L. Duncan Cancer Center, Baylor
College of Medicine, Houston, 77030, TX, USA. [email protected].
(16)Departments of Medicine and Molecular and Cellular Biology, Baylor College
of Medicine, Houston, 77030, TX, USA. [email protected]. |
Name 3 diseases for which lucatumumab is being tested? | Lucatumumab is being tested as treatment for malignancies such as chronic lymphatic leukemia (CLL), Multiple Myeloma (MM), and non-Hodgkin's lymphoma (NHL). | The costimulatory molecule CD40 is a member of the tumor necrosis factor (TNF)
receptor superfamily and is expressed on various antigen presenting cells (APCs)
as well as some tumor cells. The binding to the natural ligand CD40L, which is
expressed on T helper cells, leads to APC activation and thus enhancement of
immune responses. Treatment with anti-CD40 monoclonal antibodies has been
exploited in several cancer immunotherapy studies in mice and led to the
development of anti-CD40 antibodies for clinical use. Here, Dacetuzumab and
Lucatumumab are in the most advanced stage and are being tested as treatment for
maligcies such as chronic lymphatic leukemia (CLL), Multiple Myeloma (MM),
and non-Hodgkin's lymphoma (NHL). The promising results from these early
clinical trials have encouraged clinical drug development in order to
investigate the effect of CD40 mAbs in combination with other cancer
immunotherapies, in particular interleukin (IL)-2. An in-depth analysis of this
immunotherapy is provided elsewhere. In the present review, we provide an update
of the most recent clinical trials with anti-CD40 antibodies. We present and
discuss recent and ongoing clinical trials in this field, including clinical
studies which combine anti-CD40 treatment with other cancer-treatments, such as
Rituximab and Tremelimumab. |
Which transcription factor binding site is contained in Alu repeats? | A novel abundant NF-κB-binding site resides in specialized Alu-repetitive elements having the potential for long range transcription regulation, thus suggesting that in addition to its known role, NF-κB has a primate-specific function and a role in human evolution. | The transcription factor NF-κB is a critical regulator of immune responses. To
determine how NF-κB builds transcriptional control networks, we need to obtain a
topographic map of the factor bound to the genome and correlate it with global
gene expression. We used a ChIP cloning technique and identified novel NF-κB
target genes in response to virus infection. We discovered that most of the
NF-κB-bound genomic sites deviate from the consensus and are located away from
conventional promoter regions. Remarkably, we identified a novel abundant
NF-κB-binding site residing in specialized Alu-repetitive elements having the
potential for long range transcription regulation, thus suggesting that in
addition to its known role, NF-κB has a primate-specific function and a role in
human evolution. By combining these data with global gene expression profiling
of virus-infected cells, we found that most of the sites bound by NF-κB in the
human genome do not correlate with changes in gene expression of the nearby
genes and they do not appear to function in the context of synthetic promoters.
These results demonstrate that repetitive elements interspersed in the human
genome function as common target sites for transcription factors and may play an
important role in expanding the repertoire of binding sites to engage new genes
into regulatory networks. Using nuclear factor-κB (NF-κB) ChIP-Seq data, we present a framework for
iterative learning of regulatory networks. For every possible transcription
factor-binding site (TFBS)-putatively regulated gene pair, the relative distance
and orientation are calculated to learn which TFBSs are most likely to regulate
a given gene. Weighted TFBS contributions to putative gene regulation are
integrated to derive an NF-κB gene network. A de novo motif enrichment analysis
uncovers secondary TFBSs (AP1, SP1) at characteristic distances from NF-κB/RelA
TFBSs. Comparison with experimental ENCODE ChIP-Seq data indicates that
experimental TFBSs highly correlate with predicted sites. We observe that
RelA-SP1-enriched promoters have distinct expression profiles from that of
RelA-AP1 and are enriched in introns, CpG islands and DNase accessible sites.
Sixteen novel NF-κB/RelA-regulated genes and TFBSs were experimentally
validated, including TANK, a negative feedback gene whose expression is
NF-κB/RelA dependent and requires a functional interaction with the AP1 TFBSs.
Our probabilistic method yields more accurate NF-κB/RelA-regulated networks than
a traditional, distance-based approach, confirmed by both analysis of gene
expression and increased informativity of Genome Ontology annotations. Our
analysis provides new insights into how co-occurring TFBSs and local chromatin
context orchestrate activation of NF-κB/RelA sub-pathways differing in
biological function and temporal expression patterns. |
What is ferroptosis? | Ferroptosis is a newly defined iron-dependent, non-apoptotic mode of cell death with necrotic morphology. Ferroptosis is a new mode of regulated cell death, which is completely distinct from other cell death modes based on morphological, biochemical, and genetic criteria. Ferroptosis is a form of oxidative cell death and has become a chemotherapeutic target for cancer treatment | PURPOSE: Ferroptosis is a new mode of regulated cell death, which is completely
distinct from other cell death modes based on morphological, biochemical, and
genetic criteria. This study evaluated the therapeutic role of ferroptosis in
classic chemotherapy drugs, including the underlying mechanism.
MATERIALS AND METHODS: Cell viabilitywas detected by using the
methylthiazoltetrazlium dye uptake method. RNAiwas used to knockout
iron-responsive element binding protein 2, and polymerase chain reaction,
western blot was used to evaluate the efficiency. Intracellular reduced
glutathione level and glutathione peroxidases activitywere determined by related
assay kit. Intracellularreactive oxygen species levelswere determined by
flowcytometry. Electron microscopywas used to observe ultrastructure changes in
cell.
