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Moustafa A, Li W, Anderson EL, Wong EHM, Dulai PS, Sandborn WJ, Biggs W, Yooseph S, Jones MB, Venter JC, Nelson KE, Chang JT, Telenti A, Boland BS. Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease. Clin Transl Gastroenterol 2018; 9:e132. [PMID: 29345635 PMCID: PMC5795019 DOI: 10.1038/ctg.2017.58] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 12/15/2017] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals. Genetic risk scores, computed on 159 single nucleotide variants, and human leukocyte antigen (HLA) types differentiated IBD patients from healthy controls. RESULTS Genetic risk was associated with the need for use of biologics in IBD and, modestly, with the composition of the gut microbiome. As compared with healthy controls, IBD patients had hallmarks of stool microbiome dysbiosis, with loss of a diversified core microbiome, enrichment and depletion of specific bacteria, and enrichment of bacterial virulence factors. CONCLUSIONS We show that genetic risk may have a role in early risk stratification in the care of IBD patients and propose that expression of virulence factors in a dysbiotic microbiome may contribute to pathogenesis in IBD.
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Affiliation(s)
| | - Weizhong Li
- Human Longevity Inc., San Diego, CA, USA
- J. Craig Venter Institute, La Jolla, CA, USA
| | | | | | - Parambir S Dulai
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | - William J Sandborn
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | | | | | | | - J Craig Venter
- Human Longevity Inc., San Diego, CA, USA
- J. Craig Venter Institute, La Jolla, CA, USA
| | | | - John T Chang
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
| | | | - Brigid S Boland
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
- Inflammatory Bowel Disease Center, University of California San Diego, La Jolla, CA, USA
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Hui KY, Fernandez-Hernandez H, Hu J, Schaffner A, Pankratz N, Hsu NY, Chuang LS, Carmi S, Villaverde N, Li X, Rivas M, Levine AP, Bao X, Labrias PR, Haritunians T, Ruane D, Gettler K, Chen E, Li D, Schiff ER, Pontikos N, Barzilai N, Brant SR, Bressman S, Cheifetz AS, Clark LN, Daly MJ, Desnick RJ, Duerr RH, Katz S, Lencz T, Myers RH, Ostrer H, Ozelius L, Payami H, Peter Y, Rioux JD, Segal AW, Scott WK, Silverberg MS, Vance JM, Ubarretxena-Belandia I, Foroud T, Atzmon G, Pe'er I, Ioannou Y, McGovern DPB, Yue Z, Schadt EE, Cho JH, Peter I. Functional variants in the LRRK2 gene confer shared effects on risk for Crohn's disease and Parkinson's disease. Sci Transl Med 2018; 10:eaai7795. [PMID: 29321258 PMCID: PMC6028002 DOI: 10.1126/scitranslmed.aai7795] [Citation(s) in RCA: 237] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/31/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022]
Abstract
Crohn's disease (CD), a form of inflammatory bowel disease, has a higher prevalence in Ashkenazi Jewish than in non-Jewish European populations. To define the role of nonsynonymous mutations, we performed exome sequencing of Ashkenazi Jewish patients with CD, followed by array-based genotyping and association analysis in 2066 CD cases and 3633 healthy controls. We detected association signals in the LRRK2 gene that conferred risk for CD (N2081D variant, P = 9.5 × 10-10) or protection from CD (N551K variant, tagging R1398H-associated haplotype, P = 3.3 × 10-8). These variants affected CD age of onset, disease location, LRRK2 activity, and autophagy. Bayesian network analysis of CD patient intestinal tissue further implicated LRRK2 in CD pathogenesis. Analysis of the extended LRRK2 locus in 24,570 CD cases, patients with Parkinson's disease (PD), and healthy controls revealed extensive pleiotropy, with shared genetic effects between CD and PD in both Ashkenazi Jewish and non-Jewish cohorts. The LRRK2 N2081D CD risk allele is located in the same kinase domain as G2019S, a mutation that is the major genetic cause of familial and sporadic PD. Like the G2019S mutation, the N2081D variant was associated with increased kinase activity, whereas neither N551K nor R1398H variants on the protective haplotype altered kinase activity. We also confirmed that R1398H, but not N551K, increased guanosine triphosphate binding and hydrolyzing enzyme (GTPase) activity, thereby deactivating LRRK2. The presence of shared LRRK2 alleles in CD and PD provides refined insight into disease mechanisms and may have major implications for the treatment of these two seemingly unrelated diseases.
