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Smemo S, Campos LC, Moskowitz IP, Krieger JE, Pereira AC, Nobrega MA. Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease. Hum Mol Genet 2012; 21:3255-63. [PMID: 22543974 PMCID: PMC3384386 DOI: 10.1093/hmg/dds165] [Citation(s) in RCA: 145] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 03/31/2012] [Accepted: 04/20/2012] [Indexed: 12/20/2022] Open
Abstract
Recent studies have identified the genetic underpinnings of a growing number of diseases through targeted exome sequencing. However, this strategy ignores the large component of the genome that does not code for proteins, but is nonetheless biologically functional. To address the possible involvement of regulatory variation in congenital heart diseases (CHDs), we searched for regulatory mutations impacting the activity of TBX5, a dosage-dependent transcription factor with well-defined roles in the heart and limb development that has been associated with the Holt-Oram syndrome (heart-hand syndrome), a condition that affects 1/100 000 newborns. Using a combination of genomics, bioinformatics and mouse genetic engineering, we scanned ∼700 kb of the TBX5 locus in search of cis-regulatory elements. We uncovered three enhancers that collectively recapitulate the endogenous expression pattern of TBX5 in the developing heart. We re-sequenced these enhancer elements in a cohort of non-syndromic patients with isolated atrial and/or ventricular septal defects, the predominant cardiac defects of the Holt-Oram syndrome, and identified a patient with a homozygous mutation in an enhancer ∼90 kb downstream of TBX5. Notably, we demonstrate that this single-base-pair mutation abrogates the ability of the enhancer to drive expression within the heart in vivo using both mouse and zebrafish transgenic models. Given the population-wide frequency of this variant, we estimate that 1/100 000 individuals would be homozygous for this variant, highlighting that a significant number of CHD associated with TBX5 dysfunction might arise from non-coding mutations in TBX5 heart enhancers, effectively decoupling the heart and hand phenotypes of the Holt-Oram syndrome.
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MESH Headings
- Abnormalities, Multiple/embryology
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/metabolism
- Animals
- Animals, Genetically Modified
- Base Sequence
- Enhancer Elements, Genetic
- Heart/embryology
- Heart Defects, Congenital/embryology
- Heart Defects, Congenital/genetics
- Heart Defects, Congenital/metabolism
- Heart Septal Defects, Atrial/embryology
- Heart Septal Defects, Atrial/genetics
- Heart Septal Defects, Atrial/metabolism
- Homozygote
- Humans
- Lower Extremity Deformities, Congenital/embryology
- Lower Extremity Deformities, Congenital/genetics
- Lower Extremity Deformities, Congenital/metabolism
- Mice
- Molecular Sequence Data
- Point Mutation
- T-Box Domain Proteins/genetics
- T-Box Domain Proteins/metabolism
- Upper Extremity Deformities, Congenital/embryology
- Upper Extremity Deformities, Congenital/genetics
- Upper Extremity Deformities, Congenital/metabolism
- Zebrafish
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Affiliation(s)
| | - Luciene C. Campos
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Ivan P. Moskowitz
- Department of Pediatrics, and
- Department of Pathology, University of Chicago, Chicago, IL, USA, and
| | - José E. Krieger
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
| | - Alexandre C. Pereira
- Heart Institute (InCor), University of São Paulo Medical School, São Paulo, Brazil
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402
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Melanoma Genetics: Recent Findings Take Us Beyond Well-Traveled Pathways. J Invest Dermatol 2012; 132:1763-74. [DOI: 10.1038/jid.2012.75] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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403
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Lara-Pezzi E, Dopazo A, Manzanares M. Understanding cardiovascular disease: a journey through the genome (and what we found there). Dis Model Mech 2012; 5:434-43. [PMID: 22730474 PMCID: PMC3380707 DOI: 10.1242/dmm.009787] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cardiovascular disease (CVD) is a major cause of mortality and hospitalization worldwide. Several risk factors have been identified that are strongly associated with the development of CVD. However, these explain only a fraction of cases, and the focus of research into the causes underlying the unexplained risk has shifted first to genetics and more recently to genomics. A genetic contribution to CVD has long been recognized; however, with the exception of certain conditions that show Mendelian inheritance, it has proved more challenging than anticipated to identify the precise genomic components responsible for the development of CVD. Genome-wide association studies (GWAS) have provided information about specific genetic variations associated with disease, but these are only now beginning to reveal the underlying molecular mechanisms. To fully understand the biological implications of these associations, we need to relate them to the exquisite, multilayered regulation of protein expression, which includes chromatin remodeling, regulatory elements, microRNAs and alternative splicing. Understanding how the information contained in the DNA relates to the operation of these regulatory layers will allow us not only to better predict the development of CVD but also to develop more effective therapies.
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Affiliation(s)
| | - Ana Dopazo
- Genomics Unit, Centro Nacional de Investigaciones, Cardiovasculares (CNIC), Melchor Fernández Almagro 3, 28029 Madrid, Spain
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404
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Lambrechts D, Truong T, Justenhoven C, Humphreys MK, Wang J, Hopper JL, Dite GS, Apicella C, Southey MC, Schmidt MK, Broeks A, Cornelissen S, van Hien R, Sawyer E, Tomlinson I, Kerin M, Miller N, Milne RL, Zamora MP, Arias Pérez JI, Benítez J, Hamann U, Ko YD, Brüning T, Chang-Claude J, Eilber U, Hein R, Nickels S, Flesch-Janys D, Wang-Gohrke S, John EM, Miron A, Winqvist R, Pylkäs K, Jukkola-Vuorinen A, Grip M, Chenevix-Trench G, Beesley J, Chen X, Menegaux F, Cordina-Duverger E, Shen CY, Yu JC, Wu PE, Hou MF, Andrulis IL, Selander T, Glendon G, Mulligan AM, Anton-Culver H, Ziogas A, Muir KR, Lophatananon A, Rattanamongkongul S, Puttawibul P, Jones M, Orr N, Ashworth A, Swerdlow A, Severi G, Baglietto L, Giles G, Southey M, Marmé F, Schneeweiss A, Sohn C, Burwinkel B, Yesilyurt BT, Neven P, Paridaens R, Wildiers H, Brenner H, Müller H, Arndt V, Stegmaier C, Meindl A, Schott S, Bartram CR, Schmutzler RK, Cox A, Brock IW, Elliott G, Cross SS, Fasching PA, Schulz-Wendtland R, Ekici AB, Beckmann MW, Fletcher O, Johnson N, Silva IDS, Peto J, Nevanlinna H, Muranen TA, Aittomäki K, Blomqvist C, Dörk T, Schürmann P, Bremer M, Hillemanns P, Bogdanova NV, Antonenkova NN, Rogov YI, Karstens JH, Khusnutdinova E, Bermisheva M, Prokofieva D, Gancev S, Jakubowska A, Lubinski J, Jaworska K, Durda K, Nordestgaard BG, Bojesen SE, Lanng C, Mannermaa A, Kataja V, Kosma VM, Hartikainen JM, Radice P, Peterlongo P, Manoukian S, Bernard L, Couch FJ, Olson JE, Wang X, Fredericksen Z, Alnæs GG, Kristensen V, Børresen-Dale AL, Devilee P, Tollenaar RA, Seynaeve CM, Hooning MJ, García-Closas M, Chanock SJ, Lissowska J, Sherman ME, Hall P, Liu J, Czene K, Kang D, Yoo KY, Noh DY, Lindblom A, Margolin S, Dunning AM, Pharoah PD, Easton DF, Guénel P, Brauch H. 11q13 is a susceptibility locus for hormone receptor positive breast cancer. Hum Mutat 2012; 33:1123-32. [PMID: 22461340 PMCID: PMC3370081 DOI: 10.1002/humu.22089] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 03/08/2012] [Indexed: 01/07/2023]
Abstract
A recent two-stage genome-wide association study (GWAS) identified five novel breast cancer susceptibility loci on chromosomes 9, 10, and 11. To provide more reliable estimates of the relative risk associated with these loci and investigate possible heterogeneity by subtype of breast cancer, we genotyped the variants rs2380205, rs1011970, rs704010, rs614367, and rs10995190 in 39 studies from the Breast Cancer Association Consortium (BCAC), involving 49,608 cases and 48,772 controls of predominantly European ancestry. Four of the variants showed clear evidence of association (P ≤ 3 × 10(-9) ) and weak evidence was observed for rs2380205 (P = 0.06). The strongest evidence was obtained for rs614367, located on 11q13 (per-allele odds ratio 1.21, P = 4 × 10(-39) ). The association for rs614367 was specific to estrogen receptor (ER)-positive disease and strongest for ER plus progesterone receptor (PR)-positive breast cancer, whereas the associations for the other three loci did not differ by tumor subtype.
