201
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Yosef N, Regev A. Writ large: Genomic dissection of the effect of cellular environment on immune response. Science 2017; 354:64-68. [PMID: 27846493 DOI: 10.1126/science.aaf5453] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cells of the immune system routinely respond to cues from their local environment and feed back to their surroundings through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell states, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules in achieving and maintaining appropriate responses to a changing environment. These provide a first step toward a systematic understanding of molecular circuits in complex tissues.
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Affiliation(s)
- Nir Yosef
- Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA. .,Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. .,Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
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202
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Rhinn H, Abeliovich A. Differential Aging Analysis in Human Cerebral Cortex Identifies Variants in TMEM106B and GRN that Regulate Aging Phenotypes. Cell Syst 2017; 4:404-415.e5. [PMID: 28330615 DOI: 10.1016/j.cels.2017.02.009] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/14/2017] [Accepted: 02/03/2017] [Indexed: 10/19/2022]
Abstract
Human age-associated traits, such as cognitive decline, can be highly variable across the population, with some individuals exhibiting traits that are not expected at a given chronological age. Here we present differential aging (Δ-aging), an unbiased method that quantifies individual variability in age-associated phenotypes within a tissue of interest, and apply this approach to the analysis of existing transcriptome-wide cerebral cortex gene expression data from several cohorts totaling 1,904 autopsied human brain samples. We subsequently performed a genome-wide association study and identified the TMEM106B and GRN gene loci, previously associated with frontotemporal dementia, as determinants of Δ-aging in the cerebral cortex with genome-wide significance. TMEM106B risk variants are associated with inflammation, neuronal loss, and cognitive deficits, even in the absence of known brain disease, and their impact is highly selective for the frontal cerebral cortex of older individuals (>65 years). The methodological framework we describe can be broadly applied to the analysis of quantitative traits associated with aging or with other parameters.
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Affiliation(s)
- Herve Rhinn
- Departments of Pathology, Cell Biology, and Neurology, Columbia University, New York, NY 10032, USA; Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY 10032, USA.
| | - Asa Abeliovich
- Departments of Pathology, Cell Biology, and Neurology, Columbia University, New York, NY 10032, USA; Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY 10032, USA.
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203
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Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK, Jeffrey KL. Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Sci Immunol 2017; 2:eaag3160. [PMID: 28783698 PMCID: PMC5549562 DOI: 10.1126/sciimmunol.aag3160] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/08/2017] [Indexed: 12/29/2022]
Abstract
Epigenetic "readers" that recognize defined posttranslational modifications on histones have become desirable therapeutic targets for cancer and inflammation. SP140 is one such bromodomain- and plant homeodomain (PHD)-containing reader with immune-restricted expression, and single-nucleotide polymorphisms (SNPs) within SP140 associate with Crohn's disease (CD). However, the function of SP140 and the consequences of disease-associated SP140 SNPs have remained unclear. We show that SP140 is critical for transcriptional programs that uphold the macrophage state. SP140 preferentially occupies promoters of silenced, lineage-inappropriate genes bearing the histone modification H3K27me3, such as the HOXA cluster in human macrophages, and ensures their repression. Depletion of SP140 in mouse or human macrophages resulted in severely compromised microbe-induced activation. We reveal that peripheral blood mononuclear cells (PBMCs) or B cells from individuals carrying CD-associated SNPs within SP140 have defective SP140 messenger RNA splicing and diminished SP140 protein levels. Moreover, CD patients carrying SP140 SNPs displayed suppressed innate immune gene signatures in a mixed population of PBMCs that stratified them from other CD patients. Hematopoietic-specific knockdown of Sp140 in mice resulted in exacerbated dextran sulfate sodium (DSS)-induced colitis, and low SP140 levels in human CD intestinal biopsies correlated with relatively lower intestinal innate cytokine levels and improved response to anti-tumor necrosis factor (TNF) therapy. Thus, the epigenetic reader SP140 is a key regulator of macrophage transcriptional programs for cellular state, and a loss of SP140 due to genetic variation contributes to a molecularly defined subset of CD characterized by ineffective innate immunity, normally critical for intestinal homeostasis.
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Affiliation(s)
- Stuti Mehta
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - D Alexander Cronkite
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Megha Basavappa
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Tahnee L Saunders
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Fatemeh Adiliaghdam
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hajera Amatullah
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Sara A Morrison
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jose D Pagan
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Robert M Anthony
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Pierre Tonnerre
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - James C Lee
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, U.K
| | - Sreehaas Digumarthi
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Lorena Pantano
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Shannan J Ho Sui
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Chan Zhou
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Alan C Mullen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Vinod Kumar
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Terry K Means
- Center for Immunology and Inflammatory Diseases, Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA 02129, USA
| | - Kate L Jeffrey
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA.
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204
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Lawlor N, Khetan S, Ucar D, Stitzel ML. Genomics of Islet (Dys)function and Type 2 Diabetes. Trends Genet 2017; 33:244-255. [PMID: 28245910 DOI: 10.1016/j.tig.2017.01.010] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 01/30/2017] [Indexed: 12/28/2022]
Abstract
Pancreatic islet dysfunction and beta cell failure are hallmarks of type 2 diabetes mellitus (T2DM) pathogenesis. In this review, we discuss how genome-wide association studies (GWASs) and recent developments in islet (epi)genome and transcriptome profiling (particularly single cell analyses) are providing novel insights into the genetic, environmental, and cellular contributions to islet (dys)function and T2DM pathogenesis. Moving forward, study designs that interrogate and model genetic variation [e.g., allelic profiling and (epi)genome editing] will be critical to dissect the molecular genetics of T2DM pathogenesis, to build next-generation cellular and animal models, and to develop precision medicine approaches to detect, treat, and prevent islet (dys)function and T2DM.
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Affiliation(s)
- Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Shubham Khetan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics & Genome Sciences, University of Connecticut, Farmington, CT 06032, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Department of Genetics & Genome Sciences, University of Connecticut, Farmington, CT 06032, USA; Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA.
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205
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Confounding effects of microbiome on the susceptibility of TNFSF15 to Crohn's disease in the Ryukyu Islands. Hum Genet 2017; 136:387-397. [PMID: 28197769 DOI: 10.1007/s00439-017-1764-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022]
Abstract
Crohn's disease (CD) involves chronic inflammation in the gastrointestinal tract due to dysregulation of the host immune response to the gut microbiome. Even though the host-microbiome interactions are likely contributors to the development of CD, a few studies have detected genetic variants that change bacterial compositions and increase CD risk. We focus on one of the well-replicated susceptible genes, tumor necrosis factor superfamily member 15 (TNFSF15), and apply statistical analyses for personal profiles of genotypes and salivary microbiota collected from CD cases and controls in the Ryukyu Islands, southernmost islands of the Japanese archipelago. Our association test confirmed the susceptibility of TNFSF15 in the Ryukyu Islands. We found that the recessive model was supported to fit the observed genotype frequency of risk alleles slightly better than the additive model, defining the genetic effect on CD if a pair of the chromosomes in an individual consists of all risk alleles. The combined analysis of haplotypes and salivary microbiome from a small set of samples showed a significant association of the genetic effect with the increase of Prevotella, which led to a significant increase of CD risk. However, the genetic effect on CD disappeared if the abundance of Prevotella was low, suggesting the genetic contribution to CD is conditionally independent given a fixed amount of Prevotella. Although our statistical power is limited due to the small sample size, these results support an idea that the genetic susceptibility of TNFSF15 to CD may be confounded, in part, by the increase of Prevotella.
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206
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Tao L, Reese TA. Making Mouse Models That Reflect Human Immune Responses. Trends Immunol 2017; 38:181-193. [PMID: 28161189 DOI: 10.1016/j.it.2016.12.007] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 12/19/2016] [Accepted: 12/30/2016] [Indexed: 02/08/2023]
Abstract
Humans are infected with a variety of acute and chronic pathogens over the course of their lives, and pathogen-driven selection has shaped the immune system of humans. The same is likely true for mice. However, laboratory mice we use for most biomedical studies are bred in ultra-hygienic environments, and are kept free of specific pathogens. We review recent studies that indicate that pathogen infections are important for the basal level of activation and the function of the immune system. Consideration of these environmental exposures of both humans and mice can potentially improve mouse models of human disease.
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Affiliation(s)
- Lili Tao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tiffany A Reese
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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207
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208
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Kelly DE, Hansen MEB, Tishkoff SA. Global variation in gene expression and the value of diverse sampling. CURRENT OPINION IN SYSTEMS BIOLOGY 2017; 1:102-108. [PMID: 28596996 PMCID: PMC5458633 DOI: 10.1016/j.coisb.2016.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The genomics era has accelerated our understanding of how genetic and epigenetic factors influence both normal variable traits and disease risk in humans. However, the majority of "omics" studies have focused on individuals living in urban centers, primarily from Europe and Asia, neglecting much of the genetic and environmental variation that exists across worldwide populations. Comparative studies of gene regulation in ethnically diverse populations are informing our understanding of how evolutionary forces have shaped the genetic and molecular mechanisms underlying complex traits, and studying gene expression in different environmental contexts is enabling the dissection of disease-related pathways such as immune response. Such approaches are vital to the equitable application of genomics and medicine.
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Affiliation(s)
- Derek E. Kelly
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Sarah A. Tishkoff
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Genomics and Computational Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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209
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Ji SG, Juran BD, Mucha S, Folseraas T, Jostins L, Melum E, Kumasaka N, Atkinson EJ, Schlicht EM, Liu JZ, Shah T, Gutierrez-Achury J, Boberg KM, Bergquist A, Vermeire S, Eksteen B, Durie PR, Farkkila M, Müller T, Schramm C, Sterneck M, Weismüller TJ, Gotthardt DN, Ellinghaus D, Braun F, Teufel A, Laudes M, Lieb W, Jacobs G, Beuers U, Weersma RK, Wijmenga C, Marschall HU, Milkiewicz P, Pares A, Kontula K, Chazouillères O, Invernizzi P, Goode E, Spiess K, Moore C, Sambrook J, Ouwehand WH, Roberts DJ, Danesh J, Floreani A, Gulamhusein AF, Eaton JE, Schreiber S, Coltescu C, Bowlus CL, Luketic VA, Odin JA, Chopra KB, Kowdley KV, Chalasani N, Manns MP, Srivastava B, Mells G, Sandford RN, Alexander G, Gaffney DJ, Chapman RW, Hirschfield GM, de Andrade M, Rushbrook SM, Franke A, Karlsen TH, Lazaridis KN, Anderson CA. Genome-wide association study of primary sclerosing cholangitis identifies new risk loci and quantifies the genetic relationship with inflammatory bowel disease. Nat Genet 2017; 49:269-273. [PMID: 27992413 PMCID: PMC5540332 DOI: 10.1038/ng.3745] [Citation(s) in RCA: 201] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 11/18/2016] [Indexed: 02/07/2023]
Abstract
Primary sclerosing cholangitis (PSC) is a rare progressive disorder leading to bile duct destruction; ∼75% of patients have comorbid inflammatory bowel disease (IBD). We undertook the largest genome-wide association study of PSC (4,796 cases and 19,955 population controls) and identified four new genome-wide significant loci. The most associated SNP at one locus affects splicing and expression of UBASH3A, with the protective allele (C) predicted to cause nonstop-mediated mRNA decay and lower expression of UBASH3A. Further analyses based on common variants suggested that the genome-wide genetic correlation (rG) between PSC and ulcerative colitis (UC) (rG = 0.29) was significantly greater than that between PSC and Crohn's disease (CD) (rG = 0.04) (P = 2.55 × 10-15). UC and CD were genetically more similar to each other (rG = 0.56) than either was to PSC (P < 1.0 × 10-15). Our study represents a substantial advance in understanding of the genetics of PSC.