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Affiliation(s)
- Ken Y Hui
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA
| | | | - Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Adam Schaffner
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shai Carmi
- Braun School of Public Health and Community Medicine, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 9112102, Israel
| | - Nicole Villaverde
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xianting Li
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Manual Rivas
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Adam P Levine
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Xiuliang Bao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Philippe R Labrias
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Talin Haritunians
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Darren Ruane
- Department of Immunology and Inflammation, Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Kyle Gettler
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics, Yale University, New Haven, CT 06520, USA
| | - Ernie Chen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dalin Li
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Elena R Schiff
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nikolas Pontikos
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - Nir Barzilai
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven R Brant
- Harvey M. and Lyn P. Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Susan Bressman
- Alan and Barbara Mirken Department of Neurology, Beth Israel Medical Center, New York, NY 10003, USA
| | - Adam S Cheifetz
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA
| | - Lorraine N Clark
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark J Daly
- Department of Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Taub Institute for Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Robert J Desnick
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15261, USA
| | - Seymour Katz
- New York University School of Medicine, New York City, NY 10016, USA
- North Shore University-Long Island Jewish Medical Center, Manhasset, NY, USA
- St. Francis Hospital, Roslyn, NY 11576, USA
| | - Todd Lencz
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY 11030, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA 02114, USA
| | - Harry Ostrer
- Departments of Pathology and Pediatrics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Laurie Ozelius
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Deparment of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Haydeh Payami
- Departments of Neurology and Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35805, USA
| | - Yakov Peter
- Department of Biology, Touro College, Queens, NY 10033, USA
- Department of Pulmonary Medicine, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10033, USA
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, Quebec H1T1C8, Canada
- Faculté de Médecine, Université de Montréal, Montreal, Quebec H1T1C8, Canada
| | - Anthony W Segal
- Centre for Molecular Medicine, Division of Medicine, University College, London WC1E 6JF, UK
| | - William K Scott
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Mark S Silverberg
- Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, Toronto, Ontario M5T3L9, USA
- Department of Medicine, University of Toronto, Toronto, Ontario M5G1X5, Canada
| | - Jeffery M Vance
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Gil Atzmon
- Departments of Genetics and Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Faculty of Natural Sciences, University of Haifa, Haifa 3498838, Israel
| | - Itsik Pe'er
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
| | - Yiannis Ioannou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dermot P B McGovern
- Translational Genomics Group, F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Zhenyu Yue
- Departments of Neurology and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Sema4, a Mount Sinai venture, Stamford, CT 06902, USA
| | - Judy H Cho
- Section of Digestive Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics, Yale University, New Haven, CT 06520, USA
- Section of Gastroenterology and Hepatology, Department of Pediatrics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
- Institute for Genetics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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Abstract
The MHC/HLA region has been consistently associated with a large number of complex traits, including but not limited to, most immune-mediated ones. Efforts to pinpoint drivers of this commonly encountered association peak at the short arm of chromosome 6, however, have been challenging, owing to the high density of genes and the long and extended linkage disequilibrium that are characteristic of this region.The development of methods to impute classical HLA alleles and amino acids from SNP genotyping data has offered an important additional layer of information to the investigators seeking to fine map the signal in the region. As a result, imputation-aided association analyses are now typically employed to shed light on the relationship of this locus with disease susceptibility and response to drugs.In this chapter we discuss how the signal in the HLA region can be interrogated in practice, from performing the imputation to understanding its output and to incorporating it into downstream analysis. In addition, we recount some of the analytical approaches that are commonly used and suggest ways in which the findings from such imputation-aided analyses can be interpreted.
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154
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Imhann F, Vila AV, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut 2018; 67:108-119. [PMID: 27802154 PMCID: PMC5699972 DOI: 10.1136/gutjnl-2016-312135] [Citation(s) in RCA: 487] [Impact Index Per Article: 81.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Revised: 08/15/2016] [Accepted: 09/14/2016] [Indexed: 02/02/2023]
Abstract
OBJECTIVE Patients with IBD display substantial heterogeneity in clinical characteristics. We hypothesise that individual differences in the complex interaction of the host genome and the gut microbiota can explain the onset and the heterogeneous presentation of IBD. Therefore, we performed a case-control analysis of the gut microbiota, the host genome and the clinical phenotypes of IBD. DESIGN Stool samples, peripheral blood and extensive phenotype data were collected from 313 patients with IBD and 582 truly healthy controls, selected from a population cohort. The gut microbiota composition was assessed by tag-sequencing the 16S rRNA gene. All participants were genotyped. We composed genetic risk scores from 11 functional genetic variants proven to be associated with IBD in genes that are directly involved in the bacterial handling in the gut: NOD2, CARD9, ATG16L1, IRGM and FUT2. RESULTS Strikingly, we observed significant alterations of the gut microbiota of healthy individuals with a high genetic risk for IBD: the IBD genetic risk score was significantly associated with a decrease in the genus Roseburia in healthy controls (false discovery rate 0.017). Moreover, disease location was a major determinant of the gut microbiota: the gut microbiota of patients with colonic Crohn's disease (CD) is different from that of patients with ileal CD, with a decrease in alpha diversity associated to ileal disease (p=3.28×10-13). CONCLUSIONS We show for the first time that genetic risk variants associated with IBD influence the gut microbiota in healthy individuals. Roseburia spp are acetate-to-butyrate converters, and a decrease has already been observed in patients with IBD.
