Genome-Wide Association Identifies Nine Common
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Genome-Wide Transcriptional Sequencing Identifies Novel Mutations in Metabolic Genes in Human Hepatocellular Carcinoma DAOUD M
CANCER GENOMICS & PROTEOMICS 11 : 1-12 (2014) Genome-wide Transcriptional Sequencing Identifies Novel Mutations in Metabolic Genes in Human Hepatocellular Carcinoma DAOUD M. MEERZAMAN 1,2 , CHUNHUA YAN 1, QING-RONG CHEN 1, MICHAEL N. EDMONSON 1, CARL F. SCHAEFER 1, ROBERT J. CLIFFORD 2, BARBARA K. DUNN 3, LI DONG 2, RICHARD P. FINNEY 1, CONSTANCE M. CULTRARO 2, YING HU1, ZHIHUI YANG 2, CU V. NGUYEN 1, JENNY M. KELLEY 2, SHUANG CAI 2, HONGEN ZHANG 2, JINGHUI ZHANG 1,4 , REBECCA WILSON 2, LAUREN MESSMER 2, YOUNG-HWA CHUNG 5, JEONG A. KIM 5, NEUNG HWA PARK 6, MYUNG-SOO LYU 6, IL HAN SONG 7, GEORGE KOMATSOULIS 1 and KENNETH H. BUETOW 1,2 1Center for Bioinformatics and Information Technology, National Cancer Institute, Rockville, MD, U.S.A.; 2Laboratory of Population Genetics, National Cancer Institute, National Cancer Institute, Bethesda, MD, U.S.A.; 3Basic Prevention Science Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, MD, U.S.A; 4Department of Biotechnology/Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, U.S.A.; 5Department of Internal Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Korea; 6Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, Korea; 7Department of Internal Medicine, College of Medicine, Dankook University, Cheon-An, Korea Abstract . We report on next-generation transcriptome Worldwide, liver cancer is the fifth most common cancer and sequencing results of three human hepatocellular carcinoma the third most common cause of cancer-related mortality (1). tumor/tumor-adjacent pairs. -
Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways
biomolecules Article Whole Genome Sequencing of Familial Non-Medullary Thyroid Cancer Identifies Germline Alterations in MAPK/ERK and PI3K/AKT Signaling Pathways Aayushi Srivastava 1,2,3,4 , Abhishek Kumar 1,5,6 , Sara Giangiobbe 1, Elena Bonora 7, Kari Hemminki 1, Asta Försti 1,2,3 and Obul Reddy Bandapalli 1,2,3,* 1 Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; [email protected] (A.S.); [email protected] (A.K.); [email protected] (S.G.); [email protected] (K.H.); [email protected] (A.F.) 2 Hopp Children’s Cancer Center (KiTZ), D-69120 Heidelberg, Germany 3 Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany 4 Medical Faculty, Heidelberg University, D-69120 Heidelberg, Germany 5 Institute of Bioinformatics, International Technology Park, Bangalore 560066, India 6 Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576104, India 7 S.Orsola-Malphigi Hospital, Unit of Medical Genetics, 40138 Bologna, Italy; [email protected] * Correspondence: [email protected]; Tel.: +49-6221-42-1709 Received: 29 August 2019; Accepted: 10 October 2019; Published: 13 October 2019 Abstract: Evidence of familial inheritance in non-medullary thyroid cancer (NMTC) has accumulated over the last few decades. However, known variants account for a very small percentage of the genetic burden. Here, we focused on the identification of common pathways and networks enriched in NMTC families to better understand its pathogenesis with the final aim of identifying one novel high/moderate-penetrance germline predisposition variant segregating with the disease in each studied family. -
Identification of Candidate Biomarkers and Pathways Associated with Type 1 Diabetes Mellitus Using Bioinformatics Analysis
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.08.447531; this version posted June 9, 2021. 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. Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis Basavaraj Vastrad1, Chanabasayya Vastrad*2 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karnataka, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India bioRxiv preprint doi: https://doi.org/10.1101/2021.06.08.447531; this version posted June 9, 2021. 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. Abstract Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein-protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were then performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. -