RESULTS: Among five chemotherapeutic drugs screened in this study, cisplatin was
found to be an inducer for both ferroptosis and apoptosis in A549 and HCT116
cells. The depletion of reduced glutathione caused by cisplatin and the
inactivation of glutathione peroxidase played the vital role in the underlying
mechanism. Besides, combination therapy of cisplatin and erastin showed
significant synergistic effect on their anti-tumor activity.
CONCLUSION: Ferroptosis had great potential to become a new approach in
anti-tumor therapies and make up for some classic drugs, which open up a new way
for their utility in clinic. Ferroptosis is an iron-dependent form of regulated nonapoptotic cell death,
which contributes to damage in models of acute kidney injury (AKI). Heme
oxygenase-1 (HO-1) is a cytoprotective enzyme induced in response to cellular
stress, and is protective against AKI because of its antiapoptotic and
anti-inflammatory properties. However, the role of HO-1 in regulating
ferroptosis is unclear. The purpose of this study was to elucidate the role of
HO-1 in regulating ferroptotic cell death in renal proximal tubule cells (PTCs).
Immortalized PTCs obtained from HO-1+/+ and HO-1-/- mice were treated with
erastin or RSL3, ferroptosis inducers, in the presence or absence of
antioxidants, an iron source, or an iron chelator. Cells were assessed for
changes in morphology and metabolic activity as an indicator of cell viability.
Treatment of HO-1+/+ PTCs with erastin resulted in a time- and dose-dependent
increase in HO-1 gene expression and protein levels compared with
vehicle-treated controls. HO-1-/- cells showed increased dose-dependent erastin-
or RSL3-induced cell death in comparison to HO-1+/+ PTCs. Iron supplementation
with ferric ammonium citrate in erastin-treated cells decreased cell viability
further in HO-1-/- PTCs compared with HO-1+/+ cells. Cotreatment with
ferrostatin-1 (ferroptosis inhibitor), deferoxamine (iron chelator), or
N-acetyl-l-cysteine (glutathione replenisher) significantly increased cell
viability and attenuated erastin-induced ferroptosis in both HO-1+/+ and HO-1-/-
PTCs. These results demonstrate an important antiferroptotic role of HO-1 in
renal epithelial cells. Clinical studies have suggested that myocardial iron is a risk factor for left
ventricular remodeling in patients after myocardial infarction. Ferroptosis has
recently been reported as a mechanism of iron-dependent nonapoptotic cell death.
However, ferroptosis in the heart is not well understood. Mechanistic target of
rapamycin (mTOR) protects the heart against pathological stimuli such as
ischemia. To define the role of cardiac mTOR on cell survival in iron-mediated
cell death, we examined cardiomyocyte (CM) cell viability under excess iron and
ferroptosis conditions. Adult mouse CMs were isolated from cardiac-specific mTOR
transgenic mice, cardiac-specific mTOR knockout mice, or control mice. CMs were
treated with ferric iron [Fe(III)]-citrate, erastin, a class 1 ferroptosis
inducer, or Ras-selective lethal 3 (RSL3), a class 2 ferroptosis inducer.
Live/dead cell viability assays revealed that Fe(III)-citrate, erastin, and RSL3
induced cell death. Cotreatment with ferrostatin-1, a ferroptosis inhibitor,
inhibited cell death in all conditions. mTOR overexpression suppressed
Fe(III)-citrate, erastin, and RSL3-induced cell death, whereas mTOR deletion
exaggerated cell death in these conditions. 2',7'-Dichlorodihydrofluorescein
diacetate measurement of reactive oxygen species (ROS) production showed that
erastin-induced ROS production was significantly lower in mTOR transgenic versus
control CMs. These findings suggest that ferroptosis is a significant type of
cell death in CMs and that mTOR plays an important role in protecting CMs
against excess iron and ferroptosis, at least in part, by regulating ROS
production. Understanding the effects of mTOR in preventing iron-mediated cell
death will provide a new therapy for patients with myocardial infarction. NEW &
NOTEWORTHY Ferroptosis has recently been reported as a new form of
iron-dependent nonapoptotic cell death. However, ferroptosis in the heart is not
well characterized. Using cultured adult mouse cardiomyocytes, we demonstrated
that the mechanistic target of rapamycin plays an important role in protecting
cardiomyocytes against excess iron and ferroptosis. Ferroptosis is a newly defined iron-dependent, non-apoptotic mode of cell death
with necrotic morphology. Distinctive from other death mechanisms, ferroptosis
requires cellular iron and lipid peroxides, and is dictated by specific cellular
metabolic processes. Importantly, ferroptosis has been implicated in a plethora
of human diseases. This paper reviews the recent advances and outstanding
questions of the field by focusing on the role of cellular metabolism in
ferroptosis. The relevance of ferroptosis to disease and therapy is also
discussed. Ferroptosis is a form of oxidative cell death and has become a chemotherapeutic
target for cancer treatment. BAY 11-7085 (BAY), which is a well-known IκBα
inhibitor, suppressed viability in cancer cells via induction of ferroptotic
death in an NF-κB-independent manner. Reactive oxygen species scavenging, relief
of lipid peroxidation, replenishment of glutathione and thiol-containing agents,
as well as iron chelation, rescued BAY-induced cell death. BAY upregulated a
variety of Nrf2 target genes related to redox regulation, particularly heme
oxygenase-1 (HO-1). Studies with specific inhibitors and shRNA interventions
suggested that the hierarchy of induction is Nrf2-SLC7A11-HO-1. SLC7A11
inhibition by erastin, sulfasalazine, or shRNA interference sensitizes
BAY-induced cell death. Overexperession of SLC7A11 attenuated BAY-inhibited cell
viability. The ferroptotic process induced by hHO-1 overexpression further
indicated that HO-1 is a key mediator of BAY-induced ferroptosis that operates
through cellular redox regulation and iron accumulation. BAY causes
compartmentalization of HO-1 into the nucleus and mitochondrion, and followed
mitochondrial dysfunctions, leading to lysosome targeting for mitophagy. In this
study, we first discovered that BAY induced ferroptosis via Nrf2-SLC7A11-HO-1
pathway and HO-1 is a key mediator by responding to the cellular redox status. |
What disease is treated with Laparoscopic Heller Myotomy (LHM)? | To compare the outcome of per oral endoscopic myotomy (POEM) and laparoscopic Heller myotomy (LHM) for the treatment of esophageal achalasia | BACKGROUND AND AIM: This retrospective cohort study compared clinical outcomes
and quality of life after peroral endoscopic myotomy (POEM) against laparoscopic
Heller myotomy (LHM) for treatment of achalasia.