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Affiliation(s)
- Floris Imhann
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Arnau Vich Vila
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Marc Jan Bonder
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Pediatrics, Groningen, the Netherlands
| | - Dirk Gevers
- Broad Institute of Harvard and MIT, Boston, USA
| | - Marijn C. Visschedijk
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lieke M. Spekhorst
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rudi Alberts
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Hendrik M. van Dullemen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Rinze W.F. Ter Steege
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Curtis Huttenhower
- Broad Institute of Harvard and MIT, Boston, USA,Biostatistics Department, Harvard School of Public Health, Boston, USA
| | - Gerard Dijkstra
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
| | - Ramnik J. Xavier
- Broad Institute of Harvard and MIT, Boston, USA,Massachusetts General Hospital, Boston, USA
| | - Eleonora A.M. Festen
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands,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
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands
| | - Rinse K. Weersma
- University of Groningen, University Medical Center Groningen, Department of Gastroenterology and Hepatology, Groningen, the Netherlands
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155
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Zhang Y, Tian L, Sleiman P, Ghosh S, Hakonarson H. Bayesian analysis of genome-wide inflammatory bowel disease data sets reveals new risk loci. Eur J Hum Genet 2017; 26:265-274. [PMID: 29203833 DOI: 10.1038/s41431-017-0041-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 10/17/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified and validated 200 risk loci for inflammatory bowel disease (IBD) to date, including risk loci for both Crohn's disease and ulcerative colitis. Previously studies mainly used single SNP testing methods and only reported the most significant association within each locus. Advanced methods are needed to detect additional joint effects of multiple SNPs and fine map causal variants in presence of strong linkage disequilibrium. In this study, we applied a powerful Bayesian method to analyze an existing Immunochip data sets for IBD from the international inflammatory bowel disease genetics consortium. The method jointly tested single and set-based SNPs in a unified framework and filtered indirect associations due to linkage disequilibrium, thereby fine-mapping the most likely IBD variants. Using an independent collection of individuals from 11 IBD GWAS as validation, our approach discovered and validated 9 completely new IBD loci and 5 independent signals (excluding the major histocompatibility complex) near known IBD loci reaching genome-wide significance. Several of the replicated new loci implicated functionally more interpretable genes than previous reports. The epigenetic marks at our detected IBD signals demonstrated significant activation signatures in blood cell types and correspondingly substantial repression in stem cells, suggesting regulatory links between genetic variants and IBD. Our analysis of the currently largest IBD datasets therefore added new insights that will be integral to the ongoing efforts in IBD genetics.
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Affiliation(s)
- Yu Zhang
- Department of Statistics, The Pennsylvania State University, University Park, 16802, USA.
| | - Lifeng Tian
- Bioinformatics Scientist, Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Patrick Sleiman
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Soumitra Ghosh
- Target Sciences, GlaxoSmithKline, King of Prussia, PA, 19406, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Center for Applied Genomics, Devision of Human Genetics, The Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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156
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Harkey MA, Villagran AM, Venkataraman GM, Leisenring WM, Hullar MAJ, Torok-Storb BJ. Associations between gastric dilatation-volvulus in Great Danes and specific alleles of the canine immune-system genes DLA88, DRB1, and TLR5. Am J Vet Res 2017; 78:934-945. [PMID: 28738011 DOI: 10.2460/ajvr.78.8.934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether specific alleles of candidate genes of the major histocompatibility complex (MHC) and innate immune system were associated with gastric dilatation-volvulus (GDV) in Great Danes. ANIMALS 42 healthy Great Danes (control group) and 39 Great Danes with ≥ 1 GDV episode. PROCEDURES Variable regions of the 2 most polymorphic MHC genes (DLA88 and DRB1) were amplified and sequenced from the dogs in each group. Similarly, regions of 3 genes associated with the innate immune system (TLR5, NOD2, and ATG16L1), which have been linked to inflammatory bowel disease, were amplified and sequenced. Alleles were evaluated for associations with GDV, controlling for age and dog family. RESULTS Specific alleles of genes DLA88, DRB1, and TLR5 were significantly associated with GDV. One allele of each gene had an OR > 2 in the unadjusted univariate analyses and retained a hazard ratio > 2 after controlling for temperament, age, and familial association in the multivariate analysis. CONCLUSIONS AND CLINICAL RELEVANCE The 3 GDV-associated alleles identified in this study may serve as diagnostic markers for identification of Great Danes at risk for GDV. Additional research is needed to determine whether other dog breeds have the same genetic associations. These findings also provided a new target for research into the etiology of, and potential treatments for, GDV in dogs.