Characterization at the Molecular Level Using Robust Biochemical Approaches of a New Kinase Protein Béatrice Vallée, Michel Doudeau, Fabienne Godin, Hélène Bénédetti
Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein Béatrice Vallée, Michel Doudeau, Fabienne Godin, Hélène Bénédetti To cite this version: Béatrice Vallée, Michel Doudeau, Fabienne Godin, Hélène Bénédetti. Characterization at the Molec- ular Level using Robust Biochemical Approaches of a New Kinase Protein. Journal of visualized experiments : JoVE, JoVE, 2019, pp.e59820. 10.3791/59820. hal-02282630 HAL Id: hal-02282630 https://hal.archives-ouvertes.fr/hal-02282630 Submitted on 17 Jun 2020 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. Characterization at the Molecular Level using Robust Biochemical Approaches of a New Kinase Protein AUTHORS 1 1 1 1 Béatrice Vallée M Michel Doudeau F Fabienne Godin Hélène Bénédetti AFFILIATIONS 1 Centre de Biophysique Moléculaire, CNRS, UPR 4301, University of Orléans and INSERM CORRESPONDING AUTHOR Béatrice Vallée [email protected] Abstract actosidase-based-screening-assay-for-identification Extensive whole genome sequencing has identified many engineered to its sequence or via an antibody specifically Open Reading Frames (ORFs) providing many potential targeting it. These protein complexes may then be separated proteins. These proteins may have important roles for the by SDS-PAGE (Sodium Dodecyl Sulfate PolyAcrylamide Gel) cell and may unravel new cellular processes. -
Global Genomic and Transcriptomic Analysis of Human Pancreatic Islets Reveals Novel Genes Influencing Glucose Metabolism
Global genomic and transcriptomic analysis of human pancreatic islets reveals novel genes influencing glucose metabolism João Fadistaa,1, Petter Vikmana, Emilia Ottosson Laaksoa, Inês Guerra Molleta, Jonathan Lou Esguerraa, Jalal Taneeraa, Petter Storma, Peter Osmarka, Claes Ladenvalla, Rashmi B. Prasada, Karin B. Hanssona, Francesca Finotellob, Kristina Uvebranta, Jones K. Oforia, Barbara Di Camillob, Ulrika Krusa, Corrado M. Cilioa, Ola Hanssona, Lena Eliassona, Anders H. Rosengrena, Erik Renströma, Claes B. Wollheima,c, and Leif Groopa,1 aLund University Diabetes Centre, Department of Clinical Sciences, Skåne University Hospital Malmö, Lund University, 20502 Malmö, Sweden; bDepartment of Information Engineering, University of Padova, 35131 Padova, Italy; and cDepartment of Cell Physiology and Metabolism, University of Geneva, 1211 Geneva 4, Switzerland Edited by Tak W. Mak, The Campbell Family Institute for Breast Cancer Research at Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, Canada, and approved August 14, 2014 (received for review February 11, 2014) Genetic variation can modulate gene expression, and thereby pheno- Results typic variation and susceptibility to complex diseases such as type 2 Genes Showing Differential Expression Between Islets from diabetes (T2D). Here we harnessed the potential of DNA and RNA Normoglycemic and Hyperglycemic Donors. To obtain a profile of sequencing in human pancreatic islets from 89 deceased donors to gene expression variation in human islets, we sequenced the poly- identify genes of potential importance in the pathogenesis of T2D. We adenylated fraction of RNA from 89 individuals with different present a catalog of genetic variants regulating gene expression degrees of glucose tolerance, using 101 base pairs paired-end on an (eQTL) and exon use (sQTL), including many long noncoding RNAs, Illumina HiSeq sequencer (Dataset S1 and SI Appendix,Fig.S1). -
Discovery and Evaluation of Inhibitor of LARP6 As Specific Antifibrotic