METHODS: Patient demographics, operation time, intraoperative blood loss,
hospital stay, time to resume diet and analgesic requirement were recorded.
Clinical outcomes including recurrence of dysphagia, need for reintervention,
and occurrence of gastroesophageal reflux disease (GERD) were recorded.
RESULTS: From 2001 to 2014, 33 patients underwent POEM whereas 23 patients
received LHM. Patients LHM had with longer mean operative time (P = 0.02), more
blood loss (P = 0.001) and higher requirement for analgesics (P = 0.009) than
those treated by POEM. Hospital stay and time to resume diet were similar. Both
POEM and LHM achieved similar dysphagia scores at postoperative 4 weeks, 3
months and 6 months. Twenty-six percent of LHM patients and 15.2% of POEM
patients sustained gastroesophageal reflux disease (GERD) after treatment
(P = 0.311). Six patients required regular proton pump inhibitor three after
POEM and three after LHM (P = 0.639). Thirteen percent of LHM patients sustained
recurrent dysphagia and one required reintervention. There was no recurrence in
the POEM group. Follow-up duration (mean [SD]) for the LHM group was
significantly longer (60 [42] months vs 6 [4] months; P = 0.001). There was also
no difference in all four aspects of GERD-related quality of life outcomes.
CONCLUSION: Compared to LHM, POEM achieved shorter operative time, less blood
loss and pain. POEM is comparable to LHM for treatment of achalasia with similar
incidence of GERD after the procedure. BACKGROUND AND STUDY AIMS: Type III achalasia is characterized by rapidly
propagating pressurization attributable to spastic contractions. Although
laparoscopic Heller myotomy (LHM) is the current gold standard management for
type III achalasia, peroral endoscopic myotomy (POEM) is conceivably superior
because it allows for a longer myotomy. Our aims were to compare the efficacy
and safety of POEM with LHM for type III achalasia patients.
PATIENTS AND METHODS: A retrospective study of 49 patients who underwent POEM
for type III achalasia across eight centers were compared to 26 patients who
underwent LHM at a single institution. Procedural data were abstracted and pre-
and post-procedural symptoms were recorded. Clinical response was defined by
improvement of symptoms and decrease in Eckardt stage to ≤ 1. Secondary outcomes
included length of myotomy, procedure duration, length of hospital stay, and
rate of adverse events.
RESULTS: Clinical response was significantly more frequent in the POEM cohort
(98.0 % vs 80.8 %; P = 0.01). POEM patients had significantly shorter mean
procedure time than LHM patients (102 min vs 264 min; P < 0.01) despite longer
length of myotomy (16 cm vs 8 cm; P < 0.01). There was no significant difference
between POEM and LHM in the length of hospital stay (3.3 days vs 3.2 days;
P = 0.68), respectively. Rate of adverse events was significantly less in the
POEM group (6 % vs 27 %; P < 0.01).
CONCLUSIONS: POEM allows for a longer myotomy than LHM, which may result in
improved clinical outcomes. POEM appears to be an effective and safe alternative
to LHM in patients with type III achalasia. INTRODUCTION: Per-oral endoscopic myotomy (POEM) is a less invasive therapy for
achalasia with a shorter hospitalization but with similar short- and long-term
outcomes as a laparoscopic Heller myotomy (LHM). Previous literature comparing
POEM to LHM has focused primarily on postoperative outcome parameters such as
complications, dysphagia scores and gastro-esophageal reflux severity. This
study specifically compares postoperative pain following POEM to pain following
LHM, the current gold-standard operation.
METHODS: A retrospective review of all patients undergoing POEM or LHM for
achalasia was performed from 2006 to 2015. Data collection included
demographics, comorbidities, length of stay (LOS) and pain scores (arrival to
the recovery room, 1 h postoperative, average first 24 h and upon discharge).
Statistical analysis was performed using Student's t test and Chi-square test.
RESULTS: Forty-four POEM patients and 122 LHM patients were identified. The
average age (52.2 ± 20.75 vs 50.9 ± 17.89 years, p = 0.306) and BMI (28.1 ± 7.62
vs 27.6 ± 7.07 kg/m2, p = 0.824) did not differ between the POEM and LHM groups,
respectively; however, the American Society of Anesthesiology scores were higher
in the POEM patients (2.43 ± 0.62 vs 2.11 ± 0.71, p = 0.011). There were no
differences in rates of smoking, diabetes, cardiac disease or pulmonary disease.