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157
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Abstract
PURPOSE OF REVIEW To review the advances in our understanding of the genetics of inclusion body myositis (IBM) in the past year. RECENT FINDINGS One large genetic association study focusing on immune-related genes in IBM has refined the association within the human leukocyte antigen (HLA) region to HLA-DRB1 alleles, and identified certain amino acid positions in HLA-DRB1 that may explain this risk. A suggestive association with CCR5 may indicate genetic overlap with other autoimmune diseases. Sequencing studies of candidate genes involved in related neuromuscular or neurodegenerative diseases have identified rare variants in VCP and SQSTM1. Proteomic studies of rimmed vacuoles in IBM and subsequent genetic analyses of candidate genes identified rare missense variants in FYCO1. Complex, large-scale mitochondrial deletions in cytochrome c oxidase-deficient muscle fibres expand our understanding of mitochondrial abnormalities in IBM. SUMMARY The pathogenesis of IBM is likely multifactorial, including inflammatory and degenerative changes, and mitochondrial abnormalities. There has been considerable progress in our understanding of the genetic architecture of IBM, using complementary genetic approaches to investigate these different pathways.
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Affiliation(s)
- Simon Rothwell
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester
| | - James B. Lilleker
- Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester
- Greater Manchester Neurosciences Centre, Manchester Academic Health Science Centre, Salford Royal NHS Foundation Trust, Stott Lane, Salford
| | - Janine A. Lamb
- Centre for Epidemiology, Division of Population Health, Health Services Research and Primary Care, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
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158
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Haber R, El Gemayel M. Comorbidities in rosacea: A systematic review and update. J Am Acad Dermatol 2017; 78:786-792.e8. [PMID: 29107339 DOI: 10.1016/j.jaad.2017.09.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 08/23/2017] [Accepted: 09/04/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Rosacea is linked to abnormalities of cutaneous vasculature and dysregulation of the inflammatory response. Recent reports on rosacea have shown a significant association with cardiovascular, gastrointestinal, and psychiatric diseases, all of which may affect morbidity and mortality among these patients. OBJECTIVE To review available data regarding comorbidities associated with rosacea, discuss their pathogenesis, and highlight the evaluation of affected patients. METHODS We performed a complete and systematic literature review in PubMed/Medline, Embase, and the Cochrane Collaboration databases, searching for all articles on possible associated diseases that have been reported with rosacea, with no limits on publication date, participant age, sex, or nationality. RESULTS A total of 29 studies were included in this systematic review, including 14 case-control, 8 cross-sectional, and 7 cohort studies. Statistically significant association with rosacea has been mostly demonstrated with depression (n = 117,848 patients), hypertension (n = 18,176), cardiovascular diseases (n = 9739), anxiety disorder (n = 9079), dyslipidemia (n = 7004), diabetes mellitus (n = 6306), migraine (n = 6136), rheumatoid arthritis (n = 4192), Helicobacter pylori infection (n = 1722), ulcerative colitis (n = 1424), and dementia (n = 1194). LIMITATIONS Limitations included the accuracy of the published data, potential patient selection, and possible confounding factors. The true nature of the drawn correlations is uncertain, and causality cannot be established. CONCLUSIONS Rosacea is associated with a number of systemic disorders. Recognition of these conditions is critical to providing appropriate screening and management of affected patients.
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Affiliation(s)
- Roger Haber
- Department of Dermatology, Saint George Hospital University Medical Center, Beirut, Lebanon; Faculty of Medicine, Balamand University, Lebanon.
| | - Maria El Gemayel
- Department of Internal Medicine, Hotel Dieu de France University Hospital, Beirut, Lebanon; Faculty of Medicine, Saint Joseph University, Beirut, Lebanon
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159
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Weiss E, Katta R. Diet and rosacea: the role of dietary change in the management of rosacea. Dermatol Pract Concept 2017; 7:31-37. [PMID: 29214107 PMCID: PMC5718124 DOI: 10.5826/dpc.0704a08] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/21/2017] [Indexed: 12/19/2022] Open
Abstract
Dietary change may play a role in the therapy of rosacea. Certain foods and beverages may act as "triggers" for rosacea exacerbations. These may be divided into heat-related, alcohol-related, capsaicin-related, and cinnamaldehyde-related. One potential pathogenic mechanism may be via the activation of transient receptor potential cation channels, which result in neurogenic vasodilatation. Further research is needed on the role of the gut skin connection in rosacea. Epidemiologic studies suggest that patients with rosacea have a higher prevalence of gastrointestinal disease, and one study reported improvement in rosacea following successful treatment of small intestinal bacterial overgrowth. While further research is required in this area, patients may be advised on measures to support a healthy gut microbiome, including the consumption of a fiber-rich (prebiotic) diet.
