Linkage and Association Studies in African
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The Tumor Suppressor CIC Directly Regulates MAPK Pathway Genes Via Histone Deacetylation Simon Weissmann1,2, Paul A
Published OnlineFirst May 29, 2018; DOI: 10.1158/0008-5472.CAN-18-0342 Cancer Genome and Epigenome Research The Tumor Suppressor CIC Directly Regulates MAPK Pathway Genes via Histone Deacetylation Simon Weissmann1,2, Paul A. Cloos1,2, Simone Sidoli2,3, Ole N. Jensen2,3, Steven Pollard4, and Kristian Helin1,2,5 Abstract Oligodendrogliomas are brain tumors accounting for approximately 10% of all central nervous system can- Low MAPK signaling High MAPK signaling cers. CIC is a transcription factor that is mutated in most RTKs patients with oligodendrogliomas; these mutations are believed to be a key oncogenic event in such cancers. MEK Analysis of the Drosophila melanogaster ortholog of ERK SIN3 CIC, Capicua, indicates that CIC loss phenocopies CIC HDAC activation of the EGFR/RAS/MAPK pathway, and HMG C-term studies in mammalian cells have demonstrated a role SIN3 CIC HDAC for CIC in repressing the transcription of the PEA3 HMG C-term Ac Ac subfamily of ETS transcription factors. Here, we address Ac Ac the mechanism by which CIC represses transcription and assess the functional consequences of CIC inacti- vation. Genome-wide binding patterns of CIC in several cell types revealed that CIC target genes were enriched ETV, DUSP, CCND1/2, SHC3,... for MAPK effector genes involved in cell-cycle regulation Normal Astrocytoma and proliferation. CIC binding to target genes was Glioblastoma multiforme abolished by high MAPK activity, which led to their 1p/19q deletion CIC-Mutants transcriptional activation. CIC interacted with the SIN3 SIN3 deacetylation complex and, based on our results, we SIN3 CIC suggest that CIC functions as a transcriptional repressor HDAC HDAC HMG C-term through the recruitment of histone deacetylases. -
Genes Involved and Proteins
Atlas of Genetics and Cytogenetics in Oncology and Haematology OPEN ACCESS JOURNAL AT INIST-CNRS Scope The Atlas of Genetics and Cytogenetics in Oncology and Haematology is a peer reviewed on-line journal in open access, devoted to genes, cytogenetics, and clinical entities in cancer, and cancer-prone diseases. It presents structured review articles ("cards") on genes, leukaemias, solid tumours, cancer-prone diseases, more traditional review articles on these and also on surrounding topics ("deep insights"), case reports in hematology, and educational items in the various related topics for students in Medicine and in Sciences. Editorial correspondance Jean-Loup Huret Genetics, Department of Medical Information, University Hospital F-86021 Poitiers, France tel +33 5 49 44 45 46 or +33 5 49 45 47 67 [email protected] or [email protected] Staff Mohammad Ahmad, Mélanie Arsaban, Houa Delabrousse, Marie-Christine Jacquemot-Perbal, Maureen Labarussias, Vanessa Le Berre, Anne Malo, Catherine Morel-Pair, Laurent Rassinoux, Sylvie Yau Chun Wan - Senon, Alain Zasadzinski. Philippe Dessen is the Database Director, and Alain Bernheim the Chairman of the on-line version (Gustave Roussy Institute – Villejuif – France). The Atlas of Genetics and Cytogenetics in Oncology and Haematology (ISSN 1768-3262) is published 12 times a year by ARMGHM, a non profit organisation, and by the INstitute for Scientific and Technical Information of the French National Center for Scientific Research (INIST-CNRS) since 2008. The Atlas is hosted by INIST-CNRS (http://www.inist.fr) http://AtlasGeneticsOncology.org © ATLAS - ISSN 1768-3262 The PDF version of the Atlas of Genetics and Cytogenetics in Oncology and Haematology is a reissue of the original articles published in collaboration with the Institute for Scientific and Technical Information (INstitut de l’Information Scientifique et Technique - INIST) of the French National Center for Scientific Research (CNRS) on its electronic publishing platform I-Revues. -
Targeting the DEK Oncogene in Head and Neck Squamous Cell Carcinoma: Functional and Transcriptional Consequences