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Affiliation(s)
| | - Therese Truong
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Christina Justenhoven
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Germany
| | - Manjeet K. Humphreys
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jean Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John L. Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia
| | - Gillian S. Dite
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia
| | - Carmel Apicella
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Annegien Broeks
- Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Sten Cornelissen
- Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Richard van Hien
- Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Elinor Sawyer
- Division of Cancer Studies, NIHR Comprehensive Biomedical Research Centre, Guy's & St. Thomas' NHS Foundation Trust in partnership with King's College London, London, United Kingdom
| | - Ian Tomlinson
- Welcome Trust Centre for Human Genetics and Oxford Biomedical Research Centre, University of Oxford, United Kingdom
| | - Michael Kerin
- Clinical Science Institute. University Hospital Galway, Galway, Ireland
| | - Nicola Miller
- Clinical Science Institute. University Hospital Galway, Galway, Ireland
| | - Roger L. Milne
- Genetic and Molecular Epidemiology Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - M. Pilar Zamora
- Servicio de Oncología Médica, Hospital Universitario La Paz, Madrid, Spain
| | | | - Javier Benítez
- Human Genetics Group, Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany
| | - The GENICA Network
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Molecular Genetics of Breast Cancer, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, Institute of Pathology, Medical Faculty of the University of Bonn, Bonn, Germany, Institute for Prevention and Occupational Medicine of the German Social Accident Insurance (IPA), Bochum, Germany; Institute and Outpatient Clinic of Occupational Medicine, Saarland University Medical Center and Saarland University Faculty of Medicine, Homburg, German
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ursel Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rebecca Hein
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Nickels
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Flesch-Janys
- Institute for Medical Biometrics and Epidemiology, University Clinic Hamburg-Eppendorf, Hamburg, Germany
| | - Shan Wang-Gohrke
- Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - Esther M. John
- Cancer Prevention Institute of California, Fremont, CA, USA and Stanford University School of Medicine and Stanford Cancer Institute, Stanford, CA, USA
| | | | - Robert Winqvist
- Laboratory of Cancer Genetics, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Katri Pylkäs
- Laboratory of Cancer Genetics, Department of Clinical Genetics and Biocenter Oulu, University of Oulu, Oulu, Finland
| | | | - Mervi Grip
- Department of Surgery, Oulu University Hospital, University of Oulu, Oulu, Finland
| | | | | | - Xiaoqing Chen
- Queensland Institute of Medical Research, Brisbane, Australia
| | | | | | - Florence Menegaux
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Emilie Cordina-Duverger
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Chen-Yang Shen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Taiwan Biobank, Taipei, Taiwan
| | - Jyh-Cherng Yu
- Department of Surgery, Tri-Service General Hospital, Taipei, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan; Taiwan Biobank, Taipei, Taiwan
| | - Ming-Feng Hou
- Cancer Center and Department of Surgery, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung, Taiwan
| | - Irene L. Andrulis
- Ontario Cancer Genetics Network, Cancer Care Ontario; Fred A. Litwin Center for Cancer Genetics, Samuel Lunenfeld Research Institute, Mount Sinai Hospital; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Teresa Selander
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gord Glendon
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, California, USA
| | - Kenneth R. Muir
- Health Sciences Research Institute, Warwick Medical School, Warwick University, Coventry, UK
| | - Artitaya Lophatananon
- Health Sciences Research Institute, Warwick Medical School, Warwick University, Coventry, UK
| | - Suthee Rattanamongkongul
- Department of Preventive Medicine, Srinakhrainwirot University, Ongkharak, Nakhon Nayok, Thailand
| | - Puttisak Puttawibul
- Department of Surgery, Medical School, Prince Songkla University, Songkla, Thailand
| | - Michael Jones
- Section of Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Nicholas Orr
- Breakthrough Breast Cancer Research Centre, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Alan Ashworth
- Breakthrough Breast Cancer Research Centre, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - Anthony Swerdlow
- Section of Epidemiology, The Institute of Cancer Research, Sutton, Surrey, UK
| | - Gianluca Severi
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Laura Baglietto
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Graham Giles
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, The University of Melbourne, Melbourne, Australia
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Melissa Southey
- Cancer Epidemiology Centre, The Cancer Council Victoria, Melbourne, Australia
| | - Federik Marmé
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Christof Sohn
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Patrick Neven
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Robert Paridaens
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Hans Wildiers
- Multidisciplinary Breast Center, University Hospital Gasthuisberg, Leuven, Belgium
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Heiko Müller
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | | | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technical University of Munich, Munich, Germany
| | - Sarah Schott
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
| | - Claus R. Bartram
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany
| | - Rita K. Schmutzler
- Division of Molecular Gyneco-Oncology, Department of Gynaecology and Obstetrics, Center of Molecular Medicine Cologne (CMMC), University Hospital of Cologne, Cologne, Germany
| | - Angela Cox
- Institute for Cancer Studies, Department of Oncology, University of Sheffield, UK
| | - Ian W. Brock
- Institute for Cancer Studies, Department of Oncology, University of Sheffield, UK
| | - Graeme Elliott
- Institute for Cancer Studies, Department of Oncology, University of Sheffield, UK; current address: University of Manchester, Manchester, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, UK
| | - Peter A. Fasching
- University Breast Center, Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany; David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, CA, USA
| | | | - Arif B. Ekici
- Institute of Human Genetics, Friedrich Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Matthias W. Beckmann
- University Breast Center, Department of Gynecology and Obstetrics, University Hospital Erlangen, Erlangen, Germany
| | - Olivia Fletcher
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | - Nichola Johnson
- Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
| | | | - Julian Peto
- London School of Hygiene and Tropical Medicine, London, UK
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Biomedicum Helsinki, Helsinki, Finland
| | - Taru A. Muranen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Biomedicum Helsinki, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Central Hospital, Helsinki, Finland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Thilo Dörk
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Peter Schürmann
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Michael Bremer
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Peter Hillemanns
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Natalia V. Bogdanova
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | | | - Yuri I. Rogov
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Johann H. Karstens
- Department of Obstetrics and Gynaecology, Hannover Medical School, Hannover, Germany
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | - Darya Prokofieva
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
| | | | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubinski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Katarzyna Jaworska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Postgraduate School of Molecular Medicine, Warsaw Medical University, Warsaw, Poland
| | - Katarzyna Durda
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Børge G. Nordestgaard
- Copenhagen General Population Study and Department of Clinical Biochemistry, Herlev University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Stig E. Bojesen
- Copenhagen General Population Study and Department of Clinical Biochemistry, Herlev University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Charlotte Lanng
- Department of Breast Surgery, Herlev University Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Arto Mannermaa
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Biocenter Kuopio and Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Vesa Kataja
- School of Medicine, Institute of Clinical Medicine, Oncology, University of Eastern Finland, Biocenter Kuopio and Department of Oncology, Kuopio University Hospital, Kuopio, Finland
| | - Veli-Matti Kosma
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Biocenter Kuopio and Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Jaana M. Hartikainen
- School of Medicine, Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Biocenter Kuopio and Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy and IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Paolo Peterlongo
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Preventive and Predicted Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy and IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Preventive and Predictive Medicine, Fondazione IRCCS Istituto Nazionale Tumori (INT), Milan, Italy
| | - Loris Bernard
- Department of Experimental Oncology, Istituto Europeo di Oncologia (IEO), Milan, Italy and Consortium for Genomics Technology (Cogentech) Milan, Italy
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Janet E. Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Xianshu Wang
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | | | - Grethe Grenaker Alnæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), UiO, Norway
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
- Faculty of Medicine (Faculty Division Ahus), UiO, Norway
| | - Peter Devilee
- Department of Human Genetics, and Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Caroline M. Seynaeve
- Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus MC-Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Rotterdam Family Cancer Clinic, Erasmus MC-Daniel den Hoed Cancer Center, Rotterdam, The Netherlands
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA; Division of Genetics and Epidemiology, Institute of Cancer Research and Breakthrough Breast Cancer Research Centre, London, UK
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Mark E. Sherman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Jianjun Liu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Daehee Kang
- Seoul National University College of Medicine, Seoul, Korea
| | - Keun-Young Yoo
- Seoul National University College of Medicine, Seoul, Korea
| | - Dong-Young Noh
- Seoul National University College of Medicine, Seoul, Korea
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Sara Margolin
- Department of Oncology Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Pascal Guénel
- Inserm (National Institute of Health and Medical Research), CESP (Center for Research in Epidemiology and Population Health), U1018, Environmental Epidemiology of Cancer Team, Villejuif, France
- University Paris-Sud, UMRS 1018, Villejuif, France
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, and University Tübingen, Germany
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405
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Abstract
Affecting about 1 in 12 Americans annually, depression is a leading cause of the global disease burden. While a range of effective antidepressants are now available, failure and relapse rates remain substantial, with intolerable side effect burden the most commonly cited reason for discontinuation. Thus, understanding individual differences in susceptibility to antidepressant therapy side effects will be essential to optimize depression treatment. Here we perform genome-wide association studies (GWAS) to identify genetic variation influencing susceptibility to citalopram-induced side effects. The analysis sample consisted of 1762 depression patients, successfully genotyped for 421K single-nucleotide polymorphisms (SNPs), from the Sequenced Treatment Alternatives to Relieve Depression (STAR(*)D) study. Outcomes included five indicators of citalopram side effects: general side effect burden, overall tolerability, sexual side effects, dizziness and vision/hearing side effects. Two SNPs met our genome-wide significance criterion (q<0.1), ensuring that, on average, only 10% of significant findings are false discoveries. In total, 12 additional SNPs demonstrated suggestive associations (q<0.5). The top finding was rs17135437, an intronic SNP within EMID2, mediating the effects of citalopram on vision/hearing side effects (P=3.27 × 10(-8), q=0.026). The second genome-wide significant finding, representing a haplotype spanning ∼30 kb and eight genotyped SNPs in a gene desert on chromosome 13, was associated with general side effect burden (P=3.22 × 10(-7), q=0.096). Suggestive findings were also found for SNPs at LAMA1, AOX2P, EGFLAM, FHIT and RTP2. Although our findings require replication and functional validation, this study demonstrates the potential of GWAS to discover genes and pathways that potentially mediate adverse effects of antidepressant medications.
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406
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The chromosome 9p21.3 coronary heart disease risk allele is associated with altered gene expression in normal heart and vascular tissues. PLoS One 2012; 7:e39574. [PMID: 22768093 PMCID: PMC3387158 DOI: 10.1371/journal.pone.0039574] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 05/22/2012] [Indexed: 12/31/2022] Open
Abstract
Genome-wide association studies have identified a coronary artery disease (CAD) risk locus in a non-coding region at 9p21.3, the nearest genes being CDKN2A and CDKN2B. To understand the pathways by which this locus might influence CAD susceptibility, we investigated associations between the 9p21.3 risk genotype and global gene expression in heart tissue from donors with no diagnosed heart disease (n = 108, predominant cause of death, cerebral vascular accident) and in carotid plaque (n = 106), aorta (n = 104) and mammary artery (n = 88) tissues from heart valve and carotid endarterectomy patients. Genotyping was performed with Taqman assays and Illumina arrays, and gene expression profiles generated with Affymetrix microarrays. Associations were analyzed with an additive genetic model. In heart tissue, 46 genes were putatively altered in association with the 9p21.3 risk allele (70% down-regulated, fold-change >1.1 per allele, p<0.05 adjusted for age, gender, ethnicity, cause of death). These genes were enriched for biomarkers of myocardial infarction (p = 1.53×10−9), response to wounding (p = 2.65×10−10) and inflammatory processes (p<1.97×10−7). Among the top 10 most down-regulated genes, 7 genes shared a set of transcription factor binding sites within conserved promoter regions (p<1.14×10−5), suggesting they may be co-regulated. Canonical pathway modelling of the most differentially expressed transcripts across all tissues (154 genes, 60% down-regulated, fold-change >1.1 per allele, p<0.01) showed that 75% of the genes could be transcriptionally regulated through the cell cycle G1 phase progression pathway (p<1.08×10−258), in which CDKN2A and CDKN2B play a regulatory role. These data suggest that the cell cycle G1 phase progression pathway is activated in individuals with the 9p21.3 risk allele. This may contribute to a proliferative phenotype that promotes adverse cardiac hypertrophy and vascular remodeling, leading to an increased CAD risk.
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407
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Genetic and functional analyses implicate the NUDT11, HNF1B, and SLC22A3 genes in prostate cancer pathogenesis. Proc Natl Acad Sci U S A 2012; 109:11252-7. [PMID: 22730461 DOI: 10.1073/pnas.1200853109] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
One of the central goals of human genetics is to discover the genes and pathways driving human traits. To date, most of the common risk alleles discovered through genome-wide association studies (GWAS) map to nonprotein-coding regions. Because of our relatively poorer understanding of this part of the genome, the functional consequences of trait-associated variants pose a considerable challenge. To identify the genes through which risk loci act, we hypothesized that the risk variants are regulatory elements. For each of 12 known risk polymorphisms, we evaluated the correlation between risk allele status and transcript abundance for all annotated protein-coding transcripts within a 1-Mb interval. A total of 103 transcripts were evaluated in 662 prostate tissue samples [normal (n = 407) and tumor (n = 255)] from 483 individuals [European Americans (n = 233), Japanese (n = 127), and African Americans (n = 123)]. In a pooled analysis, 4 of the 12 risk variants were strongly associated with five transcripts (NUDT11, MSMB, NCOA4, SLC22A3, and HNF1B) in histologically normal tissue (P ≤ 0.001). Although associations were also observed in tumor tissue, they tended to be more attenuated. Previously, we showed that MSMB and NCOA4 participate in prostate cancer pathogenesis. Suppressing the expression of NUDT11, SLC22A3, and HNF1B influences cellular phenotypes associated with tumor-related properties in prostate cancer cells. Taken together, the data suggest that these transcripts contribute to prostate cancer pathogenesis.
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408
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Abstract
Differential gene expression is the fundamental mechanism underlying animal development and cell differentiation. However, it is a challenge to identify comprehensively and accurately the DNA sequences that are required to regulate gene expression: namely, cis-regulatory modules (CRMs). Three major features, either singly or in combination, are used to predict CRMs: clusters of transcription factor binding site motifs, non-coding DNA that is under evolutionary constraint and biochemical marks associated with CRMs, such as histone modifications and protein occupancy. The validation rates for predictions indicate that identifying diagnostic biochemical marks is the most reliable method, and understanding is enhanced by the analysis of motifs and conservation patterns within those predicted CRMs.