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Affiliation(s)
- Emma Weiss
- Baylor College of Medicine, Houston, TX, USA
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160
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Yadav P, Ellinghaus D, Rémy G, Freitag-Wolf S, Cesaro A, Degenhardt F, Boucher G, Delacre M, Peyrin-Biroulet L, Pichavant M, Rioux JD, Gosset P, Franke A, Schumm LP, Krawczak M, Chamaillard M, Dempfle A, Andersen V. Genetic Factors Interact With Tobacco Smoke to Modify Risk for Inflammatory Bowel Disease in Humans and Mice. Gastroenterology 2017; 153:550-565. [PMID: 28506689 PMCID: PMC5526723 DOI: 10.1053/j.gastro.2017.05.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 03/28/2017] [Accepted: 05/08/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The role of tobacco smoke in the etiology of inflammatory bowel disease (IBD) is unclear. We investigated interactions between genes and smoking (gene-smoking interactions) that affect risk for Crohn's disease (CD) and ulcerative colitis (UC) in a case-only study of patients and in mouse models of IBD. METHODS We used 55 Immunochip-wide datasets that included 19,735 IBD cases (10,856 CD cases and 8879 UC cases) of known smoking status. We performed 3 meta-analyses each for CD, UC, and IBD (CD and UC combined), comparing data for never vs ever smokers, never vs current smokers, and never vs former smokers. We studied the effects of exposure to cigarette smoke in Il10-/- and Nod2-/- mice, as well as in Balb/c mice without disruption of these genes (wild-type mice). Mice were exposed to the smoke of 5 cigarettes per day, 5 days a week, for 8 weeks, in a ventilated smoking chamber, or ambient air (controls). Intestines were collected and analyzed histologically and by reverse transcription polymerase chain reaction. RESULTS We identified 64 single nucleotide polymorphisms (SNPs) for which the association between the SNP and IBD were modified by smoking behavior (meta-analysis Wald test P < 5.0 × 10-5; heterogeneity Cochrane Q test P > .05). Twenty of these variants were located within the HLA region at 6p21. Analysis of classical HLA alleles (imputed from SNP genotypes) revealed an interaction with smoking. We replicated the interaction of a variant in NOD2 with current smoking in relation to the risk for CD (frameshift variant fs1007insC; rs5743293). We identified 2 variants in the same genomic region (rs2270368 and rs17221417) that interact with smoking in relation to CD risk. Approximately 45% of the SNPs that interact with smoking were in close vicinity (≤1 Mb) to SNPs previously associated with IBD; many were located near or within genes that regulate mucosal barrier function and immune tolerance. Smoking modified the disease risk of some variants in opposite directions for CD vs UC. Exposure of Interleukin 10 (il10)-deficient mice to cigarette smoke accelerated development of colitis and increased expression of interferon gamma in the small intestine compared to wild-type mice exposed to smoke. NOD2-deficient mice exposed to cigarette smoke developed ileitis, characterized by increased expression of interferon gamma, compared to wild-type mice exposed to smoke. CONCLUSIONS In an analysis of 55 Immunochip-wide datasets, we identified 64 SNPs whose association with risk for IBD is modified by tobacco smoking. Gene-smoking interactions were confirmed in mice with disruption of Il10 and Nod2-variants of these genes have been associated with risk for IBD. Our findings from mice and humans revealed that the effects of smoking on risk for IBD depend on genetic variants.
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Affiliation(s)
- Pankaj Yadav
- Institute of Medical Informatics and Statistics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Gaëlle Rémy
- University of Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Anabelle Cesaro
- University of Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | | | - Myriam Delacre
- University of Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France
| | | | - Laurent Peyrin-Biroulet
- Department of Gastroenterology and Inserm U954, Nancy University Hospital, Lorraine University, 54500 Vandoeuvre-lès-Nancy, France
| | - Muriel Pichavant
- University of Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montreal, Quebec, Canada,Faculté de Médecine, Université de Montréal, Montreal, Quebec, Canada
| | - Philippe Gosset
- University of Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - L. Philip Schumm
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Mathias Chamaillard
- University of Lille, CNRS, Inserm, CHRU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d’Infection et d’Immunité de Lille, F-59000 Lille, France
| | - Astrid Dempfle
- Institute of Medical Informatics and Statistics, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Vibeke Andersen
- Molecular Diagnostic and Clinical Research Unit, Institut for Regional Sundhedsforskning, Center Sønderjylland, University of Southern Denmark, Odense, Denmark; Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark; Laboratory Center, Hospital of Southern Jutland, Aabenraa, Denmark.