Targeting the DEK oncogene in head and neck squamous cell carcinoma: functional and transcriptional consequences A dissertation submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirements to the degree of Doctor of Philosophy (Ph.D.) in the Department of Cancer and Cell Biology of the College of Medicine March 2015 by Allie Kate Adams B.S. The Ohio State University, 2009 Dissertation Committee: Susanne I. Wells, Ph.D. (Chair) Keith A. Casper, M.D. Peter J. Stambrook, Ph.D. Ronald R. Waclaw, Ph.D. Susan E. Waltz, Ph.D. Kathryn A. Wikenheiser-Brokamp, M.D., Ph.D. Abstract Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies worldwide with over 50,000 new cases in the United States each year. For many years tobacco and alcohol use were the main etiological factors; however, it is now widely accepted that human papillomavirus (HPV) infection accounts for at least one-quarter of all HNSCCs. HPV+ and HPV- HNSCCs are studied as separate diseases as their prognosis, treatment, and molecular signatures are distinct. Five-year survival rates of HNSCC hover around 40-50%, and novel therapeutic targets and biomarkers are necessary to improve patient outcomes. Here, we investigate the DEK oncogene and its function in regulating HNSCC development and signaling. DEK is overexpressed in many cancer types, with roles in molecular processes such as transcription, DNA repair, and replication, as well as phenotypes such as apoptosis, senescence, and proliferation. DEK had never been previously studied in this tumor type; therefore, our studies began with clinical specimens to examine DEK expression patterns in primary HNSCC tissue. -
Endocrine System Local Gene Expression
Copyright 2008 By Nathan G. Salomonis ii Acknowledgments Publication Reprints The text in chapter 2 of this dissertation contains a reprint of materials as it appears in: Salomonis N, Hanspers K, Zambon AC, Vranizan K, Lawlor SC, Dahlquist KD, Doniger SW, Stuart J, Conklin BR, Pico AR. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics. 2007 Jun 24;8:218. The co-authors listed in this publication co-wrote the manuscript (AP and KH) and provided critical feedback (see detailed contributions at the end of chapter 2). The text in chapter 3 of this dissertation contains a reprint of materials as it appears in: Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005;6(2):R12. Epub 2005 Jan 28. The co-authors listed in this publication developed the hierarchical clustering method (KP), co-designed the study (NC, AZ, BC), provided statistical guidance (KV), co- contributed to GenMAPP 2.0 (SD) and performed quantitative mRNA analyses (GD). The text of this dissertation contains a reproduction of a figure from: Yeo G, Holste D, Kreiman G, Burge CB. Variation in alternative splicing across human tissues. Genome Biol. 2004;5(10):R74. Epub 2004 Sep 13. The reproduction was taken without permission (chapter 1), figure 1.3. iii Personal Acknowledgments The achievements of this doctoral degree are to a large degree possible due to the contribution, feedback and support of many individuals. To all of you that helped, I am extremely grateful for your support. -
Differential DNA Methylation and Changing Cell-Type Proportions As Fibrotic Stage Progresses in NAFLD
Johnson et al. Clin Epigenet (2021) 13:152 https://doi.org/10.1186/s13148-021-01129-y RESEARCH Open Access Diferential DNA methylation and changing cell-type proportions as fbrotic stage progresses in NAFLD Nicholas D. Johnson1,2†, Xiumei Wu3†, Christopher D. Still4, Xin Chu4, Anthony T. Petrick4, Glenn S. Gerhard5, Karen N. Conneely1,2† and Johanna K. DiStefano3*† Abstract Background: Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fbrosis in a subset of patients. DNA methyla- tion (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profles difer across tissues and cell types, and DNAm may play a role in cell-type diferentiation. Previous work investigating the relationship between DNAm and fbrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated. Results: Here, we performed an epigenome-wide analysis using Infnium MethylationEPIC array data from 325 indi- viduals with NAFLD, including 119 with severe fbrosis and 206 with no histological evidence of fbrosis. After adjust- ment for latent confounders, we identifed 7 CpG sites whose DNAm associated with fbrosis (p < 5.96 10–8). Analysis of RNA-seq data collected from a subset of individuals (N 56) revealed that gene expression at 288 genes× associated with DNAm at one or more of the 7 fbrosis-related CpGs.= DNAm-based estimates of cell-type proportions showed that estimated proportions of natural killer cells increased, while epithelial cell proportions decreased with disease stage. Finally, we used an elastic net regression model to assess DNAm as a biomarker of fbrotic stage and found that our model predicted fbrosis with a sensitivity of 0.93 and provided information beyond a model based solely on cell- type proportions. -