The average pain scores upon arrival to the recovery room and 1 h
postoperatively were lower in the POEM group (2.3 ± 3.014 vs 3.61 ± 3 0.418,
p = 0.025 and 2.2 ± 2.579 vs 3.46 ± 3.063, p = 0.034, respectively). There was
no difference in the average pain score over the first 24 h (2.7 ± 2.067 vs
3.29 ± 1.980, p = 0.472) or at the time of discharge (1.6 ± 2.420 vs
2.09 ± 2.157, p = 0.0657) between the POEM and LHM groups. After standardizing
opioid administration against 10 mg of oral morphine, the POEM group used
significantly less narcotics that the LHM group (35.8 vs 101.8 mg, p < 0.001)
while hospitalized. The average LOS for the POEM group was 31.2 h and 55.79 for
the LHM group (p < 0.0001). At discharge, fewer POEM patients required a
prescription for a narcotic analgesic (6.81 vs 92.4 %, p < 0.0001).
CONCLUSION: POEM demonstrated significantly less postoperative pain upon arrival
to the recovery room and 1 h postoperatively. To achieve similar pain scores
during the first 24 h and at discharge, LHM patients required more narcotic
analgesic administration. Despite a significantly shorter LOS, fewer POEM
patients require a prescription for narcotic analgesics compared to LHM. POEM is
a less painful procedure for achalasia than LHM, permitting earlier hospital
discharge with little need for home narcotic use. AIMS AND OBJECTIVES: Laparoscopic Heller myotomy (LHM) is the preferred surgical
method for treating achalasia. However, peroral endoscopic myotomy (POEM) is
providing good short-term results. The objective of this systematic review and
meta-analysis was to compare the safety and efficacy of LHM and POEM.
MATERIALS AND METHODS: A search of PubMed, Cochrane database, Medline, Embase,
Science Citation Index, and current contents for English-language articles
comparing LHM and POEM between 2007 and 2016 was performed. Variables analyzed
included prior endoscopic treatment, prior medical treatment, prior Heller
myotomy, operative time, overall complications rate, postoperative
gastroesophageal reflux disease (GERD), length of hospital stay, postoperative
pain score, and long-term GERD.
RESULTS: Seven trials consisting of 483 (LHM=250, POEM=233) patients were
analyzed. Preoperative variables, for example, prior endoscopic treatment [odds
ratio (OR), 1.32; 95% confidence interval (CI), 0.23-4.61; P=0.96], prior
medical treatment [weighted mean difference (WMD), 1.22; 95% CI, 0.52-2.88;
P=0.65], and prior Heller myotomy (WMD, 0.47; 95% CI, 0.13-1.67; P=0.25) were
comparable. Operative time was 26.28 minutes, nonsignificantly longer for LHM
(WMD, 26.28; 95% CI, -11.20 to 63.70; P=0.17). There was a comparable overall
complication rate (OR, 1.25; 95% CI, 0.56-2.77; P=0.59), postoperative GERD rate
(OR, 1.27; 95% CI, 0.70-2.30; P=0.44), length of hospital stay (WMD, 0.30; 95%
CI, -0.24 to 0.85; P=0.28), postoperative pain score (WMD, -0.26; 95% CI, -1.58
to 1.06; P=0.70), and long-term GERD (WMD, 1.06; 95% CI, 0.27-4.1; P=0.08) for
both procedures. There was a significantly higher short-term clinical treatment
failure rate for LHM (OR, 9.82; 95% CI, 2.06-46.80; P<0.01).
CONCLUSIONS: POEM compares favorably to LHM for achalasia treatment in
short-term perioperative outcomes. However, there was a significantly higher
clinical treatment failure rate for LHM on short-term postoperative follow-up.
Presently long-term postoperative follow-up data for POEM beyond 1 year are
unavailable and eagerly awaited. BACKGROUND: Although laparoscopic Heller myotomy (LHM) has been the standard of
care for achalasia, per oral endoscopic myotomy (POEM) has gained popularity as
a viable alternative. This retrospective study aimed to compare patient-reported
outcomes between LHM and POEM in a consecutive series of achalasia patients with
more than 1 year of follow-up.
STUDY DESIGN: We reviewed demographic and procedure-related data for patients
who underwent either LHM or POEM for achalasia between January 2011 and May
2016. Phone interviews were conducted assessing post-procedure achalasia
symptoms via the Eckardt score and achalasia severity questionnaire (ASQ).
Demographics, disease factors, and survey results were compared between LHM and
POEM patients using univariate analysis. Significant predictors of procedure
failure were analyzed using univariate and multivariate analysis.
RESULTS: There were no serious complications in 110 consecutive patients who
underwent LHM or POEM during the study period, and 96 (87%) patients completed
phone surveys. There was a nonsignificant trend toward better patient-reported
outcomes with POEM. There were significant differences in patient
characteristics including sex, achalasia type, mean residual lower esophageal
pressure (rLESP), and follow-up time. The only univariate predictors of an
unsatisfactory Eckardt score or ASQ were longer follow-up and lower rLESP, with
follow-up length being the only predictor on multivariate analysis.
CONCLUSIONS: There were significant demographic and clinical differences in
patient selection for POEM vs LHM in our group. Although the 2 procedures have
similar patient-reported effectiveness, subjective outcomes seem to decline as a
result of time rather than procedure type. BACKGROUND AND AIMS: Peroral endoscopic myotomy (POEM) may be associated with
higher rates of gastroesophageal reflux disease (GERD) than laparoscopic
Heller's myotomy with fundoplication (LHM), since POEM is not combined with a
fundoplication. However, peri-esophageal anti-reflux barriers are preserved in
POEM, which might prevent GERD. Hence, we sought to compare the objective
esophageal pH study findings in achalasia patients after POEM and LHM.
METHODS: Achalasia patients undergoing POEM from 2014 to 2015 at our institution
were matched 1:3 with LHM patients using propensity score matching.