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161
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Bayesian analysis of genetic association across tree-structured routine healthcare data in the UK Biobank. Nat Genet 2017; 49:1311-1318. [PMID: 28759005 PMCID: PMC5580804 DOI: 10.1038/ng.3926] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/06/2017] [Indexed: 12/15/2022]
Abstract
Genetic discovery from the multitude of phenotypes extractable from routine healthcare data can transform our understanding of the human phenome and accelerate progress towards precision medicine. However, a critical question when analysing high-dimensional and heterogeneous data is how to best interrogate increasingly specific subphenotypes whilst retaining statistical power to detect genetic associations. Here we develop and employ a novel Bayesian analysis framework that exploits the hierarchical structure of diagnosis classifications to analyse genetic variants against UK Biobank disease phenotypes derived from self-reporting and hospital episode statistics. Our method displays a more than 20% increase in power to detect genetic effects over other approaches and identifies novel associations between classical human leukocyte antigen (HLA) alleles and common immune-mediated diseases (IMDs). By applying the approach to genetic risk scores (GRSs) we reveal the extent of genetic sharing between IMDs and expose differences in disease perception or diagnosis with potential clinical implications.
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162
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Zhang C, de Smith AJ, Smirnov IV, Wiencke JK, Wiemels JL, Witte JS, Walsh KM. Non-additive and epistatic effects of HLA polymorphisms contributing to risk of adult glioma. J Neurooncol 2017; 135:237-244. [PMID: 28721485 DOI: 10.1007/s11060-017-2569-7] [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] [Received: 04/20/2017] [Accepted: 07/13/2017] [Indexed: 01/15/2023]
Abstract
Although genome-wide association studies have identified several susceptibility loci for adult glioma, little is known regarding the potential contribution of genetic variation in the human leukocyte antigen (HLA) region to glioma risk. HLA associations have been reported for various malignancies, with many studies investigating selected candidate HLA polymorphisms. However, no systematic analysis has been conducted in glioma patients, and no investigation into potential non-additive effects has been described. We conducted comprehensive genetic analyses of HLA variants among 1746 adult glioma patients and 2312 controls of European-ancestry from the GliomaScan Consortium. Genotype data were generated with the Illumina 660-Quad array, and we imputed HLA alleles using a reference panel of 5225 individuals in the Type 1 Diabetes Genetics Consortium who underwent high-resolution HLA typing via next-generation sequencing. Case-control comparisons were adjusted for population stratification using ancestry-informative principal components. Because alleles in different loci across the HLA region are linked, we created multigene haplotypes consisting of the genes DRB1, DQA1, and DQB1. Although none of the haplotypes were associated with glioma in additive models, inclusion of a dominance term significantly improved the model for multigene haplotype HLA-DRB1*1501-DQA1*0102-DQB1*0602 (P = 0.002). Heterozygous carriers of the haplotype had an increased risk of glioma [odds ratio (OR) 1.23; 95% confidence interval (CI) 1.01-1.49], while homozygous carriers were at decreased risk compared with non-carriers (OR 0.64; 95% CI 0.40-1.01). Our results suggest that the DRB1*1501-DQA1*0102-DQB1*0602 haplotype may contribute to the risk of glioma in a non-additive manner, with the positive dominance effect partly explained by an epistatic interaction with HLA-DRB1*0401-DQA1*0301-DQB1*0301.
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Affiliation(s)
- Chenan Zhang
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ivan V Smirnov
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - John K Wiencke
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Joseph L Wiemels
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.,Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
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163
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Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KKH, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature 2017; 547:173-178. [PMID: 28658209 PMCID: PMC5511510 DOI: 10.1038/nature22969] [Citation(s) in RCA: 378] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 05/07/2017] [Indexed: 12/19/2022]
Abstract
Inflammatory bowel diseases are chronic gastrointestinal inflammatory disorders that affect millions of people worldwide. Genome-wide association studies have identified 200 inflammatory bowel disease-associated loci, but few have been conclusively resolved to specific functional variants. Here we report fine-mapping of 94 inflammatory bowel disease loci using high-density genotyping in 67,852 individuals. We pinpoint 18 associations to a single causal variant with greater than 95% certainty, and an additional 27 associations to a single variant with greater than 50% certainty. These 45 variants are significantly enriched for protein-coding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-specific epigenetic marks (n = 10), with the last category showing enrichment in specific immune cells among associations stronger in Crohn's disease and in gut mucosa among associations stronger in ulcerative colitis. The results of this study suggest that high-resolution fine-mapping in large samples can convert many discoveries from genome-wide association studies into statistically convincing causal variants, providing a powerful substrate for experimental elucidation of disease mechanisms.