An RNA-Seq-Based Resource for Pain and Sensory Neuroscience Research
bioRxiv preprint doi: https://doi.org/10.1101/165431; this version posted October 13, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Comparative transcriptome profiling of the human and mouse dorsal root ganglia: An RNA-seq-based resource for pain and sensory neuroscience research Short Title: Human and mouse DRG comparative transcriptomics Pradipta Ray 1, 2 #, Andrew Torck 1 , Lilyana Quigley 1, Andi Wangzhou 1, Matthew Neiman 1, Chandranshu Rao 1, Tiffany Lam 1, Ji-Young Kim 1, Tae Hoon Kim 2, Michael Q. Zhang 2, Gregory Dussor 1 and Theodore J. Price 1, # 1 The University of Texas at Dallas, School of Behavioral and Brain Sciences 2 The University of Texas at Dallas, Department of Biological Sciences # Corresponding authors Theodore J Price Pradipta Ray School of Behavioral and Brain Sciences School of Behavioral and Brain Sciences The University of Texas at Dallas The University of Texas at Dallas BSB 14.102G BSB 10.608 800 W Campbell Rd 800 W Campbell Rd Richardson TX 75080 Richardson TX 75080 972-883-4311 972-883-7262 [email protected] [email protected] Number of pages: 27 Number of figures: 9 Number of tables: 8 Supplementary Figures: 4 Supplementary Files: 6 Word count: Abstract = 219; Introduction = 457; Discussion = 1094 Conflict of interest: The authors declare no conflicts of interest Patient anonymity and informed consent: Informed consent for human tissue sources were obtained by Anabios, Inc. (San Diego, CA). Human studies: This work was approved by The University of Texas at Dallas Institutional Review Board (MR 15-237). -
Clinical Factors That Influence the Cellular Responses of Saphenous
Clinical factors that influence the cellular responses of saphenous veins used for arterial bypass Michael Sobel, MD,a,b Shinsuke Kikuchi, MD,c Lihua Chen,b Gale L. Tang, MD,a,b Tom N. Wight, PhD,d and Richard D. Kenagy, PhD,b Seattle, Wash; and Asahikawa, Japan ABSTRACT Objective: When an autogenous vein is harvested and used for arterial bypass, it suffers physical and biologic injuries that may set in motion the cellular processes that lead to wall thickening, fibrosis, stenosis, and ultimately graft failure. Whereas the injurious effects of surgical preparation of the vein conduit have been extensively studied, little is known about the influence of the clinical environment of the donor leg from which the vein is obtained. Methods: We studied the cellular responses of fresh saphenous vein samples obtained before implantation in 46 patients undergoing elective lower extremity bypass surgery. Using an ex vivo model of response to injury, we quantified the outgrowth of cells from explants of the adventitial and medial layers of the vein. We correlated this cellular outgrowth with the clinical characteristics of the patients, including the Wound, Ischemia, and foot Infection classification of the donor leg for ischemia, wounds, and infection as well as smoking and diabetes. Results: Cellular outgrowth was significantly faster and more robust from the adventitial layer than from the medial layer. The factors of leg ischemia (P < .001), smoking (P ¼ .042), and leg infection (P ¼ .045) were associated with impaired overall outgrowth from the adventitial tissue on multivariable analysis. Only ischemia (P ¼ .046) was associated with impaired outgrowth of smooth muscle cells (SMCs) from the medial tissue. -
Identification of Novel Regulatory Genes in Acetaminophen