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Affiliation(s)
- Sun-Gou Ji
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Brian D Juran
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Sören Mucha
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Trine Folseraas
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, United Kingdom,Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, United Kingdom
| | - Espen Melum
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Natsuhiko Kumasaka
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Erik M Schlicht
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Jimmy Z Liu
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Tejas Shah
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Javier Gutierrez-Achury
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Kirsten M Boberg
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Annika Bergquist
- Department of Gastroenterology and Hepatology, Karolinska University Hospital Huddinge, Karolinska Instituet, Stockholm, Sweden
| | - Severine Vermeire
- Department of Clinical and Experimental Medicine, Katholieke Universiteit Leuven, Lueven, Belgium,Department of Gastroenterology, University Hospital Lueven, Lueven, Belgium
| | - Bertus Eksteen
- Snyder Institute for Chronic Diseases, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Peter R Durie
- Physiology and Experimental Medicine, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martti Farkkila
- Helsinki University and Helsinki University Hospital, Clinic of Gastroenterology, Helsinki, Finland
| | - Tobias Müller
- Department of Internal Medicine, Hepatology and Gastroenterology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martina Sterneck
- Department of Hepatobiliary Surgery and Transplantation, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias J Weismüller
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany,Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany,Department of Internal Medicine 1, University Hospital of Bonn, Bonn, Germany
| | - Daniel N Gotthardt
- Department of Medicine, University Hospital of Heidelberg, Heidelberg, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Felix Braun
- Department of General, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Medical Centre Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andreas Teufel
- Department of Medicine I, University Medical Center, Regensburg, Germany
| | - Mattias Laudes
- Clinic of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gunnar Jacobs
- Institute of Epidemiology and Biobank PopGen, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ulrich Beuers
- Department of Gastroenterology and Hepatology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Hanns-Ulrich Marschall
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Piotr Milkiewicz
- Liver and Internal Medicine Unit, Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Albert Pares
- Liver Unit, Hospital Clínic, IDIBAPS, CIBERehd, University of Barcelona, Barcelona, Spain
| | - Kimmo Kontula
- Helsinki University, Department of Medicine, University of Helsinki, Helsinki, Finland
| | - Olivier Chazouillères
- AP-HP Hôpital Saint Antoine, Department of Hepatology, UPMC University Paris 06, Paris, France
| | - Pietro Invernizzi
- Center for Autoimmune Liver Diseases, Humanitas Clinical and Research Center, Rozzano, Milano, Italy
| | - Elizabeth Goode
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Kelly Spiess
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Carmel Moore
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom
| | - Jennifer Sambrook
- INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,Department of Hematology, University of Cambridge, Long Road, Cambridge CB2 0PT, United Kingdom
| | - Willem H Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,Department of Hematology, University of Cambridge, Long Road, Cambridge CB2 0PT, United Kingdom,NHS Blood and Transplant, Long Road, Cambridge CB2 0PT, United Kingdom
| | - David J Roberts
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,NHS Blood and Transplant - Oxford Centre, Level 2, John Radcliffe Hospital, Headley Way, Oxford OX3 9BQ, United Kingdom,Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, United Kingdom
| | - John Danesh
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom,INTERVAL Coordinating Centre, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, United Kingdom
| | - Annarosa Floreani
- Department of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, Italy
| | - Aliya F Gulamhusein
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - John E Eaton
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany,Department for General Internal Medicine, University Hospital Schleswig-Holstein Campus Kiel, Kiel 24105, Germany
| | | | - Christopher L Bowlus
- Division of Gastroenterology and Hepatology, University of California, Davis, California, United States of America
| | - Velimir A Luketic
- Gastroenterology and Hepatology Section, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Joseph A Odin
- Department of Medicine, The Mount Sinai School of Medicine, New York, New York, United States of America
| | - Kapil B Chopra
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Kris V Kowdley
- Liver Care Network and Organ Care Research, Swedish Medical Center, Seattle, Washington, United States of America
| | - Naga Chalasani
- Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany,Integrated Research and Treatment Center-Transplantation (IFB-tx), Hannover Medical School, Hannover, Germany
| | - Brijesh Srivastava
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - George Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom,Division of Gastroenterology and Hepatology, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Graeme Alexander
- Department of Medicine, Division of Hepatology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel J Gaffney
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Roger W Chapman
- Department of Translational Gastroenterology, Oxford University Hospitals NHS Trust, Oxford, United Kingdom
| | - Gideon M Hirschfield
- Centre for Liver Research, NIHR Biomedical Research Unit, University of Birmingham, Birmingham, United Kingdom,University of Toronto and Liver Center, Toronto Western Hospital, Toronto, ON, Canada
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America
| | | | | | | | - Simon M Rushbrook
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom H Karlsen
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Institute of Clinical Medicine, University of Oslo, Oslo, Norway,Section of Gastroenterology, Department of Transplantation Medicine, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Konstantinos N Lazaridis
- Center for Basic Research in Digestive Diseases, Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine, Rochester, Minnesota, United States of America,Corresponding authors: Correspondence should be addressed to C.A.A. () or K.N.L. () or
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom,Corresponding authors: Correspondence should be addressed to C.A.A. () or K.N.L. () or
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210
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Escudero-Hernández C, Peña AS, Bernardo D. Immunogenetic Pathogenesis of Celiac Disease and Non-celiac Gluten Sensitivity. Curr Gastroenterol Rep 2017; 18:36. [PMID: 27216895 DOI: 10.1007/s11894-016-0512-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Celiac disease is the most common oral intolerance in Western countries. It results from an immune response towards gluten proteins from certain cereals in genetically predisposed individuals (HLA-DQ2 and/or HLA-DQ8). Its pathogenesis involves the adaptive (HLA molecules, transglutaminase 2, dendritic cells, and CD4(+) T-cells) and the innate immunity with an IL-15-mediated response elicited in the intraepithelial compartment. At present, the only treatment is a permanent strict gluten-free diet (GFD). Multidisciplinary studies have provided a deeper insight of the genetic and immunological factors and their interaction with the microbiota in the pathogenesis of the disease. Similarly, a better understanding of the composition of the toxic gluten peptides has improved the ways to detect them in food and drinks and how to monitor GFD compliance via non-invasive approaches. This review, therefore, addresses the major findings obtained in the last few years including the re-discovery of non-celiac gluten sensitivity.
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Affiliation(s)
- Celia Escudero-Hernández
- Mucosal Immunology Laboratory, IBGM, Facultad de Medicina, Dpto. Pediatría e Inmunología, University of Valladolid-Consejo Superior de Investigaciones Científicas, (4th floor) Av. Ramón y Cajal 7, 47005, Valladolid, Spain
| | - Amado Salvador Peña
- VU Medical Center Amsterdam, Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108 Room 10E65, 1081 HZ, Amsterdam, The Netherlands
| | - David Bernardo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, 28006, Spain.
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211
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Abstract
Whole-genome and exome sequencing in human populations has revealed the tolerance of each gene for loss-of-function variation. By understanding this tolerance, it has become increasingly possible to identify genes that would make safe therapeutic targets and to identify rare genetic risk factors and phenotypes at the scale of individual genomes. To date, the vast majority of surveyed loss-of-function variants are in protein-coding regions of the genome mainly due to the focus on these regions by exome-based sequencing projects and their relative ease of interpretability. As whole-genome sequencing becomes more prevalent, new strategies will be required to uncover impactful variation in non-coding regions of the genome where the architecture of genome function is more complex. In this review, we investigate recent studies of loss-of-function variation and emerging approaches for interpreting whole-genome sequencing data to identify rare and impactful non-coding loss-of-function variants.
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Affiliation(s)
- Zachary Zappala
- Department of Genetics, Stanford University, California, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, California, USA
- Department of Pathology, Stanford University, California, USA
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212
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Moreno-Moral A, Pesce F, Behmoaras J, Petretto E. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease. Methods Mol Biol 2017; 1488:337-362. [PMID: 27933533 DOI: 10.1007/978-1-4939-6427-7_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.
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Affiliation(s)
- Aida Moreno-Moral
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Francesco Pesce
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, Hammersmith Campus, Imperial Centre for Translational and Experimental Medicine, London, UK
| | - Jacques Behmoaras
- Centre for Complement and Inflammation Research, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Enrico Petretto
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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213
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Lee CH, Cook S, Lee JS, Han B. Comparison of Two Meta-Analysis Methods: Inverse-Variance-Weighted Average and Weighted Sum of Z-Scores. Genomics Inform 2016; 14:173-180. [PMID: 28154508 PMCID: PMC5287121 DOI: 10.5808/gi.2016.14.4.173] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 12/03/2016] [Accepted: 12/03/2016] [Indexed: 12/22/2022] Open
Abstract
The meta-analysis has become a widely used tool for many applications in bioinformatics, including genome-wide association studies. A commonly used approach for meta-analysis is the fixed effects model approach, for which there are two popular methods: the inverse variance-weighted average method and weighted sum of z-scores method. Although previous studies have shown that the two methods perform similarly, their characteristics and their relationship have not been thoroughly investigated. In this paper, we investigate the optimal characteristics of the two methods and show the connection between the two methods. We demonstrate that the each method is optimized for a unique goal, which gives us insight into the optimal weights for the weighted sum of z-scores method. We examine the connection between the two methods both analytically and empirically and show that their resulting statistics become equivalent under certain assumptions. Finally, we apply both methods to the Wellcome Trust Case Control Consortium data and demonstrate that the two methods can give distinct results in certain study designs.
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Affiliation(s)
- Cue Hyunkyu Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.; Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Seungho Cook
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.; School of Systems Biomedical Science, Soongsil University, Seoul 06978, Korea
| | - Ji Sung Lee
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.; Department of Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea
| | - Buhm Han
- Asan Institute for Life Sciences, Asan Medical Center, Seoul 05505, Korea.; Department of Convergence Medicine, University of Ulsan College of Medicine, Seoul 05505, Korea
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214
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Fischer A, Rausell A. Primary immunodeficiencies suggest redundancy within the human immune system. Sci Immunol 2016; 1:1/6/eaah5861. [PMID: 28783693 DOI: 10.1126/sciimmunol.aah5861] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/03/2016] [Accepted: 12/01/2016] [Indexed: 12/31/2022]
Abstract
Pathogen-driven evolution has shaped the complexity of the human immune system. Our genome contains at least 1854 gene products involved in immune responses. However, the redundancy and robustness of the immune system need further characterization. One way to examine this redundancy is through the study of monogenic primary immunodeficiencies (PIDs) associated with infections. Causal mutations affecting innate immunity genes are, in relative terms, close to seven times less frequent than those affecting adaptive immunity genes in PIDs. Loss-of-function mutations of innate immunity genes encoding pattern-recognition receptors (PRRs) and associated pathways rarely cause susceptibility to infections, which suggests that PRR pathways are partially redundant in the immune responses to infection. This dispensability has also been observed for constitutive products of the immune system, such as secretory immunoglobulin A, and for innate immune cells, such as natural killer and innate lymphoid cell subsets, which are not essential for viability. This Review discusses these findings in the context of their implications for the identification of previously unknown classes of PIDs and assessment of the susceptibility to infection associated with various targeted immunotherapies.
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Affiliation(s)
- Alain Fischer
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France. .,Immunology and Pediatric Hematology Department, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM UMR 1163, Paris, France.,Collège de France, Paris, France
| | - Antonio Rausell
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, Paris, France
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215
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Genetic Ancestry and Natural Selection Drive Population Differences in Immune Responses to Pathogens. Cell 2016; 167:657-669.e21. [PMID: 27768889 DOI: 10.1016/j.cell.2016.09.025] [Citation(s) in RCA: 312] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/28/2016] [Accepted: 09/15/2016] [Indexed: 12/31/2022]
Abstract
Individuals from different populations vary considerably in their susceptibility to immune-related diseases. To understand how genetic variation and natural selection contribute to these differences, we tested for the effects of African versus European ancestry on the transcriptional response of primary macrophages to live bacterial pathogens. A total of 9.3% of macrophage-expressed genes show ancestry-associated differences in the gene regulatory response to infection, and African ancestry specifically predicts a stronger inflammatory response and reduced intracellular bacterial growth. A large proportion of these differences are under genetic control: for 804 genes, more than 75% of ancestry effects on the immune response can be explained by a single cis- or trans-acting expression quantitative trait locus (eQTL). Finally, we show that genetic effects on the immune response are strongly enriched for recent, population-specific signatures of adaptation. Together, our results demonstrate how historical selective events continue to shape human phenotypic diversity today, including for traits that are key to controlling infection.