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Affiliation(s)
- Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Ming Fang
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Christ Church, University of Oxford, St Aldates OX1 1DP, UK
| | - Maša Umićević Mirkov
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Gabrielle Boucher
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Carl A Anderson
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Vibeke Andersen
- Focused research unit for Molecular Diagnostic and Clinical Research (MOK), IRS-Center Sonderjylland, Hospital of Southern Jutland, 6200 Åbenrå, Denmark.,Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense, Denmark
| | | | - Adrian Cortes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington OX3 7BN, UK.,Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, Division of Clinical Neurology, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - François Crins
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mauro D'Amato
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet, 17176 Stockholm, Sweden.,Department of Gastrointestinal and Liver Diseases, BioDonostia Health Research Institute, 20014 San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Valérie Deffontaine
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Julia Dmitrieva
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Elisa Docampo
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mahmoud Elansary
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Kyle Kai-How Farh
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Illumina, San Diego, California 92122, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Ann-Stephan Gori
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Philippe Goyette
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, SE-70182 Örebro, Sweden
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Jo Knight
- Data Science Institute and Lancaster Medical School, Lancaster University, Lancaster LA1 4YG, UK
| | - Ian C Lawrance
- Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco, Western Australia 6008, Australia.,Harry Perkins Institute for Medical Research, School of Medicine and Pharmacology, University of Western Australia, Murdoch, Western Australia 6150, Australia
| | - Charlie W Lees
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Edouard Louis
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Division of Gastroenterology, Centre Hospitalier Universitaire (CHU) de Liège, 4000 Liège, Belgium
| | - Rob Mariman
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Theo Meuwissen
- Institute of Livestock and Aquacultural Sciences, Norwegian University of Life Sciences, 1430 Ås, Norway
| | - Myriam Mni
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Yukihide Momozawa
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium.,Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Kanagawa 230-0045, Japan
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK.,Open Targets, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK
| | - Emilie Théâtre
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Gosia Trynka
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Western General Hospital University of Edinburgh, Edinburgh, UK
| | - Suzanne van Sommeren
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Severine Vermeire
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium.,Division of Gastroenterology, University Hospital Gasthuisberg, 3000 Leuven, Belgium
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.,Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA
| | | | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Richard H Duerr
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA.,Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261, USA
| | - Christopher G Mathew
- Department of Medical and Molecular Genetics, King's College London, London SE1 9RT, UK.,Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - John D Rioux
- Research Center, Montreal Heart Institute, Montréal, Québec H1T 1C8, Canada.,Faculté de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, USA
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06510, USA
| | - Michel Georges
- Unit of Medical Genomics, Groupe Interdisciplinaire de Génoprotéomique Appliquée (GIGA-R) Research Center and WELBIO, University of Liège, 4000 Liège, Belgium.,Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
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164
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Castro-Santos P, Moro-García MA, Marcos-Fernández R, Alonso-Arias R, Díaz-Peña R. ERAP1 and HLA-C interaction in inflammatory bowel disease in the Spanish population. Innate Immun 2017. [PMID: 28651467 DOI: 10.1177/1753425917716527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large genome-wide analysis studies (GWAS) and meta-analyses have dramatically increased our knowledge of the genetic risk factors of inflammatory bowel disease (IBD), identifying at least 163 loci. The endoplasmic reticulum aminopeptidase-2 ( ERAP2) gene has been reported as a potential candidate gene for IBD. GWAS have also shown the potential associations between ERAP single nucleotide polymorphisms (SNP) loci and susceptibility to several autoimmune diseases, and ERAP1 and ERAP2 polymorphisms are related to HLA class I-associated diseases, including ankylosing spondylitis and Behçet's disease. Interestingly, these associations were confined to individuals carrying HLA class I-risk alleles. The aim of this study was to investigate the association of ERAP1 and ERAP2 SNPs with IBD in a Spanish population, analysing their possible interaction with specific HLA-C alleles to IBD susceptibility. A total of 367 individuals were divided into 216 IBD cases and 151 controls. SNP genotyping was performed using TaqMan® genotyping assays, whereas HLA-C typing was analysed by sequence-specific oligonucleotide probing. Herein, we report an association of the ERAP1 SNP rs30187 with the HLA-C*07 allele. The existence of shared inflammatory pathways in immunologically related diseases together with the understanding of ERAP1 function may offer clues to novel treatment strategies.