www.nature.com/scientificreports OPEN Discovery and evaluation of inhibitor of LARP6 as specifc antifbrotic compound Received: 6 August 2018 Branko Stefanovic1, Zarko Manojlovic2, Cynthia Vied 3, Crystal-Dawn Badger3,4 & Accepted: 27 November 2018 Lela Stefanovic1 Published: xx xx xxxx Fibrosis is characterized by excessive production of type I collagen. Biosynthesis of type I collagen in fbrosis is augmented by binding of protein LARP6 to the 5′ stem-loop structure (5′SL), which is found exclusively in type I collagen mRNAs. A high throughput screen was performed to discover inhibitors of LARP6 binding to 5′SL, as potential antifbrotic drugs. The screen yielded one compound (C9) which was able to dissociate LARP6 from 5′ SL RNA in vitro and to inactivate the binding of endogenous LARP6 in cells. Treatment of hepatic stellate cells (liver cells responsible for fbrosis) with nM concentrations of C9 reduced secretion of type I collagen. In precision cut liver slices, as an ex vivo model of hepatic fbrosis, C9 attenuated the profbrotic response at 1 μM. In prophylactic and therapeutic animal models of hepatic fbrosis C9 prevented development of fbrosis or hindered the progression of ongoing fbrosis when administered at 1 mg/kg. Toxicogenetics analysis revealed that only 42 liver genes changed expression after administration of C9 for 4 weeks, suggesting minimal of target efects. Based on these results, C9 represents the frst LARP6 inhibitor with signifcant antifbrotic activity. Fibrosis is characterized by excessive synthesis of type I collagen in various organs and major complications of fbrosis are direct result of massive deposition of type I collagen in the extracellular matrix1,2. -
Identification of the Involvement of LOXL4 in Generation of Keratocystic Odontogenic Tumors by RNA-Seq Analysis
International Journal of Oral Science (2013) 6, 31–38 ß 2013 WCSS. All rights reserved 1674-2818/13 www.nature.com/ijos ORIGINAL ARTICLE Identification of the involvement of LOXL4 in generation of keratocystic odontogenic tumors by RNA-Seq analysis Wei-Peng Jiang1, Zi-Han Sima1, Hai-Cheng Wang1, Jian-Yun Zhang1, Li-Sha Sun2, Feng Chen2 and Tie-Jun Li1 Keratocystic odontogenic tumors (KCOT) are benign, locally aggressive intraosseous tumors of odontogenic origin. KCOT have a higher stromal microvessel density (MVD) than dentigerous cysts (DC) and normal oral mucosa. To identify genes in the stroma of KCOT involved in tumor development and progression, RNA sequencing (RNA-Seq) was performed using samples from KCOT and primary stromal fibroblasts isolated from gingival tissues. Seven candidate genes that possess a function potentially related to KCOT progression were selected and their expression levels were confirmed by quantitative PCR, immunohistochemistry and enzyme-linked immunosorbent assay. Expression of lysyl oxidase-like 4 (LOXL4), the only candidate gene that encodes a secreted protein, was enhanced at both the mRNA and protein levels in KCOT stromal tissues and primary KCOT stromal fibroblasts compared to control tissues and primary fibroblasts (P,0.05). In vitro, high expression of LOXL4 could enhance proliferation and migration of the human umbilical vein endothelial cells (HUVECs). There was a significant, positive correlation between LOXL4 protein expression and MVD in stroma of KCOT and control tissues (r50.882). These data suggest that abnormal expression of LOXL4 of KCOT may enhance angiogenesis in KCOT, which may help to promote the locally aggressive biological behavior of KCOT. -
Transdifferentiation of Human Mesenchymal Stem Cells