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216
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Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations. Cell 2016; 167:643-656.e17. [PMID: 27768888 PMCID: PMC5075285 DOI: 10.1016/j.cell.2016.09.024] [Citation(s) in RCA: 275] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 07/14/2016] [Accepted: 09/15/2016] [Indexed: 12/30/2022]
Abstract
Humans differ in the outcome that follows exposure to life-threatening pathogens, yet the extent of population differences in immune responses and their genetic and evolutionary determinants remain undefined. Here, we characterized, using RNA sequencing, the transcriptional response of primary monocytes from Africans and Europeans to bacterial and viral stimuli-ligands activating Toll-like receptor pathways (TLR1/2, TLR4, and TLR7/8) and influenza virus-and mapped expression quantitative trait loci (eQTLs). We identify numerous cis-eQTLs that contribute to the marked differences in immune responses detected within and between populations and a strong trans-eQTL hotspot at TLR1 that decreases expression of pro-inflammatory genes in Europeans only. We find that immune-responsive regulatory variants are enriched in population-specific signals of natural selection and show that admixture with Neandertals introduced regulatory variants into European genomes, affecting preferentially responses to viral challenges. Together, our study uncovers evolutionarily important determinants of differences in host immune responsiveness between human populations.
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217
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Wang Y, Richard R, Pan Y. Prior knowledge guided eQTL mapping for identifying candidate genes. BMC Bioinformatics 2016; 17:531. [PMID: 27964730 PMCID: PMC5155383 DOI: 10.1186/s12859-016-1387-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 11/26/2016] [Indexed: 12/03/2022] Open
Abstract
Background Expression quantitative trait loci (eQTL) mapping is often used to identify genetic loci and candidate genes correlated with traits. Although usually a group of genes affect complex traits, genes in most eQTL mapping methods are considered as independent. Recently, some eQTL mapping methods have accounted for correlated genes, used biological prior knowledge and applied these in model species such as yeast or mouse. However, biological prior knowledge might be very limited for most species. Results We proposed a data-driven prior knowledge guided eQTL mapping for identifying candidate genes. At first, quantitative trait loci (QTL) analysis was used to identify single nucleotide polymorphisms (SNP) markers that are associated with traits. Then co-expressed gene modules were generated and gene modules significantly associated with traits were selected. Prior knowledge from QTL mapping was used for eQTL mapping on the selected modules. We tested and compared prior knowledge guided eQTL mapping to the eQTL mapping with no prior knowledge in a simulation study and two barley stem rust resistance case studies. The results in simulation study and real barley case studies show that models using prior knowledge outperform models without prior knowledge. In the first case study, three gene modules were selected and one of the gene modules was enriched with defense response Gene Ontology (GO) terms. Also, one probe in the gene module is mapped to Rpg1, previously identified as resistance gene to stem rust. In the second case study, four gene modules are identified, one gene module is significantly enriched with defense response to fungus and bacterium. Conclusions Prior knowledge guided eQTL mapping is an effective method for identifying candidate genes. The case studies in stem rust show that this approach is robust, and outperforms methods with no prior knowledge in identifying candidate genes. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1387-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yunli Wang
- National Research Council Canada, 1200 Montreal Rd., Ottawa, K1A 0R6, Canada.
| | - Rene Richard
- National Research Council Canada, 46 Dineen Dr., Fredericton, E3B 9W4, Canada
| | - Youlian Pan
- National Research Council Canada, 1200 Montreal Rd., Ottawa, K1A 0R6, Canada
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218
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Te Velde AA, Bezema T, van Kampen AHC, Kraneveld AD, 't Hart BA, van Middendorp H, Hack EC, van Montfrans JM, Belzer C, Jans-Beken L, Pieters RH, Knipping K, Huber M, Boots AMH, Garssen J, Radstake TR, Evers AWM, Prakken BJ, Joosten I. Embracing Complexity beyond Systems Medicine: A New Approach to Chronic Immune Disorders. Front Immunol 2016; 7:587. [PMID: 28018353 PMCID: PMC5149516 DOI: 10.3389/fimmu.2016.00587] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/28/2016] [Indexed: 12/21/2022] Open
Abstract
In order to combat chronic immune disorders (CIDs), it is an absolute necessity to understand the bigger picture, one that goes beyond insights at a one-disease, molecular, cellular, and static level. To unravel this bigger picture we advocate an integral, cross-disciplinary approach capable of embracing the complexity of the field. This paper discusses the current knowledge on common pathways in CIDs including general psychosocial and lifestyle factors associated with immune functioning. We demonstrate the lack of more in-depth psychosocial and lifestyle factors in current research cohorts and most importantly the need for an all-encompassing analysis of these factors. The second part of the paper discusses the challenges of understanding immune system dynamics and effectively integrating all key perspectives on immune functioning, including the patient’s perspective itself. This paper suggests the use of techniques from complex systems science in describing and simulating healthy or deviating behavior of the immune system in its biopsychosocial surroundings. The patient’s perspective data are suggested to be generated by using specific narrative techniques. We conclude that to gain more insight into the behavior of the whole system and to acquire new ways of combatting CIDs, we need to construct and apply new techniques in the field of computational and complexity science, to an even wider variety of dynamic data than used in today’s systems medicine.
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Affiliation(s)
- Anje A Te Velde
- Tytgat Institute for Liver and Intestinal Research, Academic Medical Center , Amsterdam , Netherlands
| | | | - Antoine H C van Kampen
- Bioinformatics Laboratory, Clinical Epidemiology, Biostatistics and Bioinformatics (KEBB), Academic Medical Center, Amsterdam, Netherlands; Biosystems Data Analysis, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, Netherlands
| | - Aletta D Kraneveld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bert A 't Hart
- Department of Immunobiology, Biomedical Primate Research Centre, Rijswijk, Netherlands; Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands; Department of Neuroscience, University Medical Center, University of Groningen, Groningen, Netherlands
| | - Henriët van Middendorp
- Institute of Psychology, Health, Medical, and Neuropsychology Unit, Faculty of Social and Behavioural Sciences, Leiden University , Leiden , Netherlands
| | - Erik C Hack
- Laboratory of Translational Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Joris M van Montfrans
- Division of Pediatrics, Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht , Utrecht , Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University , Wageningen , Netherlands
| | - Lilian Jans-Beken
- Department of Psychology and Educational Sciences, Open University , Heerlen , Netherlands
| | - Raymond H Pieters
- Institute for Risk Assessment Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands; Institute for Life Sciences and Chemistry, HU University of Applied Sciences Utrecht, Utrecht, Netherlands
| | - Karen Knipping
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Immunology Platform, Nutricia Research, Utrecht, Netherlands
| | - Machteld Huber
- Institute for Positive Health , Amersfoort , Netherlands
| | - Annemieke M H Boots
- Department of Rheumatology and Clinical Immunology, University Medical Center Groningen, University of Groningen , Groningen , Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Netherlands; Immunology Platform, Nutricia Research, Utrecht, Netherlands
| | - Tim R Radstake
- Laboratory of Translational Immunology, Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht , Utrecht , Netherlands
| | - Andrea W M Evers
- Institute of Psychology, Health, Medical, and Neuropsychology Unit, Faculty of Social and Behavioural Sciences, Leiden University , Leiden , Netherlands
| | - Berent J Prakken
- Laboratory of Translational Immunology, Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht , Utrecht , Netherlands
| | - Irma Joosten
- Laboratory of Medical Immunology, Department of Laboratory Medicine, Radboud University Medical Centre , Nijmegen , Netherlands
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219
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Zhernakova DV, Deelen P, Vermaat M, van Iterson M, van Galen M, Arindrarto W, van 't Hof P, Mei H, van Dijk F, Westra HJ, Bonder MJ, van Rooij J, Verkerk M, Jhamai PM, Moed M, Kielbasa SM, Bot J, Nooren I, Pool R, van Dongen J, Hottenga JJ, Stehouwer CDA, van der Kallen CJH, Schalkwijk CG, Zhernakova A, Li Y, Tigchelaar EF, de Klein N, Beekman M, Deelen J, van Heemst D, van den Berg LH, Hofman A, Uitterlinden AG, van Greevenbroek MMJ, Veldink JH, Boomsma DI, van Duijn CM, Wijmenga C, Slagboom PE, Swertz MA, Isaacs A, van Meurs JBJ, Jansen R, Heijmans BT, 't Hoen PAC, Franke L. Identification of context-dependent expression quantitative trait loci in whole blood. Nat Genet 2016; 49:139-145. [PMID: 27918533 DOI: 10.1038/ng.3737] [Citation(s) in RCA: 263] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 11/02/2016] [Indexed: 02/07/2023]
Abstract
Genetic risk factors often localize to noncoding regions of the genome with unknown effects on disease etiology. Expression quantitative trait loci (eQTLs) help to explain the regulatory mechanisms underlying these genetic associations. Knowledge of the context that determines the nature and strength of eQTLs may help identify cell types relevant to pathophysiology and the regulatory networks underlying disease. Here we generated peripheral blood RNA-seq data from 2,116 unrelated individuals and systematically identified context-dependent eQTLs using a hypothesis-free strategy that does not require previous knowledge of the identity of the modifiers. Of the 23,060 significant cis-regulated genes (false discovery rate (FDR) ≤ 0.05), 2,743 (12%) showed context-dependent eQTL effects. The majority of these effects were influenced by cell type composition. A set of 145 cis-eQTLs depended on type I interferon signaling. Others were modulated by specific transcription factors binding to the eQTL SNPs.
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Affiliation(s)
- Daria V Zhernakova
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Patrick Deelen
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Martijn Vermaat
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Michiel van Galen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Wibowo Arindrarto
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter van 't Hof
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Hailiang Mei
- Sequence Analysis Support Core, Leiden University Medical Center, Leiden, the Netherlands
| | - Freerk van Dijk
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Harm-Jan Westra
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - Marijn Verkerk
- Department of Internal Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - P Mila Jhamai
- Department of Internal Medicine, ErasmusMC, Rotterdam, the Netherlands
| | - Matthijs Moed
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Szymon M Kielbasa
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Jan Bot
- SURFsara, Amsterdam, the Netherlands
| | | | - René Pool
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Jouke J Hottenga
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Coen D A Stehouwer
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Carla J H van der Kallen
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Casper G Schalkwijk
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Ettje F Tigchelaar
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Niek de Klein
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - Marian Beekman
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris Deelen
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Leonard H van den Berg
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands
| | | | - Marleen M J van Greevenbroek
- Department of Internal Medicine, Maastricht University Medical Center, Maastricht, the Netherlands.,School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Morris A Swertz
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands.,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Aaron Isaacs
- School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, Maastricht, the Netherlands.,Genetic Epidemiology Unit, Department of Epidemiology, ErasmusMC, Rotterdam, the Netherlands.,Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands
| | | | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Neuroscience Campus Amsterdam, Amsterdam, the Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Genomics Coordination Center, Groningen, the Netherlands
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220
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Abstract
The human immune system is highly variable between individuals but relatively stable over time within a given person. Recent conceptual and technological advances have enabled systems immunology analyses, which reveal the composition of immune cells and proteins in populations of healthy individuals. The range of variation and some specific influences that shape an individual's immune system is now becoming clearer. Human immune systems vary as a consequence of heritable and non-heritable influences, but symbiotic and pathogenic microbes and other non-heritable influences explain most of this variation. Understanding when and how such influences shape the human immune system is key for defining metrics of immunological health and understanding the risk of immune-mediated and infectious diseases.