IDENTIFICATION OF NOVEL REGULATORY GENES IN ACETAMINOPHEN INDUCED HEPATOCYTE TOXICITY BY A GENOME-WIDE CRISPR/CAS9 SCREEN A THESIS IN Cell Biology and Biophysics and Bioinformatics Presented to the Faculty of the University of Missouri-Kansas City in partial fulfillment of the requirements for the degree DOCTOR OF PHILOSOPHY By KATHERINE ANNE SHORTT B.S, Indiana University, Bloomington, 2011 M.S, University of Missouri, Kansas City, 2014 Kansas City, Missouri 2018 © 2018 Katherine Shortt All Rights Reserved IDENTIFICATION OF NOVEL REGULATORY GENES IN ACETAMINOPHEN INDUCED HEPATOCYTE TOXICITY BY A GENOME-WIDE CRISPR/CAS9 SCREEN Katherine Anne Shortt, Candidate for the Doctor of Philosophy degree, University of Missouri-Kansas City, 2018 ABSTRACT Acetaminophen (APAP) is a commonly used analgesic responsible for over 56,000 overdose-related emergency room visits annually. A long asymptomatic period and limited treatment options result in a high rate of liver failure, generally resulting in either organ transplant or mortality. The underlying molecular mechanisms of injury are not well understood and effective therapy is limited. Identification of previously unknown genetic risk factors would provide new mechanistic insights and new therapeutic targets for APAP induced hepatocyte toxicity or liver injury. This study used a genome-wide CRISPR/Cas9 screen to evaluate genes that are protective against or cause susceptibility to APAP-induced liver injury. HuH7 human hepatocellular carcinoma cells containing CRISPR/Cas9 gene knockouts were treated with 15mM APAP for 30 minutes to 4 days. A gene expression profile was developed based on the 1) top screening hits, 2) overlap with gene expression data of APAP overdosed human patients, and 3) biological interpretation including assessment of known and suspected iii APAP-associated genes and their therapeutic potential, predicted affected biological pathways, and functionally validated candidate genes. -
An Integrative Genomic Analysis of the Longshanks Selection Experiment for Longer Limbs in Mice
bioRxiv preprint doi: https://doi.org/10.1101/378711; this version posted August 19, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Title: 2 An integrative genomic analysis of the Longshanks selection experiment for longer limbs in mice 3 Short Title: 4 Genomic response to selection for longer limbs 5 One-sentence summary: 6 Genome sequencing of mice selected for longer limbs reveals that rapid selection response is 7 due to both discrete loci and polygenic adaptation 8 Authors: 9 João P. L. Castro 1,*, Michelle N. Yancoskie 1,*, Marta Marchini 2, Stefanie Belohlavy 3, Marek 10 Kučka 1, William H. Beluch 1, Ronald Naumann 4, Isabella Skuplik 2, John Cobb 2, Nick H. 11 Barton 3, Campbell Rolian2,†, Yingguang Frank Chan 1,† 12 Affiliations: 13 1. Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany 14 2. University of Calgary, Calgary AB, Canada 15 3. IST Austria, Klosterneuburg, Austria 16 4. Max Planck Institute for Cell Biology and Genetics, Dresden, Germany 17 Corresponding author: 18 Campbell Rolian 19 Yingguang Frank Chan 20 * indicates equal contribution 21 † indicates equal contribution 22 Abstract: 23 Evolutionary studies are often limited by missing data that are critical to understanding the 24 history of selection. Selection experiments, which reproduce rapid evolution under controlled 25 conditions, are excellent tools to study how genomes evolve under strong selection. Here we 1 bioRxiv preprint doi: https://doi.org/10.1101/378711; this version posted August 19, 2018. -
Derived Xenografts Highlights the Role of REST in Neuroendocrine Differentiation of Castration- Resistant Prostate Cancer Amilcar Flores-Morales1,2,3, Tobias B