Demographics, prior interventions, pre-treatment and 2-month post-treatment
timed barium esophagram (TBE), high-resolution esophageal manometry (HREM) and
24-h esophageal pH study findings were compared between the two groups.
RESULTS: Thirty-one patients in the POEM group and 88 patients in the LHM group
were included. Larger proportion of POEM patients had prior interventions for
achalasia as compared to LHM patients (overall: 71% vs. 44.3%; p = 0.012).
Esophageal acid exposure was significantly higher in POEM as compared to LHM
patients (abnormal total acid exposure: 48.4% vs. 13.6%; p < 0.001, abnormal
DeMeester score 54.8% vs. 17.4%; p = 0.005 respectively). In sub-group analysis,
similar results were noted on 24-h pH study after exclusion of the POEM patients
with prior LHM and corresponding matches. There was no significant difference in
the rate of GERD symptoms between POEM and LHM. There was no significant
correlation between the post-treatment basal lower esophageal sphincter pressure
and integrated relaxation pressure with abnormal acid exposure in either POEM or
LHM.
CONCLUSIONS: In patients with achalasia, POEM leads to significantly higher
rates of abnormal esophageal acid exposure, without an increase in the rate of
GERD symptoms, when compared to LHM with fundoplication. Interestingly, prior
LHM has no impact on post-POEM pH study findings. Potential of increased
esophageal acid exposure and possible consequences should be discussed with all
patients prior to POEM. Further studies are needed to determine the long-term
effects of increased acid exposure after POEM. |
Name 4 side effects of enasidenib | Enasidenib is found to be associated with certain adverse effects like elevated bilirubin level, diarrhea, differentiation syndrome, decreased potassium and calcium levels etc. | BACKGROUND: Acute myeloid leukemia is the collective name for different types of
leukemias of myeloid origin affecting blood and bone marrow. The overproduction
of immature myeloblasts (white blood cells) is the characteristic feature of
AML, thus flooding the bone marrow and reducing its capacity to produce normal
blood cells. USFDA on August 1, 2017, approved a drug named Enasidenib formerly
known as AG-221 which is being marketed under the name Idhifa to treat R/R AML
with IDH2 mutation. The present review depicts the broad profile of enasidenib
including various aspects of chemistry, preclinical, clinical studies,
pharmacokinetics, mode of action and toxicity studies.
METHODS: Various reports and research articles have been referred to summarize
different aspects related to chemistry and pharmacokinetics of enasidenib.
Clinical data was collected from various recently published clinical reports
including clinical trial outcomes.
RESULT: The various findings of enasidenib revealed that it has been designed to
allosterically inhibit mutated IDH2 to treat R/R AML patients. It has also
presented good safety and efficacy profile along with 9.3 months overall
survival rates of patients in which disease has relapsed. The drug is still
under study either in combination or solely to treat hematological maligcies.
Molecular modeling studies revealed that enasidenib binds to its target through
hydrophobic interaction and hydrogen bonding inside the binding pocket.
Enasidenib is found to be associated with certain adverse effects like elevated
bilirubin level, diarrhea, differentiation syndrome, decreased potassium and
calcium levels, etc.
CONCLUSION: Enasidenib or AG-221was introduced by FDA as an anticancer agent
which was developed as a first in class, a selective allosteric inhibitor of the
tumor target i.e. IDH2 for Relapsed or Refractory AML. Phase 1/2 clinical trial
of Enasidenib resulted in the overall survival rate of 40.3% with CR of 19.3%.
Phase III trial on the Enasidenib is still under process along with another
trial to test its potency against other cell lines. Edasidenib is associated
with certain adverse effects, which can be reduced by investigators by designing
its newer derivatives on the basis of SAR studies. Hence, it may come in the
light as a potent lead entity for anticancer treatment in the coming years. |
Is lucatumumab a polyclonal antibody? | No, lucatumumab is a a monoclonal antibody against CD40. | In this open-label, multicentre, phase 1 study a fully human anti-CD40
antagonist monoclonal antibody, lucatumumab, was evaluated in patients with
relapsed/refractory multiple myeloma (MM). The primary objective was to
determine the maximum tolerated dose (MTD) based on dose-limiting toxicities
(DLTs). Secondary objectives included safety, pharmacokinetics, pharmacodynamics
and antimyeloma activity. Twenty-eight patients, enrolled using a standard
'3 + 3' dose escalation, received one or two (n = 3) cycles of lucatumumab 1·0,
3·0, 4·5 or 6·0 mg/kg once weekly for 4 weeks. Common lucatumumab-related
adverse events were reversible, mild-to-moderate infusion reactions. Severe
adverse events were anaemia, chills, hypercalcaemia and pyrexia (7% each). DLTs
included grade 4 thrombocytopenia, grade 3 increased alanine aminotransferase
and grade 4 increased lipase (n = 1 each). The MTD was 4·5 mg/kg. At doses
≥3·0 mg/kg, sustained receptor occupancy (≥87%), observed throughout weekly
infusions up to 5 weeks after the last infusion, correlated with an estimated
half-life of 4-19 d. Twelve patients (43%) had stable disease, and one patient
(4%) maintained a partial response for ≥8 months. These findings indicate that
single-agent lucatumumab was well tolerated up to 4·5 mg/kg with modest clinical
activity in relapsed/refractory MM, warranting further study as a combination
therapy. |
What is evaluated with the SAD PERSONS scale? | SAD PERSONS scale was developed to evaluate suicide risk. | BACKGROUND: Prior studies on the association between sleep disturbances and
suicidal behavior did not explore whether or not short sleep is a marker of
suicide intent, lethality or risk.
DESIGN: Cross-sectional.