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Affiliation(s)
- Petter Brodin
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institutet, Stockholm 17165, Sweden.,Department of Neonatology, Karolinska University Hospital, Stockholm 14186, Sweden
| | - Mark M Davis
- Department of Microbiology and Immunology, Stanford University School of Medicine.,Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine.,Howard Hughes Medical Institute, Stanford University School of Medicine, California 94304, USA
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Hoffman GE, Schadt EE. variancePartition: interpreting drivers of variation in complex gene expression studies. BMC Bioinformatics 2016; 17:483. [PMID: 27884101 PMCID: PMC5123296 DOI: 10.1186/s12859-016-1323-z] [Citation(s) in RCA: 339] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 11/05/2016] [Indexed: 12/14/2022] Open
Abstract
Background As large-scale studies of gene expression with multiple sources of biological and technical variation become widely adopted, characterizing these drivers of variation becomes essential to understanding disease biology and regulatory genetics. Results We describe a statistical and visualization framework, variancePartition, to prioritize drivers of variation based on a genome-wide summary, and identify genes that deviate from the genome-wide trend. Using a linear mixed model, variancePartition quantifies variation in each expression trait attributable to differences in disease status, sex, cell or tissue type, ancestry, genetic background, experimental stimulus, or technical variables. Analysis of four large-scale transcriptome profiling datasets illustrates that variancePartition recovers striking patterns of biological and technical variation that are reproducible across multiple datasets. Conclusions Our open source software, variancePartition, enables rapid interpretation of complex gene expression studies as well as other high-throughput genomics assays. variancePartition is available from Bioconductor: http://bioconductor.org/packages/variancePartition. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1323-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gabriel E Hoffman
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA.
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, USA
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Abstract
The hematopoietic system plays a major role in human health. Two studies by Astle et al. and Chen et al. published in this issue of Cell use genome-wide association and functional genomics approaches to provide deep insights into the role of genetic variants in hematological traits. We discuss these discoveries and future strategies toward completing our understanding of the genetic basis for variation in human traits.
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Affiliation(s)
- Sarah Kim-Hellmuth
- New York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10027, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY 10013, USA; Department of Systems Biology, Columbia University, New York, NY 10027, USA.
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Capture Hi-C identifies a novel causal gene, IL20RA, in the pan-autoimmune genetic susceptibility region 6q23. Genome Biol 2016; 17:212. [PMID: 27799070 PMCID: PMC5088679 DOI: 10.1186/s13059-016-1078-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/05/2016] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific assays in T and B cell lines, we provide compelling evidence that redefines causal genes at the 6q23 locus, one of the most important loci that confers autoimmunity risk. RESULTS Although the function of disease-associated non-coding single nucleotide polymorphisms (SNPs) at 6q23 is unknown, the association is generally assigned to TNFAIP3, the closest gene. However, the DNA fragment containing the associated SNPs interacts through chromatin looping not only with TNFAIP3, but also with IL20RA, located 680 kb upstream. The risk allele of the most likely causal SNP, rs6927172, is correlated with both a higher frequency of interactions and increased expression of IL20RA, along with a stronger binding of both the NFκB transcription factor and chromatin marks characteristic of active enhancers in T-cells. CONCLUSIONS Our results highlight the importance of gene assignment for translating GWAS findings into biologically meaningful mechanisms of disease and potential therapeutic targets; indeed, monoclonal antibody therapy targeting IL-20 is effective in the treatment of rheumatoid arthritis and psoriasis, both with strong GWAS associations to this region.
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Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R, Le KT, Deelen P, Ricaño-Ponce I, Schoffelen T, Jansen AF, Swertz MA, Withoff S, van de Vosse E, van Deuren M, van de Veerdonk F, Zhernakova A, van der Meer JW, Xavier RJ, Franke L, Joosten LA, Wijmenga C, Kumar V, Netea MG. A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans. Cell 2016; 167:1099-1110.e14. [DOI: 10.1016/j.cell.2016.10.017] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/04/2016] [Accepted: 10/11/2016] [Indexed: 12/17/2022]
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225
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Malik U, Javed A, Ali A, Asghar K. Structural and functional annotation of human FAM26F: A multifaceted protein having a critical role in the immune system. Gene 2016; 597:66-75. [PMID: 27784631 DOI: 10.1016/j.gene.2016.10.029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/29/2016] [Accepted: 10/19/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Human immune system is a complex amalgam of a greatly diverse ensemble comprising of various cellular and non-cellular components, including proteins. FAM26F (family with sequence similarity 26, member F) is a relatively recently identified gene reported to play important role in diverse immune responses. Numerous studies have reported FAM26F to be differentially expressed in several viral, bacterial and parasitic infections, in certain pathophysiological conditions such as heart and liver transplantation, and in several cancers. FAM26F has also been found to be upregulated by various stimulants such as polyI:C, LPS, INF gamma and TNF alpha, and via various anticipated pathways including TLR3, TLR4 IFN-β and Dectin-1. Moreover, the synergistic expression of FAM26F on both NK-cells and myeloid dendritic cells is required to activate NK-cells against tumors via its cytoplasmic tail, thus emphasizing the therapeutic potential of FAM26F for NK sensitive tumors. Although a considerable amount of evidence is present regarding the potential role of FAM26F in immune modulation, the exact function and modulatory pathways of this gene are yet to be elucidated. We aimed to completely characterize FAM26F in order to apprehend its function and role in the immune responses. RESULTS The results revealed human FAM26F to be located at chromosomal position 6q22.1. FAM26F mRNA contains 1141bp coding region encoding a 315 amino acid long, stable protein that has been well-conserved throughout evolution. It is a signal peptide deprived transmembrane protein that is secreted through non-classical pathway. The presence of a single well-conserved Ca_hom_mod domain indicated FAM26F to be a cation channel involved in the transport of molecules. A potential N-glycosylation and 14 phosphorylation sites were also predicted, along with four interacting partners of FAM26F. The secondary and tertiary structures of FAM26F were determined. Moreover, the presence of an immunoglobulin-like fold in FAM26F emphasized its role in immune responses. CONCLUSION This is the first in silico structural and functional characterization of FAM26F which will be helpful in better understanding the role of FAM26F in the context of the immune system and may also lead to the identification of novel therapeutic targets.
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Affiliation(s)
- Uzma Malik
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan.
| | - Aneela Javed
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan.
| | - Amjad Ali
- Department of Industrial Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan.
| | - Kashif Asghar
- Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, 54000, Pakistan.
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Moyerbrailean GA, Richards AL, Kurtz D, Kalita CA, Davis GO, Harvey CT, Alazizi A, Watza D, Sorokin Y, Hauff N, Zhou X, Wen X, Pique-Regi R, Luca F. High-throughput allele-specific expression across 250 environmental conditions. Genome Res 2016; 26:1627-1638. [PMID: 27934696 PMCID: PMC5131815 DOI: 10.1101/gr.209759.116] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/13/2016] [Indexed: 11/24/2022]
Abstract
Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are complex and difficult to measure and control at the organismal level, as found in GWAS and epidemiological studies. An alternative approach focuses on the cellular environment using in vitro treatments as a proxy for the organismal environment. These cellular environments simplify the organism-level environmental exposures to provide a tractable influence on subcellular phenotypes, such as gene expression. Expression quantitative trait loci (eQTL) mapping studies identified GxE interactions in response to drug treatment and pathogen exposure. However, eQTL mapping approaches are infeasible for large-scale analysis of multiple cellular environments. Recently, allele-specific expression (ASE) analysis emerged as a powerful tool to identify GxE interactions in gene expression patterns by exploiting naturally occurring environmental exposures. Here we characterized genetic effects on the transcriptional response to 50 treatments in five cell types. We discovered 1455 genes with ASE (FDR < 10%) and 215 genes with GxE interactions. We demonstrated a major role for GxE interactions in complex traits. Genes with a transcriptional response to environmental perturbations showed sevenfold higher odds of being found in GWAS. Additionally, 105 genes that indicated GxE interactions (49%) were identified by GWAS as associated with complex traits. Examples include GIPR–caffeine interaction and obesity and include LAMP3–selenium interaction and Parkinson disease. Our results demonstrate that comprehensive catalogs of GxE interactions are indispensable to thoroughly annotate genes and bridge epidemiological and genome-wide association studies.
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Affiliation(s)
- Gregory A Moyerbrailean
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Allison L Richards
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Daniel Kurtz
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Cynthia A Kalita
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Gordon O Davis
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Chris T Harvey
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Adnan Alazizi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Donovan Watza
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA
| | - Yoram Sorokin
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Nancy Hauff
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Xiang Zhou
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Xiaoquan Wen
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Roger Pique-Regi
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, Michigan 48201, USA.,Department of Obstetrics and Gynecology, Wayne State University, Detroit, Michigan 48201, USA
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227
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Kita R, Fraser HB. Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin. PLoS Genet 2016; 12:e1006382. [PMID: 27760139 PMCID: PMC5070784 DOI: 10.1371/journal.pgen.1006382] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/23/2016] [Indexed: 12/29/2022] Open
Abstract
Sun-exposure is a key environmental variable in the study of human evolution. Several skin-pigmentation genes serve as classical examples of positive selection, suggesting that sun-exposure has significantly shaped worldwide genomic variation. Here we investigate the interaction between genetic variation and sun-exposure, and how this impacts gene expression regulation. Using RNA-Seq data from 607 human skin samples, we identified thousands of transcripts that are differentially expressed between sun-exposed skin and non-sun-exposed skin. We then tested whether genetic variants may influence each individual’s gene expression response to sun-exposure. Our analysis revealed 10 sun-exposure-dependent gene expression quantitative trait loci (se-eQTLs), including genes involved in skin pigmentation (SLC45A2) and epidermal differentiation (RASSF9). The allele frequencies of the RASSF9 se-eQTL across diverse populations correlate with the magnitude of solar radiation experienced by these populations, suggesting local adaptation to varying levels of sunlight. These results provide the first examples of sun-exposure-dependent regulatory variation and suggest that this variation has contributed to recent human adaptation. Varying levels of sun-exposure across the world have significantly shaped human evolution. Previous analyses have found several skin pigmentation genes with evidence of strong evolutionary pressures throughout human history, manifesting as large differences in the frequency of genomic variants across populations. But even within populations, individuals respond differently to sun-exposure, suggesting variation in addition to the major differences in skin pigmentation across populations. Here we investigated whether genetic variants associate with response to sun-exposure within Europeans. To measure the response we analyzed gene expression in sun-exposed and non-sun-exposed skin, and identified ten genetic variants that associated with the sun-exposure response of nearby genes. One of these genetic variants, which associated with the sun-exposure response of the gene RASSF9, showed evidence of adaptation in humans in response to solar radiation. Together this evidence suggests that the regulation of gene expression is influenced by sun-exposure and that the sun-exposure dependent effect on RASSF9 expression may have had an effect on human fitness. To our knowledge, this is the first example of an environment-dependent regulatory variant with evidence of adaptation in humans.
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Affiliation(s)
- Ryosuke Kita
- Department of Biology, Stanford University, Stanford California
| | - Hunter B. Fraser
- Department of Biology, Stanford University, Stanford California
- * E-mail:
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228
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Javed A, Leuchte N, Salinas G, Opitz L, Stahl-Hennig C, Sopper S, Sauermann U. Pre-infection transcript levels of FAM26F in peripheral blood mononuclear cells inform about overall plasma viral load in acute and post-acute phase after simian immunodeficiency virus infection. J Gen Virol 2016; 97:3400-3412. [PMID: 27902344 PMCID: PMC5203675 DOI: 10.1099/jgv.0.000632] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
CD8+ cells from simian immunodeficiency virus (SIV)-infected long-term non-progressors and some uninfected macaques can suppress viral replication in vitro without killing the infected cells. The aim of this study was to identify factors responsible for non-cytolytic viral suppression by transcriptional profiling and to investigate their potential impact on SIV replication. Results of microarray experiments and further validation with cells from infected and uninfected macaques revealed that FAM26F RNA levels distinguished CD8+ cells of controllers and non-controllers (P=0.001). However, FAM26F was also expressed in CD4+ T-cells and B-cells. FAM26F expression increased in lymphocytes after in vitro IFN-γ treatment on average 40-fold, and ex vivo FAM26F RNA levels in peripheral blood mononuclear cells correlated with plasma IFN-γ but not with IFN-α. Baseline FAM26F expression appeared to be stable for months, albeit the individual expression levels varied up to tenfold. Investigating its role in SIV-infection revealed that FAM26F was upregulated after infection (P<0.0008), but did not directly correlate with viral load in contrast to MX1 and CXCL10. However, pre-infection levels of FAM26F correlated inversely with overall plasma viral load (AUC) during the acute and post-acute phases of infection (e.g. AUC weeks post infection 0–8; no AIDS vaccine: P<0.0001, Spearman rank correlation coefficient (rs)=−0.89, n=16; immunized with an AIDS vaccine: P=0.033, rs=−0.43; n=25). FAM26F transcript levels prior to infection can provide information about the pace and strength of the antiviral immune response during the early stage of infection. FAM26F expression represented, in our experiments, one of the earliest prognostic markers, and could supplement major histocompatibility complex (MHC)-typing to predict disease progression before SIV-infection.