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409
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Maccioni L, Rachakonda PS, Scherer D, Bermejo JL, Planelles D, Requena C, Hemminki K, Nagore E, Kumar R. Variants at chromosome 20 (ASIP locus) and melanoma risk. Int J Cancer 2012; 132:42-54. [PMID: 22628150 DOI: 10.1002/ijc.27648] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 05/07/2012] [Indexed: 02/04/2023]
Abstract
Agouti signaling protein (ASIP) locus on chromosome 20q11 is implicated, as shown by genome-wide association studies, in phenotype variation and melanoma risk. We genotyped 837 melanoma cases and 1,154 controls for 21 single nucleotide polymorphisms (SNPs) informative for 495 polymorphisms at the locus. Our data showed an increased risk of melanoma (odds ratio [OR] 1.27, 95% confidence interval [95% CI] 1.03-1.57) in carriers of the rs4911414 variant, located 120 kb upstream of ASIP. The main effect of rs4911414, as reported previously, was in tandem with a 10 kb adjacent polymorphism rs1015362; two constituted risk-associated haplotype/diplotype. Except for rs1015363, none of the 12 tagging SNPs, genotyped to cover 239.9 kb region with polymorphisms linked to rs4911414 and rs1015362, were associated with melanoma. Our data confirmed a previous association of melanoma risk (OR 1.82, 95% CI 1.37-2.41) with rs4911442, located in intron 5 of the nuclear receptor coactivator 6 (NCOA6) gene. The rs910871, one of the six variants, genotyped to cover NCOA6, showed an association with melanoma risk (OR 1.33, 95% CI 1.04-1.70). Both, rs4911442 and rs910871 were in moderate linkage with a, previously reported, risk-associated rs910873 polymorphism. A haplotype from the variants within NCOA6 showed an association with risk of melanoma (OR 1.49, 95% CI 1.17-1.88). Interaction between risk-associated polymorphisms and previously genotyped melanocortin receptor 1 (MC1R) variants, in our study, was not statistically significant. Nevertheless, the carriers of the variant alleles over the background of MC1R variants were at a higher risk than the carriers not enriched for MC1R variants. Our data confirmed the association of different variants at chromosome 20q11 with melanoma risk.
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Affiliation(s)
- Livia Maccioni
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre, Heidelberg, Germany
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410
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Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus. Genome Res 2012; 22:1437-46. [PMID: 22665440 PMCID: PMC3409257 DOI: 10.1101/gr.135665.111] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Genome-wide association studies (GWAS) are identifying genetic predisposition to various diseases. The 17q24.3 locus harbors the single nucleotide polymorphism (SNP) rs1859962 that is statistically associated with prostate cancer (PCa). It defines a 130-kb linkage disequilibrium (LD) block that lies in an ∼2-Mb gene desert area. The functional biology driving the risk associated with this LD block is unknown. Here, we integrate genome-wide chromatin landscape data sets, namely, epigenomes and chromatin openness from diverse cell types. This identifies a PCa-specific enhancer within the rs1859962 risk LD block that establishes a 1-Mb chromatin loop with the SOX9 gene. The rs8072254 and rs1859961 SNPs mapping to this enhancer impose allele-specific gene expression. The variant allele of rs8072254 facilitates androgen receptor (AR) binding driving increased enhancer activity. The variant allele of rs1859961 decreases FOXA1 binding while increasing AP-1 binding. The latter is key to imposing allele-specific gene expression. The rs8072254 variant in strong LD with the rs1859962 risk SNP can account for the risk associated with this locus, while rs1859961 is a rare variant less likely to contribute to the risk associated with this LD block. Together, our results demonstrate that multiple genetic variants mapping to a unique enhancer looping to the SOX9 oncogene can account for the risk associated with the PCa 17q24.3 locus. Allele-specific recruitment of the transcription factors androgen receptor (AR) and activating protein-1 (AP-1) account for the increased enhancer activity ascribed to this PCa-risk LD block. This further supports the notion that an integrative genomics approach can identify the functional biology disrupted by genetic risk variants.
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411
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Xu F, Wang Q, Zhang F, Zhu Y, Gu Q, Wu L, Yang L, Yang X. Impact of Next-Generation Sequencing (NGS) technology on cardiovascular disease research. Cardiovasc Diagn Ther 2012; 2:138-46. [PMID: 24282707 DOI: 10.3978/j.issn.2223-3652.2012.06.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Accepted: 06/08/2012] [Indexed: 11/14/2022]
Abstract
In recent years, hundreds of gene loci associated with multiple cardiovascular pathologies and traits have been identified through high-throughput Next-Generation Sequencing (NGS) technology. Due to the increasing efficiency and decreasing cost of NGS, rapid progresses anticipated in the field of CVD research. This review summarizes the main strategies of CV research with NGS at the level of genomics, transcriptomics, epigenetics, and proteomics.
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412
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Abstract
BACKGROUND Coronary heart disease (CHD) is a leading cause of death worldwide, yet many areas of its pathogenesis remain unknown or poorly understood, leaving potential for novel preventive and therapeutic interventions. Recent major advances in genomic science and technology have opened new avenues of investigation in the pathogenesis of CHD, some of which are leading to clinical translation. SOURCES OF DATA The published literature in CHD genetics has burgeoned in the last 5 years with the reporting of genome-wide association studies (GWASs) and many other findings. AREAS OF AGREEMENT Identification of many genetic variants with small effects on CHD risk has been a common finding. These have included several predicted loci, such as those involved in conventional CHD risk factors (e.g. plasma lipids) and many novel loci, where their mechanism of action is unclear. The need for large, collaborative approaches to research has also become clear and is now an accepted modus operandi. AREAS OF CONTROVERSY The clinical utility of novel GWAS findings remains uncertain. In particular, the relative contribution of common variants of modest effect and rare variants of larger effects to risk of CHD or response to drugs is unclear. GROWING POINTS As a greater number of larger GWASs are conducted in CHD and its related phenotypes, much effort is being made to find translational applications for their findings. Therapeutics, prediction and pathology are major areas of research endeavour.
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Affiliation(s)
- Daniel I Swerdlow
- Genetic Epidemiology Group, Department of Epidemiology and Public Health, UCL Institute of Epidemiology and Health Care, University College London, UK
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413
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Li X, Zhao L, Chen Z, Lin Y, Yu P, Mao L. Continuous Electrochemical Monitoring of Extracellular Lactate Production from Neonatal Rat Cardiomyocytes following Myocardial Hypoxia. Anal Chem 2012; 84:5285-91. [DOI: 10.1021/ac300354z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Xianchan Li
- Beijing National
Laboratory for Molecular Sciences,
Key Laboratory of Analytical Chemistry for Living Biosystems, Institute
of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Lingzhi Zhao
- Beijing National
Laboratory for Molecular Sciences,
Key Laboratory of Analytical Chemistry for Living Biosystems, Institute
of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Zhenling Chen
- Beijing National
Laboratory for Molecular Sciences,
Key Laboratory of Analytical Chemistry for Living Biosystems, Institute
of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Yuqing Lin
- Beijing National
Laboratory for Molecular Sciences,
Key Laboratory of Analytical Chemistry for Living Biosystems, Institute
of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Ping Yu
- Beijing National
Laboratory for Molecular Sciences,
Key Laboratory of Analytical Chemistry for Living Biosystems, Institute
of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Lanqun Mao
- Beijing National
Laboratory for Molecular Sciences,
Key Laboratory of Analytical Chemistry for Living Biosystems, Institute
of Chemistry, the Chinese Academy of Sciences (CAS), Beijing 100190, China
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414
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Naidoo N, Pawitan Y, Soong R, Cooper DN, Ku CS. Human genetics and genomics a decade after the release of the draft sequence of the human genome. Hum Genomics 2012; 5:577-622. [PMID: 22155605 PMCID: PMC3525251 DOI: 10.1186/1479-7364-5-6-577] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Substantial progress has been made in human genetics and genomics research over the past ten years since the publication of the draft sequence of the human genome in 2001. Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome. Major developments have been made in cataloguing genetic variation, the International HapMap Project, and with respect to advances in genotyping technologies. These developments are vital for the emergence of genome-wide association studies in the investigation of complex diseases and traits. In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing studies such as the 1000 Genomes Project and the International Cancer Genome Consortium. The high-throughput sequencing and sequence-capture technologies are also providing new opportunities to study Mendelian disorders through exome sequencing and whole-genome sequencing. This paper reviews these major developments in human genetics and genomics over the past decade.
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Affiliation(s)
- Nasheen Naidoo
- Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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415
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Abstract
Cardiovascular disease encompasses a range of conditions extending from myocardial infarction to congenital heart disease, most of which are heritable. Enormous effort has been invested in understanding the genes and specific DNA sequence variants that are responsible for this heritability. Here, we review the lessons learned for monogenic and common, complex forms of cardiovascular disease. We also discuss key challenges that remain for gene discovery and for moving from genomic localization to mechanistic insights, with an emphasis on the impact of next-generation sequencing and the use of pluripotent human cells to understand the mechanism by which genetic variation contributes to disease.
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Affiliation(s)
- Sekar Kathiresan
- Center for Human Genetic Research and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA.
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416
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Montavon T, Duboule D. Landscapes and archipelagos: spatial organization of gene regulation in vertebrates. Trends Cell Biol 2012; 22:347-54. [PMID: 22560708 DOI: 10.1016/j.tcb.2012.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 03/30/2012] [Accepted: 04/03/2012] [Indexed: 11/28/2022]
Abstract
Vertebrate genes controlling critical developmental processes are often regulated by complex sets of global enhancer sequences, located at a distance, within neighboring gene deserts. Recent technological advances have made it possible to investigate the spatial organization of these 'regulatory landscapes'. The integration of such datasets with information on chromatin status, transcriptional activity and nuclear localization of these loci, as well as the effects of genetic modifications thereof, may bring a more comprehensive understanding of tissue- and/or stage-specific gene regulation in both normal and pathological contexts. Here, we review the impact of recent technological advances on our understanding of large-scale gene regulation in vertebrates, by focusing on paradigmatic gene loci.
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Affiliation(s)
- Thomas Montavon
- National Research Centre Frontiers in Genetics, University of Geneva, Geneva, Switzerland
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417
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Single polymorphism nucleotide rs1333049 on chromosome 9p21 is associated with carotid plaques but not with common carotid intima-media thickness in older adults. A combined analysis of the Three-City and the EVA studies. Atherosclerosis 2012; 222:187-90. [DOI: 10.1016/j.atherosclerosis.2012.02.038] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Revised: 02/21/2012] [Accepted: 02/23/2012] [Indexed: 01/12/2023]
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418
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Abstract
The human genome encodes thousands of long noncoding RNAs (lncRNAs). Although most remain functionally uncharacterized biological "dark matter," lncRNAs have garnered considerable attention for their diverse roles in human biology, including developmental programs and tumor suppressor gene networks. As the number of lncRNAs associated with human disease grows, ongoing research efforts are focusing on their regulatory mechanisms. New technologies that enable enumeration of lncRNA interaction partners and determination of lncRNA structure are well positioned to drive deeper understanding of their functions and involvement in pathogenesis. In turn, lncRNAs may become targets for therapeutic intervention or new tools for biotechnology.
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Affiliation(s)
- Lance Martin
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Howard Y. Chang
- Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.