PARTICIPANTS: Suicide attempters (SAs) (n=434). Controls included 83 psychiatric
inpatients who have never been SAs, and 509 healthy controls.
MEASUREMENTS: Short sleep was defined by self-assessment as ≤ 5 h per day. The
MINI and the DSM-IV version of the International Personality Disorder
Examination Screening Questionnaire were used to diagnose Axis I and Axis II
diagnoses, respectively. Suicide intent and lethality were evaluated through the
Beck's Suicidal Intent Scale (SIS) and the Risk-Rescue Rating Scale (RRRS),
respectively. Beck's Medical Lethality Scale (BMLS) was administered to assess
the degree of medical injury, and the SAD PERSONS mnemonic scale was used to
evaluate suicide risk.
STATISTICAL ANALYSES: Chi-square tests and logistic regression analyses explored
frequencies of short sleep in 3 samples. Chi-square tests explored whether or
not suicide intent, lethality and risk were greater in SAs with short-sleep
versus those without short-sleep.
RESULTS: Short sleep was more prevalent in SAs than in psychiatric controls only
in males. In female SAs, short sleep was significantly associated with several
SIS items and high scores in the SAD PERSONS.
LIMITATIONS: Sleep duration was assessed only by self-report.
CONCLUSIONS: The association between short sleep and suicidal behavior may be
partly explained by confounders. Short sleep may be a marker of severity of
suicidal behavior among female SAs. BACKGROUND: Past and repeated self-harm are long-term risks to completed
suicide. A brief rating scale to assess repetition risk of self-harm is
important for high-risk identification and early interventions in suicide
prevention. The study aimed to examine the validity of the Chinese SAD PERSONS
Scale (CSPS) and to evaluate its feasibility in clinical settings.
METHODS: One hundred and forty-seven patients with self-harm were recruited from
the Emergency Department and assessed at baseline and the sixth month. The
controls, 284 people without self-harm from the Family Medicine Department in
the same hospital were recruited and assessed concurrently. The psychometric
properties of the CSPS were examined using baseline and follow-up measurements
that assessed a variety of suicide risk factors. Clinical feasibility and
applicability of the CSPS were further evaluated by a group of general nurses
who used case vignette approach in CSPS risk assessment in clinical settings. An
open-ended question inquiring their opinions of scale adaptation to hospital
inpatient assessment for suicide risks were also analyzed using content
analysis.
RESULTS: The CSPS was significantly correlated with other scales measuring
depression, hopelessness and suicide ideation. A cut-off point of the scale was
at 4/5 in predicting 6-month self-harm repetition with the sensitivity and
specificity being 65.4% and 58.1%, respectively. Based on the areas under the
Receiver Operating Characteristic curves, the predictive validity of the scale
showed a better performance than the other scales. Fifty-four nurses, evaluating
the scale using case vignette found it a useful tool to raise the awareness of
suicide risk and a considerable tool to be adopted into nursing care.
CONCLUSIONS: The Chinese SAD PERSONS Scale is a brief instrument with acceptable
psychometric properties for self-harm prediction. However, cautions should be
paid to level of therapeutic relationships during assessment, staff workload and
adequate training for wider clinical applications. OBJECTIVES: The goal of this study was to evaluate the relationship between
various suicide screening tools and clinical impression with subsequent patient
psychiatric admission and near-term adverse emergency department (ED) events.
METHODS: We performed a prospective observational study of 50 patients with
suicidal ideation in the ED. Subjects completed a series of depression/suicide
screening tools: the Columbia Suicide Severity Scale, SAD PERSONS scale, Patient
Health Questionnaire 9, and Beck Scale for Suicidal Ideation. Clinicians were
also asked about their impression on likelihood of patient admission. Outcome
measures were as follows: need for psychiatric hospital admission, prolonged
stay at psychiatric facility, and any adverse events during ED stay including
need for unscheduled psychiatric or sedating medications, need for physical
restraints, and need for intervention by security staff.
RESULTS: The Beck Scale for Suicidal Ideation, Patient Health Questionnaire 9,
and Columbia Suicide Severity Scale did not significantly predict within-ED
adverse events or admissions to psychiatric facilities. Wald test for individual
parameters at an α of .10 level found that patients who were screened positive
by their nurse had 3.37 times the odds of adverse within-ED events; patients
with a positive SAD PERSONS score had 8.18 times the odds of psychiatric
admission greater than 5 days. However, at the α of .05 level, no screening
tools correlated with patient ED course or likelihood of psychiatric admission.
CONCLUSION: Clinical impression alone and the suicide screening tools showed
poor predictive value for near-term events. Data from this study highlight the
need for the development of ED-based suicide screening instruments capable of
identifying those patients with suicidal ideation at greatest risk. BACKGROUND: Suicide is a major public health issue, and a priority requirement
is accurately identifying high-risk individuals. The SAD PERSONS suicide risk
assessment scale is widely implemented in clinical settings despite limited
supporting evidence. This article aims to determine the ability of the SAD
PERSONS scale (SPS) to predict future suicide in the emergency department.
METHODS: Five thousand four hundred sixty-two consecutive adults were seen by
psychiatry consultation teams in two tertiary emergency departments with linkage
to population-based administrative data to determine suicide deaths within 6
months, 1, and 5 years.
RESULTS: Seventy-seven (1.4%) individuals died by suicide during the study
period. When predicting suicide at 12 months, medium- and high-risk scores on
SPS had a sensitivity of 49% and a specificity of 60%; the positive and negative
predictive values were 0.9 and 99%, respectively. Half of the suicides at both
6- and 12-month intervals were classified as low risk by SPS at index visit. The
area under the curve at 12 months for the Modified SPS was 0.59 (95% confidence
interval [CI] range 0.51-0.67). High-risk scores (compared to low risk) were
significantly associated with death by suicide over the 5-year study period
using the SPS (hazard ratio 2.49; 95% CI 1.34-4.61) and modified version (hazard
ratio 2.29; 95% CI 1.24-2.29).