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Affiliation(s)
- Aneela Javed
- Deutsches Primatenzentrum GmbH, Leibniz-Institut für Primatenforschung, Unit of Infection Models, Göttingen, Germany
| | - Nicole Leuchte
- Deutsches Primatenzentrum GmbH, Leibniz-Institut für Primatenforschung, Unit of Infection Models, Göttingen, Germany
| | - Gabriela Salinas
- Transcriptome and Genome Analysis Laboratory (TAL), Faculty of Medicine, University of Göttingen, Göttingen, Germany
| | - Lennart Opitz
- Transcriptome and Genome Analysis Laboratory (TAL), Faculty of Medicine, University of Göttingen, Göttingen, Germany
| | - Christiane Stahl-Hennig
- Deutsches Primatenzentrum GmbH, Leibniz-Institut für Primatenforschung, Unit of Infection Models, Göttingen, Germany
| | - Sieghart Sopper
- Tumor Immunology Lab, Hematology and Oncology, Medical University Innsbruck and Tyrolean Cancer Research Institute, Innsbruck, Austria
| | - Ulrike Sauermann
- Deutsches Primatenzentrum GmbH, Leibniz-Institut für Primatenforschung, Unit of Infection Models, Göttingen, Germany
- Correspondence Ulrike Sauermann
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229
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Jacobson E, Perry JK, Long DS, Vickers MH, O'Sullivan JM. A potential role for genome structure in the translation of mechanical force during immune cell development. Nucleus 2016; 7:462-475. [PMID: 27673560 PMCID: PMC5120600 DOI: 10.1080/19491034.2016.1238998] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 09/11/2016] [Accepted: 09/13/2016] [Indexed: 12/29/2022] Open
Abstract
Immune cells react to a wide range of environments, both chemical and physical. While the former has been extensively studied, there is growing evidence that physical and in particular mechanical forces also affect immune cell behavior and development. In order to elicit a response that affects immune cell behavior or development, environmental signals must often reach the nucleus. Chemical and mechanical signals can initiate signal transduction pathways, but mechanical forces may also have a more direct route to the nucleus, altering nuclear shape via mechanotransduction. The three-dimensional organization of DNA allows for the possibility that altering nuclear shape directly remodels chromatin, redistributing critical regulatory elements and proteins, and resulting in wide-scale gene expression changes. As such, integrating mechanotransduction and genome architecture into the immunology toolkit will improve our understanding of immune development and disease.
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Affiliation(s)
- Elsie Jacobson
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Jo K. Perry
- Liggins Institute, University of Auckland, Auckland, New Zealand
| | - David S. Long
- Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand
| | - Mark H. Vickers
- Liggins Institute, University of Auckland, Auckland, New Zealand
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Urrutia A, Duffy D, Rouilly V, Posseme C, Djebali R, Illanes G, Libri V, Albaud B, Gentien D, Piasecka B, Hasan M, Fontes M, Quintana-Murci L, Albert ML. Standardized Whole-Blood Transcriptional Profiling Enables the Deconvolution of Complex Induced Immune Responses. Cell Rep 2016; 16:2777-2791. [PMID: 27568558 DOI: 10.1016/j.celrep.2016.08.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/31/2016] [Accepted: 08/02/2016] [Indexed: 10/21/2022] Open
Abstract
Systems approaches for the study of immune signaling pathways have been traditionally based on purified cells or cultured lines. However, in vivo responses involve the coordinated action of multiple cell types, which interact to establish an inflammatory microenvironment. We employed standardized whole-blood stimulation systems to test the hypothesis that responses to Toll-like receptor ligands or whole microbes can be defined by the transcriptional signatures of key cytokines. We found 44 genes, identified using Support Vector Machine learning, that captured the diversity of complex innate immune responses with improved segregation between distinct stimuli. Furthermore, we used donor variability to identify shared inter-cellular pathways and trace cytokine loops involved in gene expression. This provides strategies for dimension reduction of large datasets and deconvolution of innate immune responses applicable for characterizing immunomodulatory molecules. Moreover, we provide an interactive R-Shiny application with healthy donor reference values for induced inflammatory genes.
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Affiliation(s)
- Alejandra Urrutia
- Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1223, Paris 75015, France; Department of Cancer Immunology, Genentech Inc., San Francisco, CA 94080, USA
| | - Darragh Duffy
- Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1223, Paris 75015, France; Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Vincent Rouilly
- Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Céline Posseme
- Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Raouf Djebali
- Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Gabriel Illanes
- Center for Translational Research, Institut Pasteur, Paris 75015, France; IGDA, Institut Pasteur, Paris 75015, France; Centro de Matemática, Facultad de Ciencias, Universidad de la República, 11200 Montevideo, Uruguay
| | - Valentina Libri
- Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Benoit Albaud
- Institut Curie, Centre de Recherche, Département de recherche translationnelle, Plateforme de Génomique, Paris 75005, France
| | - David Gentien
- Institut Curie, Centre de Recherche, Département de recherche translationnelle, Plateforme de Génomique, Paris 75005, France
| | - Barbara Piasecka
- Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Milena Hasan
- Center for Translational Research, Institut Pasteur, Paris 75015, France
| | - Magnus Fontes
- IGDA, Institut Pasteur, Paris 75015, France; Centre for Mathematical Sciences, Lund University, 221 00 Lund, Sweden
| | - Lluis Quintana-Murci
- Laboratory of Human Evolutionary Genetics, Department of Genomes and Genetics, Institut Pasteur, Paris 75015, France; CNRS URA3012, Paris 75015, France.
| | - Matthew L Albert
- Laboratory of Dendritic Cell Immunobiology, Department of Immunology, Institut Pasteur, Paris 75015, France; INSERM U1223, Paris 75015, France; Center for Translational Research, Institut Pasteur, Paris 75015, France; Department of Cancer Immunology, Genentech Inc., San Francisco, CA 94080, USA.
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231
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Humburg P, Maugeri N, Lee W, Mohr B, Knight JC. Characterisation of the global transcriptional response to heat shock and the impact of individual genetic variation. Genome Med 2016; 8:87. [PMID: 27553423 PMCID: PMC4995779 DOI: 10.1186/s13073-016-0345-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 08/09/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The heat shock transcriptional response is essential to effective cellular function under stress. This is a highly heritable trait but the nature and extent of inter-individual variation in heat shock response remains unresolved. METHODS We determined global transcription profiles of the heat shock response for a panel of lymphoblastoid cell lines established from 60 founder individuals in the Yoruba HapMap population. We explore the observed differentially expressed gene sets following heat shock, establishing functional annotations, underlying networks and nodal genes involving heat shock factor 1 recruitment. We define a multivariate phenotype for the global transcriptional response to heat shock using partial least squares regression and map this quantitative trait to associated genetic variation in search of the major genomic modulators. RESULTS A comprehensive dataset of differentially expressed genes following heat shock in humans is presented. We identify nodal genes downstream of heat shock factor 1 in this gene set, notably involving ubiquitin C and small ubiquitin-like modifiers together with transcription factors. We dissect a multivariate phenotype for the global heat shock response which reveals distinct clustering of individuals in terms of variance of the heat shock response and involves differential expression of genes involved in DNA replication and cell division in some individuals. We find evidence of genetic associations for this multivariate response phenotype that involves trans effects modulating expression of genes following heat shock, including HSF1 and UBQLN1. CONCLUSION This study defines gene expression following heat shock for a cohort of individuals, establishing insights into the biology of the heat shock response and hypotheses for how variation in this may be modulated by underlying genetic diversity.
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Affiliation(s)
- Peter Humburg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Narelle Maugeri
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Queensland Institute of Medical Research, Brisbane, 4029 Queensland Australia
| | - Wanseon Lee
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Bert Mohr
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Hatter Institute for Cardiovascular Research in Africa, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Julian C. Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
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232
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Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ. Characterization of candidate genes in inflammatory bowel disease-associated risk loci. JCI Insight 2016; 1:e87899. [PMID: 27668286 DOI: 10.1172/jci.insight.87899] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
GWAS have linked SNPs to risk of inflammatory bowel disease (IBD), but a systematic characterization of disease-associated genes has been lacking. Prior studies utilized microarrays that did not capture many genes encoded within risk loci or defined expression quantitative trait loci (eQTLs) using peripheral blood, which is not the target tissue in IBD. To address these gaps, we sought to characterize the expression of IBD-associated risk genes in disease-relevant tissues and in the setting of active IBD. Terminal ileal (TI) and colonic mucosal tissues were obtained from patients with Crohn's disease or ulcerative colitis and from healthy controls. We developed a NanoString code set to profile 678 genes within IBD risk loci. A subset of patients and controls were genotyped for IBD-associated risk SNPs. Analyses included differential expression and variance analysis, weighted gene coexpression network analysis, and eQTL analysis. We identified 116 genes that discriminate between healthy TI and colon samples and uncovered patterns in variance of gene expression that highlight heterogeneity of disease. We identified 107 coexpressed gene pairs for which transcriptional regulation is either conserved or reversed in an inflammation-independent or -dependent manner. We demonstrate that on average approximately 60% of disease-associated genes are differentially expressed in inflamed tissue. Last, we identified eQTLs with either genotype-only effects on expression or an interaction effect between genotype and inflammation. Our data reinforce tissue specificity of expression in disease-associated candidate genes, highlight genes and gene pairs that are regulated in disease-relevant tissue and inflammation, and provide a foundation to advance the understanding of IBD pathogenesis.
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Affiliation(s)
- Joanna M Peloquin
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology
| | - Gautam Goel
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology
| | - Lingjia Kong
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - R Balfour Sartor
- Department of Medicine, Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dermot P McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Vijay Yajnik
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease
| | - Sergio A Lira
- Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Ramnik J Xavier
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease.,Center for Computational and Integrative Biology.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Song W, Hooli B, Mullin K, Jin SC, Cella M, Ulland TK, Wang Y, Tanzi RE, Colonna M. Alzheimer's disease-associated TREM2 variants exhibit either decreased or increased ligand-dependent activation. Alzheimers Dement 2016; 13:381-387. [PMID: 27520774 DOI: 10.1016/j.jalz.2016.07.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022]
Abstract
INTRODUCTION TREM2 is a lipid-sensing activating receptor on microglia known to be important for Alzheimer's disease (AD), but whether it plays a beneficial or detrimental role in disease pathogenesis is controversial. METHODS We analyzed AD risk of TREM2 variants in the NIMH AD Genetics Initiative Study and AD Sequencing Project. We compared each variant's risk and functional impact by a reporter assay. Finally, we analyzed expression of TREM2 on human monocytes. RESULTS We provide more evidence for increased AD risk associated with several TREM2 variants, and show that these variants decreased or markedly increased binding to TREM2 ligands. We identify HDL and LDL as novel TREM2 ligands. We also show that TREM2 expression in human monocytes is minimal compared to monocyte-derived dendritic cells. DISCUSSION Our results suggest that TREM2 signaling helps protect against AD but can cause harm in excess, supporting the idea that proper TREM2 function is important to counteract disease progression.
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Affiliation(s)
- Wilbur Song
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Basavaraj Hooli
- Department of Neurology, Harvard Medical School, and Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Kristina Mullin
- Department of Neurology, Harvard Medical School, and Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sheng Chih Jin
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Tyler K Ulland
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Yaming Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rudolph E Tanzi
- Department of Neurology, Harvard Medical School, and Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, MA, USA.