Department of Bioengineering, Stanford University, Stanford, California, USA
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419
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Affiliation(s)
- Tanmoy Mondal
- From the Department of Medical and Clinical Genetics (T.M., C.K.), Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Chandrasekhar Kanduri
- From the Department of Medical and Clinical Genetics (T.M., C.K.), Institute of Biomedicine, The Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
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420
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Wiggs JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, Doheny KF, Friedman DS, Gaasterland D, Gaasterland T, Laurie C, Lee RK, Lichter PR, Loomis S, Liu Y, Medeiros FA, McCarty C, Mirel D, Moroi SE, Musch DC, Realini A, Rozsa FW, Schuman JS, Scott K, Singh K, Stein JD, Trager EH, Vanveldhuisen P, Vollrath D, Wollstein G, Yoneyama S, Zhang K, Weinreb RN, Ernst J, Kellis M, Masuda T, Zack D, Richards JE, Pericak-Vance M, Pasquale LR, Haines JL. Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. PLoS Genet 2012; 8:e1002654. [PMID: 22570617 PMCID: PMC3343074 DOI: 10.1371/journal.pgen.1002654] [Citation(s) in RCA: 229] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 03/01/2012] [Indexed: 01/07/2023] Open
Abstract
Optic nerve degeneration caused by glaucoma is a leading cause of blindness worldwide. Patients affected by the normal-pressure form of glaucoma are more likely to harbor risk alleles for glaucoma-related optic nerve disease. We have performed a meta-analysis of two independent genome-wide association studies for primary open angle glaucoma (POAG) followed by a normal-pressure glaucoma (NPG, defined by intraocular pressure (IOP) less than 22 mmHg) subgroup analysis. The single-nucleotide polymorphisms that showed the most significant associations were tested for association with a second form of glaucoma, exfoliation-syndrome glaucoma. The overall meta-analysis of the GLAUGEN and NEIGHBOR dataset results (3,146 cases and 3,487 controls) identified significant associations between two loci and POAG: the CDKN2BAS region on 9p21 (rs2157719 [G], OR = 0.69 [95%CI 0.63-0.75], p = 1.86×10⁻¹⁸), and the SIX1/SIX6 region on chromosome 14q23 (rs10483727 [A], OR = 1.32 [95%CI 1.21-1.43], p = 3.87×10⁻¹¹). In sub-group analysis two loci were significantly associated with NPG: 9p21 containing the CDKN2BAS gene (rs2157719 [G], OR = 0.58 [95% CI 0.50-0.67], p = 1.17×10⁻¹²) and a probable regulatory region on 8q22 (rs284489 [G], OR = 0.62 [95% CI 0.53-0.72], p = 8.88×10⁻¹⁰). Both NPG loci were also nominally associated with a second type of glaucoma, exfoliation syndrome glaucoma (rs2157719 [G], OR = 0.59 [95% CI 0.41-0.87], p = 0.004 and rs284489 [G], OR = 0.76 [95% CI 0.54-1.06], p = 0.021), suggesting that these loci might contribute more generally to optic nerve degeneration in glaucoma. Because both loci influence transforming growth factor beta (TGF-beta) signaling, we performed a genomic pathway analysis that showed an association between the TGF-beta pathway and NPG (permuted p = 0.009). These results suggest that neuro-protective therapies targeting TGF-beta signaling could be effective for multiple forms of glaucoma.
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Affiliation(s)
- Janey L Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States of America.
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421
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Jarinova O, Ekker M. Regulatory variations in the era of next-generation sequencing: Implications for clinical molecular diagnostics. Hum Mutat 2012; 33:1021-30. [DOI: 10.1002/humu.22083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 03/06/2012] [Indexed: 01/05/2023]
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422
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Burri A, Hysi P, Clop A, Rahman Q, Spector TD. A genome-wide association study of female sexual dysfunction. PLoS One 2012; 7:e35041. [PMID: 22509378 PMCID: PMC3324410 DOI: 10.1371/journal.pone.0035041] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/08/2012] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Female sexual dysfunction (FSD) is an important but controversial problem with serious negative impact on women's quality of life. Data from twin studies have shown a genetic contribution to the development and maintenance of FSD. METHODOLOGY/PRINCIPAL FINDINGS We performed a genome-wide association study (GWAS) on 2.5 million single-nucleotide polymorphisms (SNPs) in 1,104 female twins (25-81 years of age) in a population-based register and phenotypic data on lifelong sexual functioning. Although none reached conventional genome-wide level of significance (10 × -8), we found strongly suggestive associations with the phenotypic dimension of arousal (rs13202860, P = 1.2 × 10(-7); rs1876525, P = 1.2 × 10(-7); and rs13209281 P = 8.3 × 10(-7)) on chromosome 6, around 500 kb upstream of the locus HTR1E (5-hydroxytryptamine receptor 1E) locus, related to the serotonin brain pathways. We could not replicate previously reported candidate SNPs associated with FSD in the DRD4, 5HT2A and IL-1B loci. CONCLUSIONS/SIGNIFICANCE We report the first GWAS of FSD symptoms in humans. This has pointed to several "risk alleles" and the implication of the serotonin and GABA pathways. Ultimately, understanding key mechanisms via this research may lead to new FSD treatments and inform clinical practice and developments in psychiatric nosology.
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Affiliation(s)
- Andrea Burri
- Biological and Experimental Psychology Group, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
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423
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Camacho-Vanegas O, Camacho S, Till J, Miranda-Lorenzo I, Terzo E, Ramirez M, Schramm V, Cordovano G, Watts G, Mehta S, Kimonis V, Hoch B, Philibert K, Raabe C, Bishop D, Glucksman M, Martignetti J. Primate genome gain and loss: a bone dysplasia, muscular dystrophy, and bone cancer syndrome resulting from mutated retroviral-derived MTAP transcripts. Am J Hum Genet 2012; 90:614-27. [PMID: 22464254 DOI: 10.1016/j.ajhg.2012.02.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/19/2012] [Accepted: 02/16/2012] [Indexed: 10/28/2022] Open
Abstract
Diaphyseal medullary stenosis with malignant fibrous histiocytoma (DMS-MFH) is an autosomal-dominant syndrome characterized by bone dysplasia, myopathy, and bone cancer. We previously mapped the DMS-MFH tumor-suppressing-gene locus to chromosomal region 9p21-22 but failed to identify mutations in known genes in this region. We now demonstrate that DMS-MFH results from mutations in the most proximal of three previously uncharacterized terminal exons of the gene encoding methylthioadenosine phosphorylase, MTAP. Intriguingly, two of these MTAP exons arose from early and independent retroviral-integration events in primate genomes at least 40 million years ago, and since then, their genomic integration has gained a functional role. MTAP is a ubiquitously expressed homotrimeric-subunit enzyme critical to polyamine metabolism and adenine and methionine salvage pathways and was believed to be encoded as a single transcript from the eight previously described exons. Six distinct retroviral-sequence-containing MTAP isoforms, each of which can physically interact with archetype MTAP, have been identified. The disease-causing mutations occur within one of these retroviral-derived exons and result in exon skipping and dysregulated alternative splicing of all MTAP isoforms. Our results identify a gene involved in the development of bone sarcoma, provide evidence of the primate-specific evolution of certain parts of an existing gene, and demonstrate that mutations in parts of this gene can result in human disease despite its relatively recent origin.
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424
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Lusis AJ. Genetics of atherosclerosis. Trends Genet 2012; 28:267-75. [PMID: 22480919 DOI: 10.1016/j.tig.2012.03.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/29/2012] [Accepted: 03/01/2012] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies (GWAS) from the past several years have provided the first unbiased evidence of the genes contributing to common cardiovascular disease traits in European and some Asian populations. The results not only confirmed the importance of prior knowledge, such as the central role of lipoproteins, but also revealed that there is still much to learn about the underlying mechanisms of this disease, as most of the associated genes do not appear to be involved in pathways previously connected to atherosclerosis. In this review, I focus on the common forms of the disease and look at both human and animal model studies. I summarize what was known before GWAS, highlight how the field has been changed by GWAS, and discuss future considerations, such as the limitations of GWAS and strategies that may lead to a more complete, mechanistic understanding of atherosclerosis.
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Affiliation(s)
- Aldons J Lusis
- University of California, Los Angeles, Department of Medicine/Division of Cardiology, Los Angeles, CA 90095-1679, USA.
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425
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Abstract
PURPOSE OF REVIEW To discuss if and how the combined analysis of large-scale datasets from multiple independent sources benefits the mapping of novel genetic elements with relevance to lipoprotein metabolism and allows for conclusions on underlying molecular mechanisms. RECENT FINDINGS Genome-wide association studies (GWAS) have identified numerous genomic loci associated with plasma lipid levels and cardiovascular disease. Yet, despite being highly successful in mapping novel loci the GWAS approach falls short to systematically extract functional information from genomic data. With the aim to complement GWAS for a better insight into disease mechanisms and identification of the most promising targets for drug development, a number of high-throughput functional genomics strategies have now been applied. These include computational approaches, consideration of gene-gene and gene-environment interactions, as well as unbiased gene-expression analyses in relevant tissues. For a limited number of loci, mechanistic insight has been gained through in-vitro and in-vivo studies by knockdown and overexpression of candidate genes. SUMMARY The integration of GWAS data with existing functional genomics strategies has contributed to ascertain the relevance of a number of novel factors for lipoprotein biology and disease. However, technologies are warranted that provide a more systematic insight into the molecular function and pathogenic relevance of promising candidate genes.
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Affiliation(s)
- Heiko Runz
- Institute of Human Genetics, University of Heidelberg, Heidelberg, Germany.
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426
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Widespread site-dependent buffering of human regulatory polymorphism. PLoS Genet 2012; 8:e1002599. [PMID: 22457641 PMCID: PMC3310774 DOI: 10.1371/journal.pgen.1002599] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 02/03/2012] [Indexed: 11/19/2022] Open
Abstract
The average individual is expected to harbor thousands of variants within non-coding genomic regions involved in gene regulation. However, it is currently not possible to interpret reliably the functional consequences of genetic variation within any given transcription factor recognition sequence. To address this, we comprehensively analyzed heritable genome-wide binding patterns of a major sequence-specific regulator (CTCF) in relation to genetic variability in binding site sequences across a multi-generational pedigree. We localized and quantified CTCF occupancy by ChIP-seq in 12 related and unrelated individuals spanning three generations, followed by comprehensive targeted resequencing of the entire CTCF–binding landscape across all individuals. We identified hundreds of variants with reproducible quantitative effects on CTCF occupancy (both positive and negative). While these effects paralleled protein–DNA recognition energetics when averaged, they were extensively buffered by striking local context dependencies. In the significant majority of cases buffering was complete, resulting in silent variants spanning every position within the DNA recognition interface irrespective of level of binding energy or evolutionary constraint. The prevalence of complex partial or complete buffering effects severely constrained the ability to predict reliably the impact of variation within any given binding site instance. Surprisingly, 40% of variants that increased CTCF occupancy occurred at positions of human–chimp divergence, challenging the expectation that the vast majority of functional regulatory variants should be deleterious. Our results suggest that, even in the presence of “perfect” genetic information afforded by resequencing and parallel studies in multiple related individuals, genomic site-specific prediction of the consequences of individual variation in regulatory DNA will require systematic coupling with empirical functional genomic measurements. A comprehensive understanding of the contribution of individual genome sequences to disease and quantitative traits will require the general ability to predict consequences of genetic variation in non-protein-coding regions, particularly those involved in gene regulation. Here we tested the power to predict such consequences when presented with “complete” information encompassing the genomic DNA binding site patterns of a well-studied regulatory protein across multiple related individuals, coupled with all individual genome sequences at the binding positions. We find that, while there is reasonable ability to predict the average effects of variation within the consensus recognition sequence of a transcriptional regulator, it is not possible to determine reliably the consequences of variation at any given genomic instance. This suggests that the interpretation of individual genome sequences will require comprehensive complementation with functional genomic studies.