Transdifferentiation of Human Mesenchymal Stem Cells Dissertation zur Erlangung des naturwissenschaftlichen Doktorgrades der Julius-Maximilians-Universität Würzburg vorgelegt von Tatjana Schilling aus San Miguel de Tucuman, Argentinien Würzburg, 2007 Eingereicht am: Mitglieder der Promotionskommission: Vorsitzender: Prof. Dr. Martin J. Müller Gutachter: PD Dr. Norbert Schütze Gutachter: Prof. Dr. Georg Krohne Tag des Promotionskolloquiums: Doktorurkunde ausgehändigt am: Hiermit erkläre ich ehrenwörtlich, dass ich die vorliegende Dissertation selbstständig angefertigt und keine anderen als die von mir angegebenen Hilfsmittel und Quellen verwendet habe. Des Weiteren erkläre ich, dass diese Arbeit weder in gleicher noch in ähnlicher Form in einem Prüfungsverfahren vorgelegen hat und ich noch keinen Promotionsversuch unternommen habe. Gerbrunn, 4. Mai 2007 Tatjana Schilling Table of contents i Table of contents 1 Summary ........................................................................................................................ 1 1.1 Summary.................................................................................................................... 1 1.2 Zusammenfassung..................................................................................................... 2 2 Introduction.................................................................................................................... 4 2.1 Osteoporosis and the fatty degeneration of the bone marrow..................................... 4 2.2 Adipose and bone -
Chapter 14: Genetics of Type 2 Diabetes
CHAPTER 14 GENETICS OF TYPE 2 DIABETES Jose C. Florez, MD, PhD, Miriam S. Udler, MD, PhD, and Robert L. Hanson, MD, MPH Dr. Jose C. Florez is Chief of the Diabetes Unit and an investigator in the Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, and Co-Director of the Program in Metabolism and Institute Member in the Broad Institute, Cambridge, MA, and Associate Professor in the Department of Medicine, Harvard Medical School, Boston, MA. Dr. Miriam S. Udler is Clinical Fellow in the Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, and Postdoctoral Fellow in the Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, and Research Fellow in the Department of Medicine, Harvard Medical School, Boston, MA. Dr. Robert L. Hanson is Clinical Investigator and Head, Genetic Epidemiology and Statistics Unit in the Diabetes Epidemiology and Clinical Research Section, National Institute of Diabetes and Digestive and Kidney Diseases, Phoenix, AZ. SUMMARY Type 2 diabetes is thought to result from a has been found to have a stronger effect insufficient sample sizes to detect small combination of environmental, behavioral, than the rs7903146 SNP in TCF7L2, which effects, a nearly exclusive focus on popu- and genetic factors, with the heritability itself has only a modest effect (odds ratio lations of European descent, an imperfect of type 2 diabetes estimated to be in the ~1.4). Nonetheless, GWAS findings have capture of uncommon genetic variants, range of 25% to 72% based on family and illustrated novel pathways, pointed toward an incomplete ascertainment of alternate twin studies. -
Structural Variant Selection for High-Altitude Adaptation Using Single-Molecule 2 Long-Read Sequencing
bioRxiv preprint doi: https://doi.org/10.1101/2021.03.27.436702; this version posted March 27, 2021. 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 Structural variant selection for high-altitude adaptation using single-molecule 2 long-read sequencing 3 Jinlong Shi1,2,4*, Zhilong Jia1,2,3*, Xiaojing Zhao2*, Jinxiu Sun4*, Fan Liang5*, Minsung Park5*, Chenghui Zhao1, 4 Xiaoreng Wang2, Qi Chen4, Xinyu Song2,3, Kang Yu1, Qian Jia2, Depeng Wang5, Yuhui Xiao5, Yinzhe Liu5, Shijing 5 Wu1, Qin Zhong2, Jue Wu2, Saijia Cui2, Xiaochen Bo6, Zhenzhou Wu7, Manolis Kellis8,9, Kunlun He1,2# 6 1. Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information 7 Technology, Chinese PLA General Hospital, Beijing, China. 8 2. Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, 9 China. 10 3. Research Center of Medical Artificial Intelligence, Chinese PLA General Hospital, Beijing, China. 11 4. Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, China. 12 5. GrandOmics Biosciences Inc, Beijing, China. 13 6. Beijing Institute of Radiation Medicine, Beijing, China. 14 7. BioMind Inc, Beijing, China. 15 8. Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, 16 MA, USA. 17 9. Broad Institute of MIT and Harvard, Cambridge, MA, USA. 18 *These authors contributed equally to this work. 19 #Corresponding author: [email protected] 20 21 Abstract: (150 words) 22 Structural variants (SVs) can be important drivers of human adaptation with strong effects, but previous studies 23 have focused primarily on common variants with weak effects. -