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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Understanding human immune function using the resources from the Human Functional Genomics Project. Nat Med 2016; 22:831-3. [DOI: 10.1038/nm.4140] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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235
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Joshi AD, Andersson C, Buch S, Stender S, Noordam R, Weng LC, Weeke PE, Auer PL, Boehm B, Chen C, Choi H, Curhan G, Denny JC, De Vivo I, Eicher JD, Ellinghaus D, Folsom AR, Fuchs C, Gala M, Haessler J, Hofman A, Hu F, Hunter DJ, Janssen HL, Kang JH, Kooperberg C, Kraft P, Kratzer W, Lieb W, Lutsey PL, Murad SD, Nordestgaard BG, Pasquale LR, Reiner AP, Ridker PM, Rimm E, Rose LM, Shaffer CM, Schafmayer C, Tamimi RM, Uitterlinden AG, Völker U, Völzke H, Wakabayashi Y, Wiggs JL, Zhu J, Roden DM, Stricker BH, Tang W, Teumer A, Hampe J, Tybjærg-Hansen A, Chasman DI, Chan AT, Johnson AD. Four Susceptibility Loci for Gallstone Disease Identified in a Meta-analysis of Genome-Wide Association Studies. Gastroenterology 2016; 151:351-363.e28. [PMID: 27094239 PMCID: PMC4959966 DOI: 10.1053/j.gastro.2016.04.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS A genome-wide association study (GWAS) of 280 cases identified the hepatic cholesterol transporter ABCG8 as a locus associated with risk for gallstone disease, but findings have not been reported from any other GWAS of this phenotype. We performed a large-scale, meta-analysis of GWASs of individuals of European ancestry with available prior genotype data, to identify additional genetic risk factors for gallstone disease. METHODS We obtained per-allele odds ratio (OR) and standard error estimates using age- and sex-adjusted logistic regression models within each of the 10 discovery studies (8720 cases and 55,152 controls). We performed an inverse variance weighted, fixed-effects meta-analysis of study-specific estimates to identify single-nucleotide polymorphisms that were associated independently with gallstone disease. Associations were replicated in 6489 cases and 62,797 controls. RESULTS We observed independent associations for 2 single-nucleotide polymorphisms at the ABCG8 locus: rs11887534 (OR, 1.69; 95% confidence interval [CI], 1.54-1.86; P = 2.44 × 10(-60)) and rs4245791 (OR, 1.27; P = 1.90 × 10(-34)). We also identified and/or replicated associations for rs9843304 in TM4SF4 (OR, 1.12; 95% CI, 1.08-1.16; P = 6.09 × 10(-11)), rs2547231 in SULT2A1 (encodes a sulfoconjugation enzyme that acts on hydroxysteroids and cholesterol-derived sterol bile acids) (OR, 1.17; 95% CI, 1.12-1.21; P = 2.24 × 10(-10)), rs1260326 in glucokinase regulatory protein (OR, 1.12; 95% CI, 1.07-1.17; P = 2.55 × 10(-10)), and rs6471717 near CYP7A1 (encodes an enzyme that catalyzes conversion of cholesterol to primary bile acids) (OR, 1.11; 95% CI, 1.08-1.15; P = 8.84 × 10(-9)). Among individuals of African American and Hispanic American ancestry, rs11887534 and rs4245791 were associated positively with gallstone disease risk, whereas the association for the rs1260326 variant was inverse. CONCLUSIONS In this large-scale GWAS of gallstone disease, we identified 4 loci in genes that have putative functions in cholesterol metabolism and transport, and sulfonylation of bile acids or hydroxysteroids.
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Affiliation(s)
- Amit D. Joshi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital Boston, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
| | - Charlotte Andersson
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts.
| | - Stephan Buch
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden Germany
| | - Stefan Stender
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark
| | - Raymond Noordam
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Lu-Chen Weng
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Peter E. Weeke
- Department of Medicine, Vanderbilt University, Nashville, TN,Department of Cardiology, The Heart Centre, Rigshospitalet, Copenhagen University Hospital, Denmark
| | - Paul L. Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee,Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Bernhard Boehm
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Constance Chen
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA
| | - Hyon Choi
- Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital, Boston, MA
| | - Gary Curhan
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Renal Division, Department of Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Joshua C. Denny
- Department of Medicine, Vanderbilt University, Nashville, TN,Department of Biomedical Informatics, Vanderbilt University, Nashville, TN
| | - Immaculata De Vivo
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - John D. Eicher
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Aaron R. Folsom
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Charles Fuchs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Manish Gala
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Frank Hu
- Department of Epidemiology, Harvard School of Public Health, Boston, MA,Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Harry L.A. Janssen
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, the Netherlands,Toronto Centre for Liver Disease, Toronto Western and General Hospital, University Health Network, Toronto, Canada
| | - Jae H. Kang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard School of Public Health, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - Wolfgang Kratzer
- Department of Internal Medicine I, Ulm University Hospital, Ulm, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian Albrechts Universität Kiel, Niemannsweg 11, Kiel, Germany
| | - Pamela L. Lutsey
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Sarwa Darwish Murad
- Department of Gastroenterology and Hepatology, Erasmus MC, Rotterdam, the Netherlands
| | - Børge G. Nordestgaard
- The Copenhagen General Population Study and,Department of Clinical Biochemistry, Herlev Hospital, Herlev Denmark,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louis R. Pasquale
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Paul M Ridker
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Eric Rimm
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA,Department of Nutrition, Harvard School of Public Health, Boston, MA
| | - Lynda M. Rose
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | | | - Clemens Schafmayer
- Department of General, Abdominal, Thoracic and Transplantation Surgery, University of Kiel, Kiel, Germany
| | - Rulla M. Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,Department of Epidemiology, Harvard School of Public Health, Boston, MA
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany,German Center for Cardiovascular Research, Partner Site Greifswald,German Center for Diabetes Research, Site Greifswald
| | - Yoshiyuki Wakabayashi
- The National Heart, Lung, and Blood Institute, DNA Sequencing Core Laboratory, Bethesda, MD
| | - Janey L. Wiggs
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
| | - Jun Zhu
- The National Heart, Lung, and Blood Institute, DNA Sequencing Core Laboratory, Bethesda, MD
| | - Dan M. Roden
- Department of Medicine, Vanderbilt University, Nashville, TN
| | - Bruno H. Stricker
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Weihong Tang
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, MN
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Jochen Hampe
- Medical Department 1, University Hospital Dresden, TU Dresden, Dresden Germany
| | - Anne Tybjærg-Hansen
- Department of Clinical Biochemistry, Rigshospitalet, Copenhagen, Denmark,Department of Clinical Biochemistry, Herlev Hospital, Herlev Denmark
| | - Daniel I. Chasman
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Andrew T. Chan
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital Boston, MA,Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
| | - Andrew D. Johnson
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA,Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Framingham, MA,To whom correspondence should be addressed: Amit D. Joshi, MBBS, PhD, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, Massachusetts 02114, USA. Tel: +1 617 724 7558; Charlotte Andersson, MD, PhD, The Framingham Heart Study, 73 Mt Wayte Avenue, Framingham, Massachusetts 01702, USA. , Andrew T. Chan, MD, MPH, Massachusetts General Hospital and Harvard Medical School, Clinical and Translational Epidemiology Unit, Division of Gastroenterology, GRJ-825C, Boston, Massachusetts 02114, USA. Tel:+1 617 724 0283; Fax: +1 617 726 3673; , Andrew D. Johnson, PhD, Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, 01702, USA. Tel: +1 508 663 4082; Fax: +1 508 626 1262;
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Richard AC, Peters JE, Lee JC, Vahedi G, Schäffer AA, Siegel RM, Lyons PA, Smith KGC. Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network. Genome Med 2016; 8:76. [PMID: 27435189 PMCID: PMC4952362 DOI: 10.1186/s13073-016-0329-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/21/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Tumour necrosis factor (TNF) superfamily cytokines and their receptors regulate diverse immune system functions through a common set of signalling pathways. Genetic variants in and expression of individual TNF superfamily cytokines, receptors and signalling proteins have been associated with autoimmune and inflammatory diseases, but their interconnected biology has been largely unexplored. METHODS We took a hypothesis-driven approach using available genome-wide datasets to identify genetic variants regulating gene expression in the TNF superfamily cytokine signalling network and the association of these variants with autoimmune and autoinflammatory disease. Using paired gene expression and genetic data, we identified genetic variants associated with gene expression, expression quantitative trait loci (eQTLs), in four peripheral blood cell subsets. We then examined whether eQTLs were dependent on gene expression level or the presence of active enhancer chromatin marks. Using these eQTLs as genetic markers of the TNF superfamily signalling network, we performed targeted gene set association analysis in eight autoimmune and autoinflammatory disease genome-wide association studies. RESULTS Comparison of TNF superfamily network gene expression and regulatory variants across four leucocyte subsets revealed patterns that differed between cell types. eQTLs for genes in this network were not dependent on absolute gene expression levels and were not enriched for chromatin marks of active enhancers. By examining autoimmune disease risk variants among our eQTLs, we found that risk alleles can be associated with either increased or decreased expression of co-stimulatory TNF superfamily cytokines, receptors or downstream signalling molecules. Gene set disease association analysis revealed that eQTLs for genes in the TNF superfamily pathway were associated with six of the eight autoimmune and autoinflammatory diseases examined, demonstrating associations beyond single genome-wide significant hits. CONCLUSIONS This systematic analysis of the influence of regulatory genetic variants in the TNF superfamily network reveals widespread and diverse roles for these cytokines in susceptibility to a number of immune-mediated diseases.
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Affiliation(s)
- Arianne C. Richard
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
- />Autoimmunity Branch, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - James E. Peters
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - James C. Lee
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Golnaz Vahedi
- />Department of Genetics, Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Alejandro A. Schäffer
- />Computational Biology Branch, National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894 USA
| | - Richard M. Siegel
- />Autoimmunity Branch, National Institute for Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892 USA
| | - Paul A. Lyons
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
| | - Kenneth G. C. Smith
- />Department of Medicine and Cambridge Institute for Medical Research, The University of Cambridge, Box 139, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY UK
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237
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Immunophenotyping of rheumatoid arthritis reveals a linkage between HLA-DRB1 genotype, CXCR4 expression on memory CD4(+) T cells, and disease activity. Sci Rep 2016; 6:29338. [PMID: 27385284 PMCID: PMC4935954 DOI: 10.1038/srep29338] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/16/2016] [Indexed: 12/15/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disease that leads to destructive arthritis. Although the HLA class II locus is the strongest genetic risk factor for rheumatoid arthritis, the relationship between HLA class II alleles and lymphocyte activation remains unclear. We performed immunophenotyping of peripheral blood mononuclear cells on 91 HLA-DRB1-genotyped RA patients and 110 healthy donors. The frequency of memory CXCR4+CD4+ T cells, and not Th1 and Th17 cells, was significantly associated with disease severity by multiple linear regression analysis. RA patients with one or more susceptible HLA-DR haplotypes (shared epitope: SE) displayed a significantly higher frequency of memory CXCR4+CD4+ T cells. Moreover, the frequency of memory CXCR4+CD4+ T cells significantly correlated with the expression level of HLA-DR on B cells, which was elevated in RA patients with SE. In vitro analysis and transcriptomic pathway analysis suggested that the interaction between HLA-DR and T cell receptors is an important regulator of memory CXCR4+CD4+ T cells. Clinically, a higher frequency of memory CXCR4+CD4+ T cells predicted a better response to CTLA4-Ig. Memory CXCR4+CD4+ T cells may serve as a powerful biomarker for unraveling the linkage between HLA-DRB1 genotype and disease activity in RA.