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427
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Zhou X, Baron RM, Hardin M, Cho MH, Zielinski J, Hawrylkiewicz I, Sliwinski P, Hersh CP, Mancini JD, Lu K, Thibault D, Donahue AL, Klanderman BJ, Rosner B, Raby BA, Lu Q, Geldart AM, Layne MD, Perrella MA, Weiss ST, Choi AM, Silverman EK. Identification of a chronic obstructive pulmonary disease genetic determinant that regulates HHIP. Hum Mol Genet 2012; 21:1325-35. [PMID: 22140090 PMCID: PMC3284120 DOI: 10.1093/hmg/ddr569] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 11/16/2011] [Accepted: 11/28/2011] [Indexed: 01/11/2023] Open
Abstract
Multiple intergenic single-nucleotide polymorphisms (SNPs) near hedgehog interacting protein (HHIP) on chromosome 4q31 have been strongly associated with pulmonary function levels and moderate-to-severe chronic obstructive pulmonary disease (COPD). However, whether the effects of variants in this region are related to HHIP or another gene has not been proven. We confirmed genetic association of SNPs in the 4q31 COPD genome-wide association study (GWAS) region in a Polish cohort containing severe COPD cases and healthy smoking controls (P = 0.001 to 0.002). We found that HHIP expression at both mRNA and protein levels is reduced in COPD lung tissues. We identified a genomic region located ∼85 kb upstream of HHIP which contains a subset of associated SNPs, interacts with the HHIP promoter through a chromatin loop and functions as an HHIP enhancer. The COPD risk haplotype of two SNPs within this enhancer region (rs6537296A and rs1542725C) was associated with statistically significant reductions in HHIP promoter activity. Moreover, rs1542725 demonstrates differential binding to the transcription factor Sp3; the COPD-associated allele exhibits increased Sp3 binding, which is consistent with Sp3's usual function as a transcriptional repressor. Thus, increased Sp3 binding at a functional SNP within the chromosome 4q31 COPD GWAS locus leads to reduced HHIP expression and increased susceptibility to COPD through distal transcriptional regulation. Together, our findings reveal one mechanism through which SNPs upstream of the HHIP gene modulate the expression of HHIP and functionally implicate reduced HHIP gene expression in the pathogenesis of COPD.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Alleles
- Blotting, Western
- Bronchi/cytology
- Bronchi/metabolism
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Case-Control Studies
- Cells, Cultured
- Chromatin Immunoprecipitation
- Chromosome Mapping
- Chromosomes, Human, Pair 4/genetics
- Electrophoretic Mobility Shift Assay
- Enhancer Elements, Genetic/genetics
- Female
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Genetic Predisposition to Disease
- Genotype
- Haplotypes/genetics
- Humans
- Lung/cytology
- Lung/metabolism
- Male
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/metabolism
- Middle Aged
- Polymorphism, Single Nucleotide/genetics
- Prognosis
- Promoter Regions, Genetic/genetics
- Pulmonary Disease, Chronic Obstructive/genetics
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/pathology
- Real-Time Polymerase Chain Reaction
- Smoking/genetics
- Sp3 Transcription Factor/metabolism
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Affiliation(s)
- Xiaobo Zhou
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Rebecca M. Baron
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Megan Hardin
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Michael H. Cho
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Jan Zielinski
- Institute of Tuberculosis and Lung Diseases, Plocka 26, Warsaw 01-138, Poland
| | - Iwona Hawrylkiewicz
- Institute of Tuberculosis and Lung Diseases, Plocka 26, Warsaw 01-138, Poland
| | - Pawel Sliwinski
- Institute of Tuberculosis and Lung Diseases, Plocka 26, Warsaw 01-138, Poland
| | - Craig P. Hersh
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | | | - Ke Lu
- Channing Laboratory, Department of Medicine
| | | | | | | | | | - Benjamin A. Raby
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Quan Lu
- Harvard School of Public Health, Boston, MA 02115, USA and
| | - Adriana M. Geldart
- Newborn Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Matthew D. Layne
- Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark A. Perrella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
- Newborn Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Scott T. Weiss
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Augustine M.K. Choi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
| | - Edwin K. Silverman
- Channing Laboratory, Department of Medicine
- Division of Pulmonary and Critical Care Medicine, Department of Medicine and
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428
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Maouche S, Schunkert H. Strategies beyond genome-wide association studies for atherosclerosis. Arterioscler Thromb Vasc Biol 2012; 32:170-81. [PMID: 22258900 DOI: 10.1161/atvbaha.111.232652] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Atherosclerotic diseases, including coronary artery disease (CAD) and myocardial infarction (MI), are the leading causes of death in the world. The genetic basis of CAD and MI, which are caused by multiple interacting endogenous and exogenous factors, has gained considerable interest in the last years as genome-wide association studies (GWASs) have identified many new susceptibility loci for CAD and MI, and the underlying genes provide new insights into the genetic architecture of these diseases. Here we summarize the recent findings from GWASs of atherosclerosis and discuss their functional and biological implications. We also discuss the different post-GWAS strategies that are currently used for refining the location of causal variants, understanding their role, and shedding light on molecular mechanisms explaining their association to CAD. We finally discuss potential clinical translations of GWAS findings for individual risk prediction, advanced clinical strategies, and personalized treatments.
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Affiliation(s)
- Seraya Maouche
- Universität zu Lübeck, Medizinische Klinik II, Ratzeburger Allee 160, 23538 Lübeck, Germany
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429
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Common variants in CDKN2B-AS1 associated with optic-nerve vulnerability of glaucoma identified by genome-wide association studies in Japanese. PLoS One 2012; 7:e33389. [PMID: 22428042 PMCID: PMC3299784 DOI: 10.1371/journal.pone.0033389] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 02/13/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND To date, only a small portion of the genetic variation for primary open-angle glaucoma (POAG), the major type of glaucoma, has been elucidated. METHODS AND PRINCIPAL FINDINGS We examined our two data sets of the genome-wide association studies (GWAS) derived from a total of 2,219 Japanese subjects. First, we performed a GWAS by analyzing 653,519 autosomal common single-nucleotide polymorphisms (SNPs) in 833 POAG patients and 686 controls. As a result, five variants that passed the Bonferroni correction were identified in CDKN2B-AS1 on chromosome 9p21.3, which was already reported to be a significant locus in the Caucasian population. Moreover, we combined the data set with our previous GWAS data set derived from 411 POAG patients and 289 controls by the Mantel-Haenszel test, and all of the combined variants showed stronger association with POAG (P<5.8 × 10(-10)). We then subdivided the case groups into two subtypes based on the value of intraocular pressure (IOP)--POAG with high IOP (high pressure glaucoma, HPG) and that with normal IOP (normal pressure glaucoma, NPG)--and performed the GWAS using the two data sets, as the prevalence of NPG in Japanese is much higher than in Caucasians. The results suggested that the variants from the same CDKN2B-AS1 locus were likely to be significant for NPG patients. CONCLUSIONS AND SIGNIFICANCE In this study, we successfully identified POAG-associated variants in the CDKN2B-AS1 locus using a Japanese population, i.e., variants originally reported as being associated with the Caucasian population. Although we cannot rule out that the significance could be due to the differences in sample size between HPG and NPG, the variants could be associated specifically with the vulnerability of the optic nerve to IOP, which is useful for investigating the etiology of glaucoma.
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430
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Hsu A, Dalbeth N, Gow P, Harrison A, Highton J, Jones PB, Stamp LK, Merriman TR. No evidence for association of Chr 9p21 variant rs1333049 with gout in New Zealand case-control sample sets. Rheumatology (Oxford) 2012; 51:1129-30. [PMID: 22396608 DOI: 10.1093/rheumatology/kes029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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431
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Stylianou IM, Bauer RC, Reilly MP, Rader DJ. Genetic basis of atherosclerosis: insights from mice and humans. Circ Res 2012; 110:337-55. [PMID: 22267839 DOI: 10.1161/circresaha.110.230854] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Atherosclerosis is a complex and heritable disease involving multiple cell types and the interactions of many different molecular pathways. The genetic and molecular mechanisms of atherosclerosis have, in part, been elucidated by mouse models; at least 100 different genes have been shown to influence atherosclerosis in mice. Importantly, unbiased genome-wide association studies have recently identified a number of novel loci robustly associated with atherosclerotic coronary artery disease. Here, we review the genetic data elucidated from mouse models of atherosclerosis, as well as significant associations for human coronary artery disease. Furthermore, we discuss in greater detail some of these novel human coronary artery disease loci. The combination of mouse and human genetics has the potential to identify and validate novel genes that influence atherosclerosis, some of which may be candidates for new therapeutic approaches.
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Affiliation(s)
- Ioannis M Stylianou
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania School of Medicine, 654 BRBII/III Labs, 421 Curie Boulevard, Philadelphia, Pennsylvania, 19104-6160, USA
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432
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From candidate gene to genome-wide association studies in cardiovascular disease. Thromb Res 2012; 129:320-4. [DOI: 10.1016/j.thromres.2011.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 11/07/2011] [Accepted: 11/08/2011] [Indexed: 11/19/2022]
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433
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Liu LY, Schaub MA, Sirota M, Butte AJ. Sex differences in disease risk from reported genome-wide association study findings. Hum Genet 2012; 131:353-64. [PMID: 21858542 PMCID: PMC3260375 DOI: 10.1007/s00439-011-1081-y] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 08/08/2011] [Indexed: 01/01/2023]
Abstract
Men and women differ in susceptibility to many diseases and in responses to treatment. Recent advances in genome-wide association studies (GWAS) provide a wealth of data for associating genetic profiles with disease risk; however, in general, these data have not been systematically probed for sex differences in gene-disease associations. Incorporating sex into the analysis of GWAS results can elucidate new relationships between single nucleotide polymorphisms (SNPs) and human disease. In this study, we performed a sex-differentiated analysis on significant SNPs from GWAS data of the seven common diseases studied by the Wellcome Trust Case Control Consortium. We employed and compared three methods: logistic regression, Woolf's test of heterogeneity, and a novel statistical metric that we developed called permutation method to assess sex effects (PMASE). After correction for false discovery, PMASE finds SNPs that are significantly associated with disease in only one sex. These sexually dimorphic SNP-disease associations occur in Coronary Artery Disease and Crohn's Disease. GWAS analyses that fail to consider sex-specific effects may miss discovering sexual dimorphism in SNP-disease associations that give new insights into differences in disease mechanism between men and women.
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Affiliation(s)
- Linda Y. Liu
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, MS-5415 Room X-163, Stanford, CA 94305-5415, USA
- Lucile Packard Children’s Hospital, 725 Welch Road, Palo Alto, CA 94304, USA
| | - Marc A. Schaub
- Computer Science Department, Stanford University, 353 Serra Mall, Stanford, CA 94305, USA,
| | - Marina Sirota
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, MS-5415 Room X-163, Stanford, CA 94305-5415, USA
- Lucile Packard Children’s Hospital, 725 Welch Road, Palo Alto, CA 94304, USA
| | - Atul J. Butte
- Division of Systems Medicine, Department of Pediatrics, Stanford University School of Medicine, 1265 Welch Road, MS-5415 Room X-163, Stanford, CA 94305-5415, USA,
- Lucile Packard Children’s Hospital, 725 Welch Road, Palo Alto, CA 94304, USA
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434
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Hoffmann MM, Renner W. Insight from genome-wide association studies into coronary heart disease. Pharmacogenomics 2012; 13:361-3. [DOI: 10.2217/pgs.11.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Michael M Hoffmann
- Department of Clinical Chemistry, University Medical Center Freiburg, Freiburg, Germany
| | - Wilfried Renner
- Clinical Institute of Medical & Chemical Laboratory Diagnostics, Medical University, Graz, Austria
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435
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436
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Abstract
Over the past 50 years, we have seen dramatic changes in cardiovascular science and clinical care, accompanied by marked declines in the morbidity and mortality. Nonetheless, cardiovascular disease remains the leading cause of death and disability in the world, and its nature is changing as Americans become older, fatter, and ethnically more diverse. Instead of young or middle-aged men with ST-segment elevation myocardial infarction, the "typical" cardiac patient now presents with acute coronary syndrome or with complications related to chronic hypertension or ischemic heart disease, including heart failure, sudden death, and atrial fibrillation. Analogously, structural heart disease is now dominated by degenerative valve or congenital disease, far more common than rheumatic disease. The changing clinical scene presents cardiovascular scientists with a number of opportunities and challenges, including taking advantage of high-throughput technologies to elucidate complex disease mechanisms, accelerating development and implementation of evidence-based strategies, assessing evolving technologies of unclear value, addressing a global epidemic of cardiovascular disease, and maintaining high levels of innovation in a time of budgetary constraint and economic turmoil.