Published OnlineFirst October 1, 2018; DOI: 10.1158/1078-0432.CCR-18-0729 Biology of Human Tumors Clinical Cancer Research Proteogenomic Characterization of Patient- Derived Xenografts Highlights the Role of REST in Neuroendocrine Differentiation of Castration- Resistant Prostate Cancer Amilcar Flores-Morales1,2,3, Tobias B. Bergmann1,2, Charlotte Lavallee1,2, Tanveer S. Batth3, Dong Lin4, Mads Lerdrup5, Stine Friis1,2, Anette Bartels1,2, Gitte Kristensen6, Agnieszka Krzyzanowska7, Hui Xue4, Ladan Fazli4, Klaus H. Hansen5, Martin A. Røder6, Klaus Brasso6, Jose M. Moreira1,2, Anders Bjartell7, Yuzhuo Wang4, Jesper V. Olsen3, Colin C. Collins4, and Diego Iglesias-Gato1,2 Abstract Background: An increasing number of castration-resistant and elevated in NEPC, while the reduced levels of proteins prostate cancer (CRPC) tumors exhibit neuroendocrine (NE) involved in mitochondrial functions suggested a prevalent features. NE prostate cancer (NEPC) has poor prognosis, and glycolytic metabolism of NEPC tumors. Integration of the its development is poorly understood. REST chromatin bound regions with expression changes Experimental Design: We applied mass spectrometry– indicated a direct role of REST in regulating neuronal gene based proteomics to a unique set of 17 prostate cancer expression in prostate cancer cells. Mechanistically, deple- patient–derived xenografts (PDX) to characterize the effects tion of REST led to cell-cycle arrest in G1, which could be of castration in vivo, and the proteome differences between rescued by p53 knockdown. Finally, the expression of the NEPC and prostate adenocarcinomas. Genome-wide profiling REST-regulated gene secretagogin (SCGN) correlated with of REST-occupied regions in prostate cancer cells was corre- an increased risk of suffering disease relapse after radical lated to the expression changes in vivo to investigate the role of prostatectomy. -
A Chronological Atlas of Natural Selection in the Human Genome During the Past Half-Million Years
bioRxiv preprint doi: https://doi.org/10.1101/018929; this version posted June 19, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. A Chronological Atlas of Natural Selection in the Human Genome during the Past Half-million Years Hang Zhou1,2,10, Sile Hu1,2,10, Rostislav Matveev3,4, Qianhui Yu1,2, Jing Li1, Philipp Khaitovich1, Li Jin1,5, Michael Lachmann3,6, Mark Stoneking3, Qiaomei Fu7,8,9 & Kun Tang1 1Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China. 2University of Chinese Academy of Sceiences, Beijing 100049, China. 3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany. 4Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany. 5MOE Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai 200433, China. 6Santa Fe Institute, Santa Fe, New Mexico 87501, USA. 7Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. 8Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA 9Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China. 10These authors contributed equally to this work. Correspondence could be addressed to K.T. ([email protected]) bioRxiv preprint doi: https://doi.org/10.1101/018929; this version posted June 19, 2015. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Lymphomes Natural-Killer T Cells (NKT) : Impact Des Stimulations Antigéniques Chroniques Et Mécanismes De La Lymphomagénèse Remy Robinot
Lymphomes Natural-Killer T cells (NKT) : impact des stimulations antigéniques chroniques et mécanismes de la lymphomagénèse Remy Robinot To cite this version: Remy Robinot. Lymphomes Natural-Killer T cells (NKT) : impact des stimulations antigéniques chroniques et mécanismes de la lymphomagénèse. Cancer. Université de Lyon, 2017. Français. NNT : 2017LYSE1255. tel-01744676 HAL Id: tel-01744676 https://tel.archives-ouvertes.fr/tel-01744676 Submitted on 27 Mar 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. N° d’ordre NNT : 2017LYSE1255 Année 2017 THESE de DOCTORAT DE L’UNIVERSITE DE LYON Opérée au sein de l’Université Claude Bernard Lyon 1 Ecole Doctorale N°340 (Biologie Moléculaire Intégrative et Cellulaire) Spécialité : Immunologie et Cancérologie Discipline : Biologie Soutenue publiquement le 05/12/2017 par Rémy Robinot LYMPHOMES NATURAL-KILLER T (NKT) : Impact des stimulations antigéniques chroniques et mécanismes de lymphomagenèse Directeur de thèse : Docteur Laurent Genestier Devant le jury composé de : Docteur Véronique Maguer-Satta, DR2 CNRS Présidente Professeur Philippe Lehours, PU-PH Université de Bordeaux Rapporteur Docteur Maria Leite de Moraes, DR1 CNRS Rapporteur Professeur Philippe Gaulard, PU-PH Université Paris Est Examinateur Docteur Sylvie Hermouet, MCU-PH Université de Nantes Examinatrice Professeur Germain Gillet, PU-PH Université de Lyon Examinateur Docteur Laurent Genestier, CR INSERM Directeur de thèse UNIVERSITE CLAUDE BERNARD - LYON 1 Président de l’Université M.