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238
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Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi. Nat Med 2016; 22:952-60. [PMID: 27376574 DOI: 10.1038/nm.4139] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 06/07/2016] [Indexed: 12/14/2022]
Abstract
Little is known about the inter-individual variation of cytokine responses to different pathogens in healthy individuals. To systematically describe cytokine responses elicited by distinct pathogens and to determine the effect of genetic variation on cytokine production, we profiled cytokines produced by peripheral blood mononuclear cells from 197 individuals of European origin from the 200 Functional Genomics (200FG) cohort in the Human Functional Genomics Project (http://www.humanfunctionalgenomics.org), obtained over three different years. We compared bacteria- and fungi-induced cytokine profiles and found that most cytokine responses were organized around a physiological response to specific pathogens, rather than around a particular immune pathway or cytokine. We then correlated genome-wide single-nucleotide polymorphism (SNP) genotypes with cytokine abundance and identified six cytokine quantitative trait loci (QTLs). Among them, a cytokine QTL at the NAA35-GOLM1 locus markedly modulated interleukin (IL)-6 production in response to multiple pathogens and was associated with susceptibility to candidemia. Furthermore, the cytokine QTLs that we identified were enriched among SNPs previously associated with infectious diseases and heart diseases. These data reveal and begin to explain the variability in cytokine production by human immune cells in response to pathogens.
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239
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Abstract
The genome is often the conduit through which environmental exposures convey their effects on health and disease. Whilst not all diseases act by directly perturbing the genome, the phenotypic responses are often genetically determined. Hence, whilst diseases are often defined has having differing degrees of genetic determination, genetic and environmental factors are, with few exceptions, inseparable features of most diseases, not least type 2 diabetes. It follows that to optimize diabetes, prevention and treatment will require that the etiological roles of genetic and environmental risk factors be jointly considered. As we discuss here, studies focused on quantifying gene-environment and gene-treatment interactions are gathering momentum and may eventually yield data that helps guide health-related choices and medical interventions for type 2 diabetes and other complex diseases.
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Affiliation(s)
- Paul W Franks
- Genetic and Molecular Epidemiology Unit, Lund University Diabetes Center, Department of Clinical Sciences, Clinical Research Center, Skåne University Hospital Malmö, Lund University, Building 91, Level 10, Jan Waldenströms gata 35, 205 02, Malmö, Sweden.
- Department of Public Health and Clinical Medicine, Umeå University, 90188, Umeå, Sweden.
- Department of Nutrition, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton General Hospital Campus, DB-CVSRI, 237 Barton Street East, Room C3103, Hamilton, ON, L8L 2X2, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Department of Clinical Epidemiology and Biostatistics, Population Genomics Program, McMaster University, Hamilton, ON, Canada
- Thrombosis and Atherosclerosis Research Institute, Hamilton Health Sciences and McMaster University, Hamilton, ON, Canada
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240
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Mostafavi S, Yoshida H, Moodley D, LeBoité H, Rothamel K, Raj T, Ye CJ, Chevrier N, Zhang SY, Feng T, Lee M, Casanova JL, Clark JD, Hegen M, Telliez JB, Hacohen N, De Jager PL, Regev A, Mathis D, Benoist C. Parsing the Interferon Transcriptional Network and Its Disease Associations. Cell 2016; 164:564-78. [PMID: 26824662 DOI: 10.1016/j.cell.2015.12.032] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/22/2015] [Accepted: 12/21/2015] [Indexed: 12/17/2022]
Abstract
Type 1 interferon (IFN) is a key mediator of organismal responses to pathogens, eliciting prototypical "interferon signature genes" that encode antiviral and inflammatory mediators. For a global view of IFN signatures and regulatory pathways, we performed gene expression and chromatin analyses of the IFN-induced response across a range of immunocyte lineages. These distinguished ISGs by cell-type specificity, kinetics, and sensitivity to tonic IFN and revealed underlying changes in chromatin configuration. We combined 1,398 human and mouse datasets to computationally infer ISG modules and their regulators, validated by genetic analysis in both species. Some ISGs are controlled by Stat1/2 and Irf9 and the ISRE DNA motif, but others appeared dependent on non-canonical factors. This regulatory framework helped to interpret JAK1 blockade pharmacology, different clusters being affected under tonic or IFN-stimulated conditions, and the IFN signatures previously associated with human diseases, revealing unrecognized subtleties in disease footprints, as affected by human ancestry.
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Affiliation(s)
- Sara Mostafavi
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Statistics and Department Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Hideyuki Yoshida
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Devapregasan Moodley
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hugo LeBoité
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine Rothamel
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Towfique Raj
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Translational NeuroPsychiatric Genomics, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Chun Jimmie Ye
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nicolas Chevrier
- FAS Center for Systems Biology, Harvard University, Cambridge, MA 02138, USA
| | - Shen-Ying Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | - Ting Feng
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Mark Lee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY 10065, USA
| | | | | | | | - Nir Hacohen
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Philip L De Jager
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Program in Translational NeuroPsychiatric Genomics, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.
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Accounting for reciprocal host–microbiome interactions in experimental science. Nature 2016; 534:191-9. [DOI: 10.1038/nature18285] [Citation(s) in RCA: 176] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 04/26/2016] [Indexed: 12/13/2022]
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Yarwood A, Eyre S, Worthington J. Genetic susceptibility to rheumatoid arthritis and its implications for novel drug discovery. Expert Opin Drug Discov 2016; 11:805-13. [PMID: 27267163 DOI: 10.1080/17460441.2016.1195366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Over 100 susceptibility loci have now been identified for rheumatoid arthritis (RA), several of which are already the targets of approved RA therapies providing proof of concept for the use of genetics in novel drug development for RA. Determining how these loci contribute to disease will be key to elucidating the mechanisms driving disease development, which has the potential for major impact on therapeutic development. AREAS COVERED Here the authors review the use of genetics in drug discovery, including the use of 'omics' data to prioritise potential drug targets at susceptibility loci using RA as an exemplar. They discuss the current state of RA genetics its impact on stratified medicine, and how the findings from RA genetics studies can be used to inform drug discovery. EXPERT OPINION It is anticipated that functional characterisation of disease variants will provide biological validation of a gene as a drug target, providing safer targets, with an increased likelihood of efficacy. In the future, techniques such as genome editing may represent a plausible option for RA therapy. Technologies such as genome-wide chromatin conformation capture Hi-C and CRISPR will be crucial to inform our understanding of how diseases develop and in developing new treatments.
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Affiliation(s)
- Annie Yarwood
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre , The University of Manchester , Manchester , UK
| | - Steve Eyre
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre , The University of Manchester , Manchester , UK
| | - Jane Worthington
- a Arthritis Research UK Centre for Genetics and Genomics, Centre for Musculoskeletal Research, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre , The University of Manchester , Manchester , UK.,b NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust , Manchester Academic Health Science Centre , Manchester , UK
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243
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Li Q, Lee CH, Peters LA, Mastropaolo LA, Thoeni C, Elkadri A, Schwerd T, Zhu J, Zhang B, Zhao Y, Hao K, Dinarzo A, Hoffman G, Kidd BA, Murchie R, Adham ZA, Guo C, Kotlarz D, Cutz E, Walters TD, Shouval DS, Curran M, Dobrin R, Brodmerkel C, Snapper SB, Klein C, Brumell JH, Hu M, Nanan R, Snanter-Nanan B, Wong M, Le Deist F, Haddad E, Roifman CM, Deslandres C, Griffiths AM, Gaskin KJ, Uhlig HH, Schadt EE, Muise AM. Variants in TRIM22 That Affect NOD2 Signaling Are Associated With Very-Early-Onset Inflammatory Bowel Disease. Gastroenterology 2016; 150:1196-1207. [PMID: 26836588 PMCID: PMC4842103 DOI: 10.1053/j.gastro.2016.01.031] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 01/22/2016] [Accepted: 01/22/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Severe forms of inflammatory bowel disease (IBD) that develop in very young children can be caused by variants in a single gene. We performed whole-exome sequence (WES) analysis to identify genetic factors that might cause granulomatous colitis and severe perianal disease, with recurrent bacterial and viral infections, in an infant of consanguineous parents. METHODS We performed targeted WES analysis of DNA collected from the patient and her parents. We validated our findings by a similar analysis of DNA from 150 patients with very-early-onset IBD not associated with known genetic factors analyzed in Toronto, Oxford, and Munich. We compared gene expression signatures in inflamed vs noninflamed intestinal and rectal tissues collected from patients with treatment-resistant Crohn's disease who participated in a trial of ustekinumab. We performed functional studies of identified variants in primary cells from patients and cell culture. RESULTS We identified a homozygous variant in the tripartite motif containing 22 gene (TRIM22) of the patient, as well as in 2 patients with a disease similar phenotype. Functional studies showed that the variant disrupted the ability of TRIM22 to regulate nucleotide binding oligomerization domain containing 2 (NOD2)-dependent activation of interferon-beta signaling and nuclear factor-κB. Computational studies demonstrated a correlation between the TRIM22-NOD2 network and signaling pathways and genetic factors associated very early onset and adult-onset IBD. TRIM22 is also associated with antiviral and mycobacterial effectors and markers of inflammation, such as fecal calprotectin, C-reactive protein, and Crohn's disease activity index scores. CONCLUSIONS In WES and targeted exome sequence analyses of an infant with severe IBD characterized by granulomatous colitis and severe perianal disease, we identified a homozygous variant of TRIM22 that affects the ability of its product to regulate NOD2. Combined computational and functional studies showed that the TRIM22-NOD2 network regulates antiviral and antibacterial signaling pathways that contribute to inflammation. Further study of this network could lead to new disease markers and therapeutic targets for patients with very early and adult-onset IBD.
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Affiliation(s)
- Qi Li
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Cheng Hiang Lee
- Gastroenterology Department, The Children's Hospital at Westmead, Westmead, 2145, New South Wales, Australia,The James Fairfax Institute of Paediatric Nutrition, the University of Sydney, New South Wales, Australia
| | - Lauren A Peters
- Icahn School of Medicine at Mount Sinai, New York, New York, USA. Graduate School of Biomedical Sciences, New York, New York, USA,Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Lucas A Mastropaolo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Cornelia Thoeni
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Abdul Elkadri
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Tobias Schwerd
- Translational Gastroenterology Unit, Nuffield Department Clinical Medicine, Experimental Medicine Division, University of Oxford, and Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Jun Zhu
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Bin Zhang
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Yongzhong Zhao
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Ke Hao
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Antonio Dinarzo
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Gabriel Hoffman
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Brian A Kidd
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Ryan Murchie
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Ziad Al Adham
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada,Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Conghui Guo
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Ernest Cutz
- Division of Pathology, The Hospital for Sick Children, Toronto, Canada
| | - Thomas D Walters
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Dror S Shouval
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, USA
| | - Mark Curran
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA 19477
| | - Radu Dobrin
- Janssen R&D, LLC, 1400 McKean Road, Spring House, PA 19477
| | | | - Scott B Snapper
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Boston Children's Hospital, Harvard Medical School, Boston, USA,Division of Gastroenterology and Hepatology, Brigham & Women's Hospital, Department of Medicine, Boston, USA
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - John H Brumell
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Institute of Medical Science, University of Toronto, Toronto, ON, Canada,Molecular Genetics, University of Toronto
| | - Mingjing Hu
- Gastroenterology Department, The Children's Hospital at Westmead, Westmead, 2145, New South Wales, Australia,The James Fairfax Institute of Paediatric Nutrition, the University of Sydney, New South Wales, Australia
| | - Ralph Nanan
- Gastroenterology Department, The Children's Hospital at Westmead, Westmead, 2145, New South Wales, Australia,The James Fairfax Institute of Paediatric Nutrition, the University of Sydney, New South Wales, Australia
| | - Brigitte Snanter-Nanan
- Gastroenterology Department, The Children's Hospital at Westmead, Westmead, 2145, New South Wales, Australia,The James Fairfax Institute of Paediatric Nutrition, the University of Sydney, New South Wales, Australia
| | - Melanie Wong
- Immunology Department, The Children's Hospital at Westmead, Westmead, 2145, New South Wales, Australia
| | - Francoise Le Deist
- Department of Microbiology and Immunology, CHU Sainte Justine and Department of Microbiology, Infectiology and Immunology, University of Montreal, QC, Canada
| | - Elie Haddad
- CHU Sainte-Justine, Department of Pediatrics, Department of Microbiology, Infectiology and Immunology, University of Montreal, QC, Canada
| | - Chaim M Roifman
- Division of Immunology, Department of Pediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Canada
| | - Colette Deslandres
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, CHU Sainte-Justine, Montreal, QC, Canada
| | - Anne M Griffiths
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
| | - Kevin J Gaskin
- Gastroenterology Department, The Children's Hospital at Westmead, Westmead, 2145, New South Wales, Australia,The James Fairfax Institute of Paediatric Nutrition, the University of Sydney, New South Wales, Australia
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department Clinical Medicine, Experimental Medicine Division, University of Oxford, and Department of Pediatrics, John Radcliffe Hospital, Oxford, UK
| | - Eric E Schadt
- Icahn School of Medicine at Mount Sinai, Department of Genetics and Genomic Sciences and the Icahn Institute for Genomics and Multiscale Biology, New York, NY 10029
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada; Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.