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Affiliation(s)
- Michael S Lauer
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
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437
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Marian AJ. Molecular genetic studies of complex phenotypes. Transl Res 2012; 159:64-79. [PMID: 22243791 PMCID: PMC3259530 DOI: 10.1016/j.trsl.2011.08.001] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 08/03/2011] [Accepted: 08/04/2011] [Indexed: 01/11/2023]
Abstract
The approach to molecular genetic studies of complex phenotypes evolved considerably during the recent years. The candidate gene approach, which is restricted to an analysis of a few single-nucleotide polymorphisms (SNPs) in a modest number of cases and controls, has been supplanted by the unbiased approach of genome-wide association studies (GWAS), wherein a large number of tagger SNPs are typed in many individuals. GWAS, which are designed on the common disease-common variant hypothesis (CD-CV), identified several SNPs and loci for complex phenotypes. However, the alleles identified through GWAS are typically not causative but rather in linkage disequilibrium (LD) with the true causal variants. The common alleles, which may not capture the uncommon and rare variants, account only for a fraction of heritability of the complex traits. Hence, the focus is being shifted to rare variants-common disease (RV-CD) hypothesis, surmising that rare variants exert large effect sizes on the phenotype. In conjunctional with this conceptual shift, technologic advances in DNA sequencing techniques have dramatically enhanced whole genome or whole exome sequencing capacity. The sequencing approach affords identification of not only the rare but also the common variants. The approach-whether used in complementation with GWAS or as a stand-alone approach-could define the genetic architecture of the complex phenotypes. Robust phenotyping and large-scale sequencing studies are essential to extract the information content of the vast number of DNA sequence variants (DSVs) in the genome. To garner meaningful clinical information and link the genotype to a phenotype, the identification and characterization of a large number of causal fields beyond the information content of DNA sequence variants would be necessary. This review provides an update on the current progress and limitations in identifying DSVs that are associated with phenotypic effects.
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Affiliation(s)
- Ali J Marian
- Center for Cardiovascular Genetics, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center and Texas Heart Institute, Houston, TX 77030, USA.
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438
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Holdt LM, Teupser D. Recent Studies of the Human Chromosome 9p21 Locus, Which Is Associated With Atherosclerosis in Human Populations. Arterioscler Thromb Vasc Biol 2012; 32:196-206. [DOI: 10.1161/atvbaha.111.232678] [Citation(s) in RCA: 141] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Lesca M. Holdt
- From the LIFE-Leipzig Center for Civilization Diseases (L.M.H., D.T.), Universität Leipzig, Germany; Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics (L.M.H.), University Hospital Leipzig, Germany; and Institute of Laboratory Medicine (D.T.), Ludwig-Maximilians-University Munich, Germany
| | - Daniel Teupser
- From the LIFE-Leipzig Center for Civilization Diseases (L.M.H., D.T.), Universität Leipzig, Germany; Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics (L.M.H.), University Hospital Leipzig, Germany; and Institute of Laboratory Medicine (D.T.), Ludwig-Maximilians-University Munich, Germany
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439
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Murabito JM, White CC, Kavousi M, Sun YV, Feitosa MF, Nambi V, Lamina C, Schillert A, Coassin S, Bis JC, Broer L, Crawford DC, Franceschini N, Frikke-Schmidt R, Haun M, Holewijn S, Huffman JE, Hwang SJ, Kiechl S, Kollerits B, Montasser ME, Nolte IM, Rudock ME, Senft A, Teumer A, van der Harst P, Vitart V, Waite LL, Wood AR, Wassel CL, Absher DM, Allison MA, Amin N, Arnold A, Asselbergs FW, Aulchenko Y, Bandinelli S, Barbalic M, Boban M, Brown-Gentry K, Couper DJ, Criqui MH, Dehghan A, Heijer MD, Dieplinger B, Ding J, Dörr M, Espinola-Klein C, Felix SB, Ferrucci L, Folsom AR, Fraedrich G, Gibson Q, Goodloe R, Gunjaca G, Haltmayer M, Heiss G, Hofman A, Kieback A, Kiemeney LA, Kolcic I, Kullo IJ, Kritchevsky SB, Lackner KJ, Li X, Lieb W, Lohman K, Meisinger C, Melzer D, Mohler ER, Mudnic I, Mueller T, Navis G, Oberhollenzer F, Olin JW, O’Connell J, O’Donnell CJ, Palmas W, Penninx BW, Petersmann A, Polasek O, Psaty BM, Rantner B, Rice K, Rivadeneira F, Rotter JI, Seldenrijk A, Stadler M, Summerer M, Tanaka T, Tybjaerg-Hansen A, Uitterlinden AG, van Gilst WH, Vermeulen SH, Wild SH, Wild PS, Willeit J, Zeller T, Zemunik T, Zgaga L, Assimes TL, Blankenberg S, Boerwinkle E, Campbell H, Cooke JP, de Graaf J, Herrington D, Kardia SLR, Mitchell BD, Murray A, Münzel T, Newman A, Oostra BA, Rudan I, Shuldiner AR, Snieder H, van Duijn CM, Völker U, Wright AF, Wichmann HE, Wilson JF, Witteman JC, Liu Y, Hayward C, Borecki IB, Ziegler A, North KE, Cupples LA, Kronenberg F. Association between chromosome 9p21 variants and the ankle-brachial index identified by a meta-analysis of 21 genome-wide association studies. CIRCULATION. CARDIOVASCULAR GENETICS 2012; 5:100-12. [PMID: 22199011 PMCID: PMC3303225 DOI: 10.1161/circgenetics.111.961292] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND Genetic determinants of peripheral arterial disease (PAD) remain largely unknown. To identify genetic variants associated with the ankle-brachial index (ABI), a noninvasive measure of PAD, we conducted a meta-analysis of genome-wide association study data from 21 population-based cohorts. METHODS AND RESULTS Continuous ABI and PAD (ABI ≤0.9) phenotypes adjusted for age and sex were examined. Each study conducted genotyping and imputed data to the ≈2.5 million single nucleotide polymorphisms (SNPs) in HapMap. Linear and logistic regression models were used to test each SNP for association with ABI and PAD using additive genetic models. Study-specific data were combined using fixed effects inverse variance weighted meta-analyses. There were a total of 41 692 participants of European ancestry (≈60% women, mean ABI 1.02 to 1.19), including 3409 participants with PAD and with genome-wide association study data available. In the discovery meta-analysis, rs10757269 on chromosome 9 near CDKN2B had the strongest association with ABI (β=-0.006, P=2.46×10(-8)). We sought replication of the 6 strongest SNP associations in 5 population-based studies and 3 clinical samples (n=16 717). The association for rs10757269 strengthened in the combined discovery and replication analysis (P=2.65×10(-9)). No other SNP associations for ABI or PAD achieved genome-wide significance. However, 2 previously reported candidate genes for PAD and 1 SNP associated with coronary artery disease were associated with ABI: DAB21P (rs13290547, P=3.6×10(-5)), CYBA (rs3794624, P=6.3×10(-5)), and rs1122608 (LDLR, P=0.0026). CONCLUSIONS Genome-wide association studies in more than 40 000 individuals identified 1 genome wide significant association on chromosome 9p21 with ABI. Two candidate genes for PAD and 1 SNP for coronary artery disease are associated with ABI.
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Affiliation(s)
- Joanne M. Murabito
- NHLBI’s Framingham Heart Study, Framingham
- Dept of Med, Section of Gen Internal Med, BU School of Med
| | | | - Maryam Kavousi
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
| | - Yan V. Sun
- Dept of Epidemiology, Emory Univ School of Public Hlth, Atlanta, GA
| | - Mary F. Feitosa
- Statistical Genomics, Dept of Genetics, Washington Univ School of Med, St. Louis, MO
| | - Vijay Nambi
- Dept of Atherosclerosis & Vascular Med, BCM, Houston, TX
| | - Claudia Lamina
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
| | | | - Stefan Coassin
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
| | - Joshua C. Bis
- Cardiovascular Hlth Rsrch Unit, Dept of Med, Univ of Washington, Seattle, WA
| | - Linda Broer
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
| | - Dana C. Crawford
- Dept of Molecular Physiology & Biophysics, The Ctr for Human Genetics Rsrch, Vanderbilt Univ, Nashville, TN
| | - Nora Franceschini
- Dept of Epidemiology, UNC Gillings School of Global Public Hlth, The Univ of North Carolina, Chapel Hill, NC
| | - Ruth Frikke-Schmidt
- Dept of Clin Biochemistry, Rigshospitalet, Copenhagen Univ Hosp, Copenhagen, Denmark
| | - Margot Haun
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
| | - Suzanne Holewijn
- Dept of Gen Internal Med, Vascular Med, Radboud Univ Nijmegen Med Ctr, Nijmegen, The Netherlands
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, Inst of Genetics & Molecular Med, Western Gen Hosp, Edinburgh, Scotland, UK
| | | | - Stefan Kiechl
- Dept of Neurology, Innsbruck Med Univ, Innsbruck, Austria
| | - Barbara Kollerits
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
| | - May E. Montasser
- Endocrinology, Dept of Med, Univ of Maryland School of Med, Baltimore, MD
| | - Ilja M. Nolte
- Unit of Gen Epidemiology & Bioinformatics, Dept of Epidemiology, Univ Med Ctr Groningen, Univ of Groningen, Groningen, The Netherlands
| | - Megan E. Rudock
- Dept of Epidemiology & Prevention, Wake Forest Univ School of Med, Winston-Salem, NC
| | - Andrea Senft
- Institut für Med Biometrie & Statistik, Univ zu Lübeck, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Alexander Teumer
- Interfaculty Inst for Genetics & Functional Genomics, Ernst-Moritz-Arndt-Univ Greifswald, Greifswald, Germany
| | - Pim van der Harst
- Dept of Cardiology, Univ Med Ctr Groningen, Univ of Groningen, Groningen, The Netherlands
- Dept of Genetics, Univ Med Ctr Groningen, Univ of Groningen, Groningen, The Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, Inst of Genetics & Molecular Med, Western Gen Hosp, Edinburgh, Scotland, UK
| | | | - Andrew R. Wood
- Genetics of Complex Traits, Peninsula College of Med & Dentistry, Univ of Exeter, UK
| | | | | | - Matthew A. Allison
- Dept of Family & Preventive Med, UC San Diego, Preventive Med, La Jolla, CA
| | - Najaf Amin
- Dept of Epidemiology, Erasmus Univ Med Ctr
| | - Alice Arnold
- Dept of Biostatistics, Univ of Washington, Seattle, WA
| | - Folkert W. Asselbergs
- Dept of Cardiology, Heart & Lungs, Univ Med Ctr Utrecht, Utrecht, The Netherlands
- Julius Ctr for Hlth Sciences & Primary Care, Univ Med Ctr, Utrecht, The Netherlands
- Dept of Med Genetics, Biomedical Genetics, Univ Med Ctr, Utrecht, The Netherlands
| | | | - Stefania Bandinelli
- Geriatric Rehabilitation Unit, Azienda Sanitaria di Firenze, Florence, Italy
| | - Maja Barbalic
- Univ of Texas Hlth Science Ctr at Houston, Dept of Epidemiology, Human Genetics & Environmental Sciences, Houston, TX
| | | | | | | | - Michael H. Criqui
- Dept of Family & Preventive Med, UC San Diego, Preventive Med, La Jolla, CA
| | - Abbas Dehghan
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
| | - Martin den Heijer
- Dept of Endocrinology & Epidemiology, Biostatistics & HTA, Radboud Univ Nijmegen Med Ctr, Nijmegen, The Netherlands
| | | | - Jingzhong Ding
- Sticht Ctr on Aging, Wake Forest School of Med, Winston-Salem, NC
| | - Marcus Dörr