CONCLUSIONS: Although widely used in educational and clinical settings, these
findings do not support the use of the SPS and Modified SPS to predict suicide
in adults seen by psychiatric services in the emergency department. BACKGROUND: Instruments have been developed to facilitate suicide risk
assessment. We aimed to evaluate the evidence for these instruments including
assessment of risk of bias and diagnostic accuracy for suicide and suicide
attempt.
METHODS: PubMed (NLM), PsycInfo, Embase, Cinahl and the Cochrane Library
databases were searched until December 2014. We assessed risk of bias with
QUADAS-2. The average sensitivity and specificity of each instrument was
estimated and the certainty of the evidence was assessed with GRADE. We
considered instruments with a sensitivity > 80% and a specificity > 50% to have
sufficient diagnostic accuracy.
RESULTS: Thirty-five relevant studies were identified but 14 were considered to
have high risk of bias, leaving 21 studies evaluating altogether 15 risk
assessment instruments. We could carry out meta-analyses for five instruments.
For the outcome suicide attempt SAD PERSONS Scale had a sensitivity of 15% (95%
CI 8-24) and specificity of 97% (96-98), and the Manchester Self-Harm Rule
(MSHR) a sensitivity of 97% (97-97) and a specificity of 20% (20-21). ReACT,
which is a modification of MSHR, had a similar low specificity, as did the
Sodersjukhuset Self Harm Rule. For the outcome suicide, the Beck Hopelessness
Scale had a sensitivity of 89% (78-95) and specificity of 42% (40-43).
CONCLUSIONS: Most suicide risk assessment instruments were supported by too few
studies to allow for evaluation of accuracy. Among those that could be
evaluated, none fulfilled requirements for sufficient diagnostic accuracy. We examine the interrelations among clinicians' judgment of patients' suicide
risk, clinicians' emotional responses, and standard risk factors in the
short-term prediction of suicidal thoughts and behaviors. Psychiatric
outpatients (n = 153) with a lifetime history of suicide ideation/attempt and
their treating clinicians (n = 67) were evaluated at intake. Clinicians
completed a standard suicide risk instrument (modified SAD PERSONS scale), a
10-point Likert scale assessment of judgment of patient suicide risk (Clinician
Prediction Scale), and a measure of their emotional responses to the patient
(Therapist Response Questionnaire-Suicide Form). The Columbia Suicide Severity
Rating Scale and the Beck Scale for Suicide Ideation were administered at a
one-month follow-up assessment (n = 114, 74.5%). Clinician judgment of risk
significantly predicted suicidal thoughts and behaviors at follow-up. Both the
standard suicide risk instrument and clinician emotional responses contributed
independently to the clinician assessment of risk, which, in turn, mediated
their relationships with suicidal thoughts and behaviors. Our findings validate
the importance of clinical judgment in assessing suicide risk. Clinical judgment
appears to be informed both by concrete risk factors and clinicians' emotional
responses to suicidal patients, highlighting emotional awareness as a promising
area for research and training. Conflict of interest statement: ETHICS APPROVAL AND CONSENT TO PARTICIPATE: The
self-harm monitoring system in Oxford was approved by South Central – Berkshire
National Research Ethics Service and Derbyshire Research Ethics Committee
approved the study in Derby. Both were granted ethical approval to collect data
for both local and multicentre projects. South Manchester Research Ethics
Committee reviewed the project in Manchester. The project was deemed not to
require approval as the monitoring is conducted as part of a clinical audit
system. The Bristol Self-Harm Surveillance Centre received ethical approval from
University Hospitals Bristol NHS Foundation Trust and Southmead Research Ethics
Committee approved the research database. All centres have approval under
section 251 of the NHS Act (2006) to collect patient identifiable data without
patient consent and Oxford, Derby and Manchester have consent to send patient
details to the Data Linkage Service. COMPETING INTERESTS: D.G., K.H. and N.K.
are members of the Department of Health’s (England) National Suicide Prevention
Advisory Group. N.K. chaired the NICE guideline development group for the
longer-term management of self-harm and the NICE Topic Expert Group (which
developed the quality standards for self-harm services). He is currently chair
of the updated NICE guideline for depression. R.O.C. was a member of the NICE
guideline development group for the longer-term management of self-harm and is a
member of the Scottish Government’s suicide prevention implementation and
monitoring group. All other authors declare no conflict of interest. PUBLISHER’S
NOTE: Springer Nature remains neutral with regard to jurisdictional claims in
published maps and institutional affiliations. |
Briefly describe a deep learning system that is more accurate than human experts at detecting melanoma. | in August of 2018 a study was published where a Convolutional Neural Network's (CNN) diagnostic performance was compared with a large international group of 58 dermatologists, including 30 experts. Most dermatologists were outperformed by the CNN, the CNN had both higher sensitivity and specificity. | BACKGROUND: Computer vision may aid in melanoma detection.
OBJECTIVE: We sought to compare melanoma diagnostic accuracy of computer
algorithms to dermatologists using dermoscopic images.
METHODS: We conducted a cross-sectional study using 100 randomly selected
dermoscopic images (50 melanomas, 44 nevi, and 6 lentigines) from an
international computer vision melanoma challenge dataset (n = 379), along with
individual algorithm results from 25 teams. We used 5 methods (nonlearned and
machine learning) to combine individual automated predictions into "fusion"
algorithms. In a companion study, 8 dermatologists classified the lesions in the
100 images as either benign or maligt.