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244
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Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. NPJ Genom Med 2016; 1. [PMID: 27482468 PMCID: PMC4966659 DOI: 10.1038/npjgenmed.2016.6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Functionally altered biological mechanisms arising from disease-associated polymorphisms, remain difficult to characterise when those variants are intergenic, or, fall between genes. We sought to identify shared downstream mechanisms by which inter- and intragenic single-nucleotide polymorphisms (SNPs) contribute to a specific physiopathology. Using computational modelling of 2 million pairs of disease-associated SNPs drawn from genome-wide association studies (GWAS), integrated with expression Quantitative Trait Loci (eQTL) and Gene Ontology functional annotations, we predicted 3,870 inter–intra and inter–intra SNP pairs with convergent biological mechanisms (FDR<0.05). These prioritised SNP pairs with overlapping messenger RNA targets or similar functional annotations were more likely to be associated with the same disease than unrelated pathologies (OR>12). We additionally confirmed synergistic and antagonistic genetic interactions for a subset of prioritised SNP pairs in independent studies of Alzheimer’s disease (entropy P=0.046), bladder cancer (entropy P=0.039), and rheumatoid arthritis (PheWAS case–control P<10−4). Using ENCODE data sets, we further statistically validated that the biological mechanisms shared within prioritised SNP pairs are frequently governed by matching transcription factor binding sites and long-range chromatin interactions. These results provide a ‘roadmap’ of disease mechanisms emerging from GWAS and further identify candidate therapeutic targets among downstream effectors of intergenic SNPs.
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245
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Insight into Genotype-Phenotype Associations through eQTL Mapping in Multiple Cell Types in Health and Immune-Mediated Disease. PLoS Genet 2016; 12:e1005908. [PMID: 27015630 PMCID: PMC4807835 DOI: 10.1371/journal.pgen.1005908] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
Genome-wide association studies (GWAS) have transformed our understanding of the genetics of complex traits such as autoimmune diseases, but how risk variants contribute to pathogenesis remains largely unknown. Identifying genetic variants that affect gene expression (expression quantitative trait loci, or eQTLs) is crucial to addressing this. eQTLs vary between tissues and following in vitro cellular activation, but have not been examined in the context of human inflammatory diseases. We performed eQTL mapping in five primary immune cell types from patients with active inflammatory bowel disease (n = 91), anti-neutrophil cytoplasmic antibody-associated vasculitis (n = 46) and healthy controls (n = 43), revealing eQTLs present only in the context of active inflammatory disease. Moreover, we show that following treatment a proportion of these eQTLs disappear. Through joint analysis of expression data from multiple cell types, we reveal that previous estimates of eQTL immune cell-type specificity are likely to have been exaggerated. Finally, by analysing gene expression data from multiple cell types, we find eQTLs not previously identified by database mining at 34 inflammatory bowel disease-associated loci. In summary, this parallel eQTL analysis in multiple leucocyte subsets from patients with active disease provides new insights into the genetic basis of immune-mediated diseases. The human immune system has evolved to protect us from infection and cancer, whilst avoiding damage to healthy tissue. If this complex system goes wrong, immune cells may cause inappropriate inflammation and damage, resulting in clinical disease. Examples include inflammatory bowel disease and autoimmune vasculitis, characterised by inflammation in the gut and blood vessels respectively. Genetic studies have identified many variants in our DNA code that predispose to such immune-mediated diseases. The majority of these variants lie outside protein-coding regions, and so how they influence disease risk remains largely unclear. Examining how genetic variants affect gene expression can help bridge this gap in our knowledge, but these effects are highly dependent on the cellular or environmental context such as tissue type or cellular activation status. We investigated the genetic control of gene expression in five white blood cell subtypes taken from patients with active inflammatory bowel disease and autoimmune vasculitis, and from healthy controls. We report the novel observation of distinct variants that only affect gene expression in patients with active inflammatory disease, and show that these effects can disappear following treatment. These findings provide new insights into the genetic basis of important immune-mediated diseases.
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246
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Cistromic and genetic evidence that the vitamin D receptor mediates susceptibility to latitude-dependent autoimmune diseases. Genes Immun 2016; 17:213-9. [PMID: 26986782 PMCID: PMC4895389 DOI: 10.1038/gene.2016.12] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 02/06/2023]
Abstract
The vitamin D receptor (VDR) is a ligand-activated transcription factor that regulates gene expression in many cell types, including immune cells. It requires binding of 1,25 dihydroxy vitamin D3 (1,25D3) for activation. Many autoimmune diseases show latitude-dependent prevalence and/or association with vitamin D deficiency, and vitamin D supplementation is commonly used in their clinical management. 1,25D3 is regulated by genes associated with the risk of autoimmune diseases and predominantly expressed in myeloid cells. We determined the VDR cistrome in monocytes and monocyte-derived inflammatory (DC1) and tolerogenic dendritic cells (DC2). VDR motifs were highly overrepresented in ChIP-Seq peaks in stimulated monocyte (40%), DC1 (21%) and DC2 (47%), P<E(-100) for all. Of the nearly 11 000 VDR-binding peaks identified across the genome in DC1s, 1317 were shared with DC2s (91% of DC2 sites) and 1579 with monocytes (83% of monocyte sites). Latitude-dependent autoimmune disease risk polymorphisms were highly overrepresented within 5 kb of the peaks. Several transcription factor recognition motifs were highly overrepresented in the peaks, including those for the autoimmune risk gene, BATF. This evidence indicates that VDR regulates hundreds of myeloid cell genes and that the molecular pathways controlled by VDR in these cells are important in maintaining tolerance.
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247
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Withoff S, Li Y, Jonkers I, Wijmenga C. Understanding Celiac Disease by Genomics. Trends Genet 2016; 32:295-308. [PMID: 26972670 DOI: 10.1016/j.tig.2016.02.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 02/06/2023]
Abstract
Celiac disease (CeD) is a complex immune-mediated disease. Genetic studies have implicated 43 predisposing loci that collectively explain some 50% of the genetic variance in CeD. More than ∼90% of CeD-associated single nucleotide polymorphisms (SNPs) localize to the non-coding genome, which we need to better understand to translate genetic knowledge into clinical practice. New genomic technologies and resources are permitting a systematic analysis of the functional elements in the non-coding part of the genome. Here we explain how investigating the regulatory and epigenomic landscape will help to pinpoint the cell types involved in CeD, and the driver genes and gene regulatory networks that are affected by CeD-associated SNPs.
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Affiliation(s)
- Sebo Withoff
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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248
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Gutierrez-Arcelus M, Rich SS, Raychaudhuri S. Autoimmune diseases - connecting risk alleles with molecular traits of the immune system. Nat Rev Genet 2016; 17:160-74. [PMID: 26907721 PMCID: PMC4896831 DOI: 10.1038/nrg.2015.33] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide strategies have driven the discovery of more than 300 susceptibility loci for autoimmune diseases. However, for almost all loci, understanding of the mechanisms leading to autoimmunity remains limited, and most variants that are likely to be causal are in non-coding regions of the genome. A critical next step will be to identify the in vivo and ex vivo immunophenotypes that are affected by risk variants. To do this, key cell types and cell states that are implicated in autoimmune diseases will need to be defined. Functional genomic annotations from these cell types and states can then be used to resolve candidate genes and causal variants. Together with longitudinal studies, this approach may yield pivotal insights into how autoimmunity is triggered.
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Affiliation(s)
- Maria Gutierrez-Arcelus
- Division of Genetics, and Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Soumya Raychaudhuri
- Division of Genetics, and Division of Rheumatology, Immunology and Allergy, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts 02142, USA
- Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02115, USA
- Faculty of Medical and Human Sciences, University of Manchester, Manchester M13 9PL, UK
- Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm SE-171 77, Sweden
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249
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Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, Decara JM, Gilad Y, Ober C. Integrated analyses of gene expression and genetic association studies in a founder population. Hum Mol Genet 2016; 25:2104-2112. [PMID: 26931462 PMCID: PMC5062579 DOI: 10.1093/hmg/ddw061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 02/21/2016] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWASs) have become a standard tool for dissecting genetic contributions to disease risk. However, these studies typically require extraordinarily large sample sizes to be adequately powered. Strategies that incorporate functional information alongside genetic associations have proved successful in increasing GWAS power. Following this paradigm, we present the results of 20 different genetic association studies for quantitative traits related to complex diseases, conducted in the Hutterites of South Dakota. To boost the power of these association studies, we collected RNA-sequencing data from lymphoblastoid cell lines for 431 Hutterite individuals. We then used Sherlock, a tool that integrates GWAS and expression quantitative trait locus (eQTL) data, to identify weak GWAS signals that are also supported by eQTL data. Using this approach, we found novel associations with quantitative phenotypes related to cardiovascular disease, including carotid intima-media thickness, left atrial volume index, monocyte count and serum YKL-40 levels.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jack A Elias
- Division of Biology and Medicine, Brown University, Providence, RI 02912, USA and
| | - Geoffrey L Chupp
- Pulmonary and Critical Care, Yale School of Medicine, New Haven, CT 06519, USA
| | - Roberto M Lang
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
| | - Sanjiv J Shah
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
| | - Jeanne M Decara
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
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250
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Wang N, Gosik K, Li R, Lindsay B, Wu R. A block mixture model to map eQTLs for gene clustering and networking. Sci Rep 2016; 6:21193. [PMID: 26892775 PMCID: PMC4759821 DOI: 10.1038/srep21193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 01/19/2016] [Indexed: 01/13/2023] Open
Abstract
To study how genes function in a cellular and physiological process, a general procedure is to classify gene expression profiles into categories based on their similarity and reconstruct a regulatory network for functional elements. However, this procedure has not been implemented with the genetic mechanisms that underlie the organization of gene clusters and networks, despite much effort made to map expression quantitative trait loci (eQTLs) that affect the expression of individual genes. Here we address this issue by developing a computational approach that integrates gene clustering and network reconstruction with genetic mapping into a unifying framework. The approach can not only identify specific eQTLs that control how genes are clustered and organized toward biological functions, but also enable the investigation of the biological mechanisms that individual eQTLs perturb in a signaling pathway. We applied the new approach to characterize the effects of eQTLs on the structure and organization of gene clusters in Caenorhabditis elegans. This study provides the first characterization, to our knowledge, of the effects of genetic variants on the regulatory network of gene expression. The approach developed can also facilitate the genetic dissection of other dynamic processes, including development, physiology and disease progression in any organisms.
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Affiliation(s)
- Ningtao Wang
- Department of Biostatistics, University of Texas School of Public Health, Houston, TX 77030, USA.,Department of Public Health Sciences, The Pennsylvania State University, Hershey, PA 17033, USA
| | - Kirk Gosik
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Runze Li
- Department of Biostatistics, University of Texas School of Public Health, Houston, TX 77030, USA.,Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Bruce Lindsay
- Department of Biostatistics, University of Texas School of Public Health, Houston, TX 77030, USA
| | - Rongling Wu
- Department of Biostatistics, University of Texas School of Public Health, Houston, TX 77030, USA.,Department of Statistics, The Pennsylvania State University, University Park, PA 16802, USA
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