- Dept of Internal Med B- Cardiology, Angiology & Pneumology & Intensive Care Med, Univ Med, Greifswald
| | | | - Stephan B. Felix
- Dept of Internal Med B- Cardiology, Angiology & Pneumology & Intensive Care Med, Univ Med, Greifswald
| | - Luigi Ferrucci
- Longitudinal Studies Section, Clinical Rsrch Branch, Nat Inst on Aging, NIH, Baltimore, MD
| | - Aaron R. Folsom
- Epidemiology & Community Hlth, School of Public Hlth, Univ of Minnesota, Minneapolis, MN
| | - Gustav Fraedrich
- Dept of Vascular Surgery, Innsbruck Med Univ, Innsbruck, Austria
| | - Quince Gibson
- Endocrinology, Dept of Med, Univ of Maryland School of Med, Baltimore, MD
| | - Robert Goodloe
- The Ctr for Human Genetics Rsrch, Vanderbilt Univ, Nashville, TN
| | | | - Meinhard Haltmayer
- Dept of Lab Med, Konventhospital Barmherzige Brueder Linz, Linz, Austria
| | - Gerardo Heiss
- Dept of Epidemiology, UNC Gillings School of Global Public Hlth, The Univ of North Carolina, Chapel Hill, NC
| | - Albert Hofman
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
| | - Arne Kieback
- Dept of Internal Med B- Cardiology, Angiology & Pneumology & Intensive Care Med, Univ Med, Greifswald
| | - Lambertus A. Kiemeney
- Dept of Epidemiology, Biostatistics & HTA, Radboud Univ Nijmegen Med Ctr, Nijmegen, The Netherlands
| | - Ivana Kolcic
- Dept of Public Hlth, University of Split School of Med, Croatia
| | - Iftikhar J. Kullo
- Cardiovascular Diseases & the Gonda Vascular Ctr, Mayo Clinic, Rochester, MN
| | | | - Karl J. Lackner
- Dept of Med 2, Univ Med Ctr Mainz, Johannes Gutenberg-Univ Mainz, Germany
| | - Xiaohui Li
- Med Genetics Inst, Cedars-Sinai Med Ctr, Los Angeles, CA
| | - Wolfgang Lieb
- Inst for Community Med, Univ Med Greifswald, Germany
| | - Kurt Lohman
- Dept of Biostatistics, Wake Forest Univ School of Med, Winston-Salem, NC
| | - Christa Meisinger
- Inst of Epidemiology II, Helmholtz Zentrum München, German Rsrch Ctr for Environmental Hlth (GmbH), Neuherberg, Germany
| | - David Melzer
- Dept of Epidemiology & Public Hlth, Peninsula College of Med & Dentistry, Univ of Exeter, UK
| | - Emile R Mohler
- Perelman School of Med at the Univ of Pennsylvania, Cardiovascular Division, Vascular Med Section, Philadelphia, PA
| | | | - Thomas Mueller
- Dept of Lab Med, Konventhospital Barmherzige Brueder Linz, Linz, Austria
| | - Gerjan Navis
- Dept of Internal Med, Univ Med Ctr Groningen, Univ of Groningen, Groningen, Netherlands
| | | | | | - Jeff O’Connell
- Endocrinology, Dept of Med, Univ of Maryland School of Med, Baltimore, MD
| | - Christopher J. O’Donnell
- NHLBI’s Framingham Heart Study, Framingham
- Nat Heart, Lung, & Blood Inst, Intramural Rsrch, Bethesda, MD
| | | | - Brenda W. Penninx
- Dept of Psychiatry/EMGO Inst, VU Univ Med Ctr, Amsterdam
- Dept of Psychiatry, Univ Med Ctr Groningen, Univ of Groningen, Groningen
- Dept of Psychiatry, Leiden Univ Med Ctr, Leiden, The Netherlands
| | | | - Ozren Polasek
- Dept of Public Hlth, University of Split School of Med, Croatia
| | - Bruce M. Psaty
- Cardiovascular Hlth Rsrch Unit, Depts of Med, Epidemiology & Hlth Services, Univ of Washington
- Group Hlth Rsrch Inst, Group Hlth Cooperative, Seattle, WA
| | - Barbara Rantner
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
- Dept of Vascular Surgery, Innsbruck Med Univ, Innsbruck, Austria
| | - Ken Rice
- Dept of Biostatistics, Univ of Washington, Seattle, WA
| | - Fernando Rivadeneira
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
- Dept of Internal Med, Erasmus Univ Med Ctr, Rotterdam, The Netherlands
| | | | | | - Marietta Stadler
- Hietzing Hosp, 3rd Med Dept of Metabolic Diseases & Nephrology, Vienna, Austria
| | - Monika Summerer
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
| | | | - Anne Tybjaerg-Hansen
- Dept of Clin Biochemistry, Rigshospitalet, Copenhagen Univ Hosp, Copenhagen, Denmark
| | - Andre G. Uitterlinden
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
- Dept of Internal Med, Erasmus Univ Med Ctr, Rotterdam, The Netherlands
| | - Wiek H. van Gilst
- Dept of Cardiology, Univ Med Ctr Groningen, Univ of Groningen, Groningen, The Netherlands
| | - Sita H. Vermeulen
- Dept of Epidemiology, Biostatistics & HTA, Radboud Univ Nijmegen Med Ctr, Nijmegen, The Netherlands
| | - Sarah H. Wild
- Ctr for Pop Hlth Sciences, Univ of Edinburgh, Edinburgh, Scotland
| | - Philipp S. Wild
- Dept of Med 2, Univ Med Ctr Mainz, Johannes Gutenberg-Univ Mainz, Germany
- Ctr for Thrombosis & Hemostasis, Univ Med Ctr Mainz, Johannes Gutenberg-Univ Mainz
| | - Johann Willeit
- Dept of Neurology, Innsbruck Med Univ, Innsbruck, Austria
| | - Tanja Zeller
- Clinic for General & Interventional Cardiology, Univ Heart Ctr Hamburg, Hamburg, Germany
| | | | - Lina Zgaga
- Ctr for Pop Hlth Sciences, Univ of Edinburgh, Edinburgh, Scotland
- Andrija Stampar School of Public Health, Med School, Univ of Zagreb, Croatia
| | | | - Stefan Blankenberg
- Clinic for General & Interventional Cardiology, Univ Heart Ctr Hamburg, Hamburg, Germany
| | - Eric Boerwinkle
- Univ of Texas Hlth Science Ctr at Houston, Dept of Epidemiology, Human Genetics & Environmental Sciences, Houston, TX
| | - Harry Campbell
- Ctr for Pop Hlth Sciences, Univ of Edinburgh, Edinburgh, Scotland
| | - John P. Cooke
- Dept of Med, Stanford Univ School of Med, Stanford, CA
| | - Jacqueline de Graaf
- Dept of Gen Internal Med, Vascular Med, Radboud Univ Nijmegen Med Ctr, Nijmegen, The Netherlands
| | - David Herrington
- Dept of Internal Med, Wake Forest Univ School of Med, Winston-Salem, NC
| | | | | | - Anna Murray
- Genetics of Complex Traits, Peninsula College of Med & Dentistry, Univ of Exeter, UK
| | - Thomas Münzel
- Dept of Med 2, Univ Med Ctr Mainz, Johannes Gutenberg-Univ Mainz, Germany
| | - Anne Newman
- Dept of Epidemiology, Graduate School of Public Hlth, Univ of Pittsburgh, PA
| | - Ben A. Oostra
- Dept of Clinical Genetics, Erasmus Med Ctr, Rotterdam, The Netherlands
| | - Igor Rudan
- Ctr for Pop Hlth Sciences, Univ of Edinburgh, Edinburgh, Scotland
- Andrija Stampar School of Public Health, Med School, Univ of Zagreb, Croatia
| | - Alan R. Shuldiner
- Endocrinology, Dept of Med, Univ of Maryland School of Med, Baltimore, MD
- Geriatric Rsrch & Edu Clinical Ctr, VA Med Ctr, Baltimore, MD
| | - Harold Snieder
- Unit of Gen Epidemiology & Bioinformatics, Dept of Epidemiology, Univ Med Ctr Groningen, Univ of Groningen, Groningen, The Netherlands
| | - Cornelia M. van Duijn
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
| | - Uwe Völker
- Interfaculty Inst for Genetics & Functional Genomics, Ernst-Moritz-Arndt-Univ Greifswald, Greifswald, Germany
| | - Alan F. Wright
- MRC Human Genetics Unit, Inst of Genetics & Molecular Med, Western Gen Hosp, Edinburgh, Scotland, UK
| | - H.-Erich Wichmann
- Inst of Epidemiology I, Helmholtz Zentrum München, German Rsrch Ctr for Environmental Hlth (GmbH), Neuherberg, Germany
| | - James F. Wilson
- Ctr for Pop Hlth Sciences, Univ of Edinburgh, Edinburgh, Scotland
| | - Jacqueline C.M. Witteman
- Dept of Epidemiology, Erasmus Univ Med Ctr
- Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Hlthy Aging (NCHA) & Ctr for Med Systems Biology, Rotterdam, the Netherlands
| | - Yongmei Liu
- Dept of Epidemiology & Prevention, Wake Forest Univ School of Med, Winston-Salem, NC
| | - Caroline Hayward
- MRC Human Genetics Unit, Inst of Genetics & Molecular Med, Western Gen Hosp, Edinburgh, Scotland, UK
| | - Ingrid B. Borecki
- Statistical Genomics, Dept of Genetics, Washington Univ School of Med, St. Louis, MO
| | - Andreas Ziegler
- Institut für Med Biometrie & Statistik, Univ zu Lübeck, Universitätsklinikum Schleswig-Holstein, Lübeck, Germany
| | - Kari E. North
- Dept of Epidemiology, UNC Gillings School of Global Public Hlth, The Univ of North Carolina, Chapel Hill, NC
- Carolina Ctr for Genome Sciences, School of Public Hlth, UNC-CH, Chapel Hill, NC
| | - L. Adrienne Cupples
- NHLBI’s Framingham Heart Study, Framingham
- Dept of Biostatistics, BU, Boston, MA
| | - Florian Kronenberg
- Genetic Epidemiology, Dept of Med Genetics, Molecular & Clin Pharmacology, Innsbruck Med Univ, Innsbruck, Austria
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440
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Demaria AN, Bax JJ, Ben-Yehuda O, Feld GK, Greenberg BH, Hall J, Hlatky M, Lew WYW, Lima JAC, Maisel AS, Narayan SM, Nissen S, Sahn DJ, Tsimikas S. Highlights of the Year in JACC 2011. J Am Coll Cardiol 2012; 59:503-37. [PMID: 22281255 DOI: 10.1016/j.jacc.2011.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony N Demaria
- University of California-San Diego, San Diego, California 92122, USA.
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441
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Genomic research to identify novel pathways in the development of abdominal aortic aneurysm. Cardiol Res Pract 2012; 2012:852829. [PMID: 22400124 PMCID: PMC3286885 DOI: 10.1155/2012/852829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is a common disease with a large heritable component. There is a need to improve our understanding of AAA pathogenesis in order to develop novel treatment paradigms. Genomewide association studies have revolutionized research into the genetic variants that underpin the development of many complex diseases including AAA. This article reviews the progress that has been made to date in this regard, including mechanisms by which loci identified by GWAS may contribute to the development of AAA. It also highlights potential post-GWAS analytical strategies to improve our understanding of the disease further.
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442
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Kuo CL, Murphy AJ, Sayers S, Li R, Yvan-Charvet L, Davis JZ, Krishnamurthy J, Liu Y, Puig O, Sharpless NE, Tall AR, Welch CL. Cdkn2a is an atherosclerosis modifier locus that regulates monocyte/macrophage proliferation. Arterioscler Thromb Vasc Biol 2012; 31:2483-92. [PMID: 21868699 DOI: 10.1161/atvbaha.111.234492] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE Common genetic variants in a 58-kb region of chromosome 9p21, near the CDKN2A/CDKN2B tumor suppressor locus, are strongly associated with coronary artery disease. However, the underlying mechanism of action remains unknown. METHODS AND RESULTS We previously reported a congenic mouse model harboring an atherosclerosis susceptibility locus and the region of homology with the human 9p21 locus. Microarray and transcript-specific expression analyses showed markedly decreased Cdkn2a expression, including both p16(INK4a) and p19(ARF), but not Cdkn2b (p15(INK4b)), in macrophages derived from congenic mice compared with controls. Atherosclerosis studies in subcongenic strains revealed genetic complexity and narrowed 1 locus to a small interval including Cdkn2a/b. Bone marrow (BM) transplantation studies implicated myeloid lineage cells as the culprit cell type, rather than resident vascular cells. To directly test the role of BM-derived Cdkn2a transcripts in atherogenesis and inflammatory cell proliferation, we performed a transplantation study using Cdkn2a(-/-) cells in the Ldlr(-/-) mouse model. Cdkn2a-deficient BM recipients exhibited accelerated atherosclerosis, increased Ly6C proinflammatory monocytes, and increased monocyte/macrophage proliferation compared with controls. CONCLUSION These data provide a plausible mechanism for accelerated atherogenesis in susceptible congenic mice, involving decreased expression of Cdkn2a and increased proliferation of monocyte/macrophages, with possible relevance to the 9p21 human locus.