RESULTS: The average sensitivity and specificity of dermatologists in
classification was 82% and 59%. At 82% sensitivity, dermatologist specificity
was similar to the top challenge algorithm (59% vs. 62%, P = .68) but lower than
the best-performing fusion algorithm (59% vs. 76%, P = .02). Receiver operating
characteristic area of the top fusion algorithm was greater than the mean
receiver operating characteristic area of dermatologists (0.86 vs. 0.71,
P = .001).
LIMITATIONS: The dataset lacked the full spectrum of skin lesions encountered in
clinical practice, particularly banal lesions. Readers and algorithms were not
provided clinical data (eg, age or lesion history/symptoms). Results obtained
using our study design cannot be extrapolated to clinical practice.
CONCLUSION: Deep learning computer vision systems classified melanoma dermoscopy
images with accuracy that exceeded some but not all dermatologists. Melanoma is a fatal form of skin cancer when left undiagnosed. Computer-aided
diagnosis systems powered by convolutional neural networks (CNNs) can improve
diagnostic accuracy and save lives. CNNs have been successfully used in both
skin lesion segmentation and classification. For reasons heretofore unclear,
previous works have found image segmentation to be, conflictingly, both
detrimental and beneficial to skin lesion classification. We investigate the
effect of expanding the segmentation border to include pixels surrounding the
target lesion. Ostensibly, segmenting a target skin lesion will remove
inessential information, non-lesion skin, and artifacts to aid in
classification. Our results indicate that segmentation border enlargement
produces, to a certain degree, better results across all metrics of interest
when using a convolutional based classifier built using the transfer learning
paradigm. Consequently, preprocessing methods which produce borders larger than
the actual lesion can potentially improve classifier performance, more than both
perfect segmentation, using dermatologist created ground truth masks, and no
segmentation altogether. Cancer bears a poisoning threat to human society. Melanoma, the skin cancer,
originates from skin layers and penetrates deep into subcutaneous layers. There
exists an extensive research in melanoma diagnosis using dermatoscopic images
captured through a dermatoscope. While designing a diagnostic model for general
handheld imaging systems is an emerging trend, this article proposes a
computer-aided decision support system for macro images captured by a
general-purpose camera. General imaging conditions are adversely affected by
nonuniform illumination, which further affects the extraction of relevant
information. To mitigate it, we process an image to define a smooth illumination
surface using the multistage illumination compensation approach, and the
infected region is extracted using the proposed multimode segmentation method.
The lesion information is numerated as a feature set comprising geometry,
photometry, border series, and texture measures. The redundancy in feature set
is reduced using information theory methods, and a classification boundary is
modeled to distinguish benign and maligt samples using support vector
machine, random forest, neural network, and fast discriminative
mixed-membership-based naive Bayesian classifiers. Moreover, the experimental
outcome is supported by hypothesis testing and boxplot representation for
classification losses. The simulation results prove the significance of the
proposed model that shows an improved performance as compared with competing
arts. We tested the use of a deep learning algorithm to classify the clinical images
of 12 skin diseases-basal cell carcinoma, squamous cell carcinoma,
intraepithelial carcinoma, actinic keratosis, seborrheic keratosis, maligt
melanoma, melanocytic nevus, lentigo, pyogenic granuloma, hemangioma,
dermatofibroma, and wart. The convolutional neural network (Microsoft ResNet-152
model; Microsoft Research Asia, Beijing, China) was fine-tuned with images from
the training portion of the Asan dataset, MED-NODE dataset, and atlas site
images (19,398 images in total). The trained model was validated with the
testing portion of the Asan, Hallym and Edinburgh datasets. With the Asan
dataset, the area under the curve for the diagnosis of basal cell carcinoma,
squamous cell carcinoma, intraepithelial carcinoma, and melanoma was 0.96 ±
0.01, 0.83 ± 0.01, 0.82 ± 0.02, and 0.96 ± 0.00, respectively. With the
Edinburgh dataset, the area under the curve for the corresponding diseases was
0.90 ± 0.01, 0.91 ± 0.01, 0.83 ± 0.01, and 0.88 ± 0.01, respectively. With the
Hallym dataset, the sensitivity for basal cell carcinoma diagnosis was 87.1% ±
6.0%. The tested algorithm performance with 480 Asan and Edinburgh images was
comparable to that of 16 dermatologists. To improve the performance of
convolutional neural network, additional images with a broader range of ages and
ethnicities should be collected. Skin lesions are a severe disease globally. Early detection of melanoma in
dermoscopy images significantly increases the survival rate. However, the
accurate recognition of melanoma is extremely challenging due to the following
reasons: low contrast between lesions and skin, visual similarity between
melanoma and non-melanoma lesions, etc. Hence, reliable automatic detection of
skin tumors is very useful to increase the accuracy and efficiency of
pathologists. In this paper, we proposed two deep learning methods to address
three main tasks emerging in the area of skin lesion image processing, i.e.,
lesion segmentation (task 1), lesion dermoscopic feature extraction (task 2) and
lesion classification (task 3). A deep learning framework consisting of two
fully convolutional residual networks (FCRN) is proposed to simultaneously
produce the segmentation result and the coarse classification result. A lesion
index calculation unit (LICU) is developed to refine the coarse classification
results by calculating the distance heat-map. A straight-forward CNN is proposed
for the dermoscopic feature extraction task. The proposed deep learning
frameworks were evaluated on the ISIC 2017 dataset. Experimental results show
the promising accuracies of our frameworks, i.e., 0.753 for task 1, 0.848 for
task 2 and 0.912 for task 3 were achieved. |
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