UNIVERSITY of CALIFORNIA IRVINE Genome-Wide Analysis of NIPBL
UNIVERSITY OF CALIFORNIA IRVINE Genome-wide analysis of NIPBL/cohesin binding in mouse and human cells: Implications for gene regulation and human disease DISSERTATION Submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Sciences by Daniel Newkirk Dissertation Committee: Professor Kyoko Yokomori, Chair Professor Xing Dai Professor Bogi Anderson Assistant Professor Ali Mortazavi Associate Professor Xiaohui Xie 2015 © Daniel Newkirk 2015 Chapter 2 © 2011 Mary Ann Liebert, Inc., New Rochelle, NY i Dedication This dissertation is dedicated to my family and many friends who have encouraged me to pursue this dream ii Table of Contents Page DEDICATION ii ABBREVIATIONS: v LIST OF FIGURES vi LIST OF TABLES vii ACKNOWLEDGEMENTS viii CURRICULUM VITAE x ABSTRACT xiii CHAPTER 1: Introduction 1 CHAPTER 2: AREM 30 Abstract 31 Introduction 32 Results 35 Discussion 39 Methods 46 References 57 CHAPTER 3: Cornelia de Lange Syndrome 61 Abstract 62 Introduction 63 Results 67 Discussion 98 Methods 104 References 110 CHAPTER 4: NIPBL in HeLa 116 Abstract 117 Introduction 118 Results 120 Discussion 139 Methods 142 References 145 CHAPTER5: FSHD 147 iii Abstract 148 Introduction 150 Results 153 Discussion 168 Methods 169 References 172 CHAPTER 6: Conclusion 174 iv Abbreviations CdLS: Cornelia de Lange Syndrome ChIP-seq: Chromatin immunoprecipitation couple to high- throughput sequencing DEGs: differentially expressed genes DMRs: differentially methylated regions EM: expectation maximization FSHD: Facioscapulohumeral -
The Pdx1 Bound Swi/Snf Chromatin Remodeling Complex Regulates Pancreatic Progenitor Cell Proliferation and Mature Islet Β Cell
Page 1 of 125 Diabetes The Pdx1 bound Swi/Snf chromatin remodeling complex regulates pancreatic progenitor cell proliferation and mature islet β cell function Jason M. Spaeth1,2, Jin-Hua Liu1, Daniel Peters3, Min Guo1, Anna B. Osipovich1, Fardin Mohammadi3, Nilotpal Roy4, Anil Bhushan4, Mark A. Magnuson1, Matthias Hebrok4, Christopher V. E. Wright3, Roland Stein1,5 1 Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 2 Present address: Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 3 Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 4 Diabetes Center, Department of Medicine, UCSF, San Francisco, California 5 Corresponding author: [email protected]; (615)322-7026 1 Diabetes Publish Ahead of Print, published online June 14, 2019 Diabetes Page 2 of 125 Abstract Transcription factors positively and/or negatively impact gene expression by recruiting coregulatory factors, which interact through protein-protein binding. Here we demonstrate that mouse pancreas size and islet β cell function are controlled by the ATP-dependent Swi/Snf chromatin remodeling coregulatory complex that physically associates with Pdx1, a diabetes- linked transcription factor essential to pancreatic morphogenesis and adult islet-cell function and maintenance. Early embryonic deletion of just the Swi/Snf Brg1 ATPase subunit reduced multipotent pancreatic progenitor cell proliferation and resulted in pancreas hypoplasia. In contrast, removal of both Swi/Snf ATPase subunits, Brg1 and Brm, was necessary to compromise adult islet β cell activity, which included whole animal glucose intolerance, hyperglycemia and impaired insulin secretion. Notably, lineage-tracing analysis revealed Swi/Snf-deficient β cells lost the ability to produce the mRNAs for insulin and other key metabolic genes without effecting the expression of many essential islet-enriched transcription factors.