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Affiliation(s)
- Chao-Ling Kuo
- Division of Molecular Medicine, Department of Medicine, Columbia University, New York, NY, USA
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443
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Sakabe NJ, Savic D, Nobrega MA. Transcriptional enhancers in development and disease. Genome Biol 2012; 13:238. [PMID: 22269347 PMCID: PMC3334578 DOI: 10.1186/gb-2012-13-1-238] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 01/13/2012] [Indexed: 01/24/2023] Open
Abstract
Distal transcription enhancers are cis-regulatory elements that promote gene expression, enabling spatiotemporal control of genetic programs such as those required in metazoan developmental processes. Because of their importance, their disruption can lead to disease.
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Affiliation(s)
- Noboru Jo Sakabe
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
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444
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Davison LJ, Wallace C, Cooper JD, Cope NF, Wilson NK, Smyth DJ, Howson JM, Saleh N, Al-Jeffery A, Angus KL, Stevens HE, Nutland S, Duley S, Coulson RM, Walker NM, Burren OS, Rice CM, Cambien F, Zeller T, Munzel T, Lackner K, Blankenberg S, Fraser P, Gottgens B, Todd JA. Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. Hum Mol Genet 2012; 21:322-33. [PMID: 21989056 PMCID: PMC3276289 DOI: 10.1093/hmg/ddr468] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/27/2011] [Accepted: 10/06/2011] [Indexed: 01/13/2023] Open
Abstract
The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes.
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Affiliation(s)
- Lucy J. Davison
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Chris Wallace
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Jason D. Cooper
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Nathan F. Cope
- Nuclear Dynamics Laboratory, Babraham Institute, Cambridge, UK
| | - Nicola K. Wilson
- Haematopoetic Stem Cell Lab, Cambridge Institute for Medical Research (CIMR), NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Joanna M.M. Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Nada Saleh
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Abdullah Al-Jeffery
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Karen L. Angus
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Helen E. Stevens
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Sarah Nutland
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Simon Duley
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Richard M.R. Coulson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Neil M. Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Oliver S. Burren
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Catherine M. Rice
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Francois Cambien
- INSERM UMRS 937, Pierre and Marie Curie University and Medical School, Paris, France
| | - Tanja Zeller
- University Heart Center Hamburg, Clinical for General and Interventional Cardiology, 20246 Hamburg, Germany
| | - Thomas Munzel
- Medizinische Klinik und Poliklinik, Johannes-Gutenberg Universität Mainz, Germany and
| | - Karl Lackner
- Department of Clinical Chemistry and Laboratory Medicine, Johannes-Gutenberg Universität Mainz, Germany
| | - Stefan Blankenberg
- University Heart Center Hamburg, Clinical for General and Interventional Cardiology, 20246 Hamburg, Germany
| | | | - Peter Fraser
- Nuclear Dynamics Laboratory, Babraham Institute, Cambridge, UK
| | - Berthold Gottgens
- Haematopoetic Stem Cell Lab, Cambridge Institute for Medical Research (CIMR), NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
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445
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Visser M, Kayser M, Palstra RJ. HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res 2012; 22:446-55. [PMID: 22234890 DOI: 10.1101/gr.128652.111] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Pigmentation of skin, eye, and hair reflects some of the most evident common phenotypes in humans. Several candidate genes for human pigmentation are identified. The SNP rs12913832 has strong statistical association with human pigmentation. It is located within an intron of the nonpigment gene HERC2, 21 kb upstream of the pigment gene OCA2, and the region surrounding rs12913832 is highly conserved among animal species. However, the exact functional role of HERC2 rs12913832 in human pigmentation is unknown. Here we demonstrate that the HERC2 rs12913832 region functions as an enhancer regulating OCA2 transcription. In darkly pigmented human melanocytes carrying the rs12913832 T-allele, we detected binding of the transcription factors HLTF, LEF1, and MITF to the HERC2 rs12913832 enhancer, and a long-range chromatin loop between this enhancer and the OCA2 promoter that leads to elevated OCA2 expression. In contrast, in lightly pigmented melanocytes carrying the rs12913832 C-allele, chromatin-loop formation, transcription factor recruitment, and OCA2 expression are all reduced. Hence, we demonstrate that allelic variation of a common noncoding SNP located in a distal regulatory element not only disrupts the regulatory potential of this element but also affects its interaction with the relevant promoter. We provide the key mechanistic insight that allele-dependent differences in chromatin-loop formation (i.e., structural differences in the folding of gene loci) result in differences in allelic gene expression that affects common phenotypic traits. This concept is highly relevant for future studies aiming to unveil the functional basis of genetically determined phenotypes, including diseases.
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Affiliation(s)
- Mijke Visser
- Department of Forensic Molecular Biology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
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446
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Kanno Y, Vahedi G, Hirahara K, Singleton K, O'Shea JJ. Transcriptional and epigenetic control of T helper cell specification: molecular mechanisms underlying commitment and plasticity. Annu Rev Immunol 2012; 30:707-31. [PMID: 22224760 PMCID: PMC3314163 DOI: 10.1146/annurev-immunol-020711-075058] [Citation(s) in RCA: 260] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
T helper cell differentiation occurs in the context of the extracellular cytokine milieu evoked by diverse microbes and other pathogenic stimuli along with T cell receptor stimulation. The culmination of these signals results in specification of T helper lineages, which occurs through the combinatorial action of multiple transcription factors that establish distinctive transcriptomes. In this manner, inducible, but constitutively active, master regulators work in conjunction with factors such as the signal transducer and activator of transcriptions (STATs) that sense the extracellular environment. The acquisition of a distinctive transcriptome also depends on chromatin modifications that impact key cis elements as well as the changes in global genomic organization. Thus, signal transduction and epigenetics are linked in these processes of differentiation. In this review, recent advances in understanding T helper lineage specification and deciphering the action of transcription factors are summarized with emphasis on comprehensive views of the dynamic T cell epigenome.
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Affiliation(s)
- Yuka Kanno
- Molecular Immunology and Inflammation Branch, National Institutes of Arthritis, and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.
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447
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Abstract
Abstract
BACKGROUND
It has long been recognized that 50% of the susceptibility for coronary artery disease (CAD) is due to predisposing genetic factors. Comprehensive prevention is likely to require knowledge of these genetic factors.
CONTENT
Using a genomewide association study (GWAS), the Ottawa Heart Genomic Study and the deCODE group simultaneously identified the first genetic risk variant, at chromosome 9p21. The 9p21 variant became the first risk factor to be identified since 1964. 9p21 occurs in 75% of the population except for African Americans and is associated with a 25% increased risk for CAD with 1 copy and a 50% increased risk with 2 copies. Perhaps the most remarkable finding is that 9p21 is independent of all known risk factors, indicating there are factors contributing to the pathogenesis of CAD that are yet unknown. 9p21 in individuals with premature CAD is associated with a 2-fold increase in risk, similar to that of smoking and cholesterol. Routine genetic testing will probably remain controversial until a specific treatment is developed. Over a period of 5 years, however, GWASs have identified 30 genetic variants for CAD risk, of which only 6 act through the known risk factors.
SUMMARY
The 9p21 variant has now been established as an independent risk factor for CAD and, along with the additional 29 risk genetic variants recently identified, is likely to provide the thrust for genetic testing and personalized medicine in the near future.
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Affiliation(s)
- Robert Roberts
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Alexandre F R Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
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448
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Zeller T, Blankenberg S, Diemert P. Genomewide Association Studies in Cardiovascular Disease—An Update 2011. Clin Chem 2012; 58:92-103. [DOI: 10.1373/clinchem.2011.170431] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Abstract
BACKGROUND
Genomewide association studies have led to an enormous boost in the identification of susceptibility genes for cardiovascular diseases. This review aims to summarize the most important findings of recent years.
CONTENT
We have carefully reviewed the current literature (PubMed search terms: “genome wide association studies,” “genetic polymorphism,” “genetic risk factors,” “association study” in connection with the respective diseases, “risk score,” “transcriptome”).
SUMMARY
Multiple novel genetic loci for such important cardiovascular diseases as myocardial infarction, hypertension, heart failure, stroke, and hyperlipidemia have been identified. Given that many novel genetic risk factors lie within hitherto-unsuspected genes or influence gene expression, these findings have inspired discoveries of biological function. Despite these successes, however, only a fraction of the heritability for most cardiovascular diseases has been explained thus far. Forthcoming techniques such as whole-genome sequencing will be important to close the gap of missing heritability.
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Affiliation(s)
- Tanja Zeller
- Department of General and Interventional Cardiology, The University Heart Center at the University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Blankenberg
- Department of General and Interventional Cardiology, The University Heart Center at the University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Patrick Diemert
- Department of General and Interventional Cardiology, The University Heart Center at the University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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449
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de Gaetano G, Santimone I, Gianfagna F, Iacoviello L, Cerletti C. Variability of platelet indices and function: acquired and genetic factors. Handb Exp Pharmacol 2012:395-434. [PMID: 22918740 DOI: 10.1007/978-3-642-29423-5_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Each individual has an inherent variable risk of bleeding linked to genetic or acquired abnormal platelet number or platelet dysfunction. In contrast, it is less obvious that the variability of platelet phenotypes (number, mean platelet volume, function) may contribute to the variable individual risk of thrombosis. Interindividual variability of platelet indices or function may be either due to acquired factors, such as age, sex, metabolic variables, smoke, dietary habits, and ongoing inflammation, or due to genetic factors. Acquired variables explain a small portion of the heterogeneity of platelet parameters. Genetic factors, instead, appear to play a major role, although a consistent portion of such a genetic variance has not yet been attributed to any specific genetic factor, possibly due to the high number of DNA loci potentially involved and to the limited effect size of each individual SNP. A portion of variance remains thus unexplained, also due to variability of test performance. A major contradiction in present platelet knowledge is, indeed, the difficulty to reconcile the universally accepted importance of platelet indices or function and the lack of reliable platelet parameters in cardiovascular risk prediction models. Trials on antiplatelet drugs were generally designed to select a homogeneous sample, whose results could be applied to an "average subject," tending to exclude the deviation/extreme values. As the current indications for antiplatelet treatment in primary or secondary prevention of ischemic vascular disease still derive from the results of such clinical trials where platelet function and its variability was not investigated, we cannot at present rely upon any current platelet test to either initiate, or monitor, or modify or stop treatment with any antiplatelet drug. Evidence is, however, increasing that traditional platelet aggregometry and other more recently developed platelet function assays could be useful to optimize antiplatelet therapy and to predict major adverse cardiac events.The observation of interindividual differences in platelet response to antiplatelet drugs has enlarged the spectrum and the possible clinical relevance of the variability of platelet indices or function. The development of "personalized medicine" will benefit from the concepts discussed in this chapter.
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Affiliation(s)
- Giovanni de Gaetano
- Research Laboratories, Fondazione di Ricerca e Cura "Giovanni Paolo II", Università Cattolica, Largo Gemelli, 1, 86100, Campobasso, Italy.
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450
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Dandona S, Stewart AFR, Roberts R. Genomics: is it ready for primetime? Med Clin North Am 2012; 96:113-22. [PMID: 22391256 DOI: 10.1016/j.mcna.2012.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The next decade will focus on identifying the missing heritability of coronary artery disease (CAD). This process will involve a more comprehensive interrogation of common single nucleotide polymorphisms (SNPs) that impart modest biologic effect and an interrogation of rare SNPs that impart profound biologic effect. In parallel, an investigation of the underlying biology of the described association will likely yield novel pathways that provide therapeutic targets. Once we obtain a more complete inventory of sequence variation that predisposes to CAD, a more realistic assessment of the role of genetic risk scoring allied with standard risk algorithms will be possible.
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Affiliation(s)
- Sonny Dandona
- Faculty of Medicine, McGill University, McIntyre Medical Building, 3655 promenade Sir William Osler Montreal, Quebec H3G 1Y6, Canada
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