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Affiliation(s)
| | | | | | - Rebeca Alonso-Arias
- 1 Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile.,2 Department of Immunology, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Roberto Díaz-Peña
- 1 Faculty of Health Sciences, Universidad Autónoma de Chile, Talca, Chile.,3 Projects Unit, Sistemas Genómicos, Valencia, Spain
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165
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Magro F, Gionchetti P, Eliakim R, Ardizzone S, Armuzzi A, Barreiro-de Acosta M, Burisch J, Gecse KB, Hart AL, Hindryckx P, Langner C, Limdi JK, Pellino G, Zagórowicz E, Raine T, Harbord M, Rieder F. Third European Evidence-based Consensus on Diagnosis and Management of Ulcerative Colitis. Part 1: Definitions, Diagnosis, Extra-intestinal Manifestations, Pregnancy, Cancer Surveillance, Surgery, and Ileo-anal Pouch Disorders. J Crohns Colitis 2017; 11:649-670. [PMID: 28158501 DOI: 10.1093/ecco-jcc/jjx008] [Citation(s) in RCA: 1126] [Impact Index Per Article: 160.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/01/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Fernando Magro
- Department of Pharmacology and Therapeutics, University of Porto; MedInUP, Centre for Drug Discovery and Innovative Medicines; Centro Hospitalar São João, Porto, Portugal
| | | | - Rami Eliakim
- Department of Gastroenterology and Hepatology, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sandro Ardizzone
- Gastrointestinal Unit ASST Fatebenefratelli Sacco-University of Milan-Milan, Italy
| | - Alessandro Armuzzi
- IBD Unit Complesso Integrato Columbus, Gastroenterological and Endocrino-Metabolical Sciences Department, Fondazione Policlinico Universitario Gemelli Universita' Cattolica del Sacro Cuore, Rome, Italy
| | - Manuel Barreiro-de Acosta
- Department of Gastroenterology, IBD Unit, University Hospital Santiago De Compostela (CHUS), A Coruña, Spain
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Krisztina B Gecse
- First Department of Medicine, Semmelweis University, Budapest,Hungary
| | | | - Pieter Hindryckx
- Department of Gastroenterology, University Hospital of Ghent, Ghent, Belgium
| | - Cord Langner
- Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Jimmy K Limdi
- Department of Gastroenterology, Pennine Acute Hospitals NHS Trust; Institute of Inflammation and Repair, University of Manchester, Manchester, UK
| | - Gianluca Pellino
- Unit of General Surgery, Second University of Naples,Napoli, Italy
| | - Edyta Zagórowicz
- Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Department of Oncological Gastroenterology Warsaw; Medical Centre for Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Warsaw, Poland
| | - Tim Raine
- Department of Medicine, University of Cambridge, Cambridge,UK
| | - Marcus Harbord
- Imperial College London; Chelsea and Westminster Hospital, London,UK
| | - Florian Rieder
- Department of Pathobiology /NC22, Lerner Research Institute; Department of Gastroenterology, Hepatology and Nutrition/A3, Digestive Disease and Surgery Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DPB, Kugathasan S. Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:2082-2083. [PMID: 28478146 PMCID: PMC6033331 DOI: 10.1053/j.gastro.2017.02.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/17/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn’s disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10−8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10−6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide signifi-cance on conditioning), IL12B, PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R. Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee,Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, Medical University of South Carolina, Pediatric Center for Inflammatory Bowel Disorders, Summerville, South Carolina
| | - Jenifer Seminerio
- Department of Gastroenterology, Medical University of South Carolina Digestive Disease Center, Charleston, South Carolina
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | - Robert N. Baldassano
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine & Nursing, Baltimore, Maryland
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, Kentucky
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, North Carolina
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; Veterans Affairs Health Services Research and Development Service, Center for Innovations in Quality Effectiveness and Safety; Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, Louisiana
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, Ohio
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children’s Hospital, Chicago, Illinois
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, Virginia
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, New York
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | | | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida, Jacksonville, Florida
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, Quebec, Canada
| | - Richard H. Duerr
- Department of Medicine and Clinical and Translational Science Institute, School of Medicine and Department of Human Genetics, Graduate School of Public Health; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Personalized Medicine, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
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Small-scale intraspecific patterns of adaptive immunogenetic polymorphisms and neutral variation in Lake Superior lake trout. Immunogenetics 2017; 70:53-66. [PMID: 28547520 DOI: 10.1007/s00251-017-0996-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 04/26/2017] [Indexed: 10/19/2022]
Abstract
Many fishes express high levels of intraspecific variability, often linked to resource partitioning. Several studies show that a species' evolutionary trajectory of adaptive divergence can undergo reversals caused by changes in its environment. Such a reversal in neutral genetic and morphological variation among lake trout Salvelinus namaycush ecomorphs appears to be underway in Lake Superior. However, a water depth gradient in neutral genetic divergence was found to be associated with intraspecific diversity in the lake. To investigate patterns of adaptive immunogenetic variation among lake trout ecomorphs, we used Illumina high-throughput sequencing. The population's genetic structure of the major histocompatibility complex (MHC Class IIβ exon 2) and 18 microsatellite loci were compared to disentangle neutral and selective processes at a small geographic scale. Both MHC and microsatellite variation were partitioned more by water depth stratum than by ecomorph. Several metrics showed strong clustering by water depth in MHC alleles, but not microsatellites. We report a 75% increase in the number of MHC alleles shared between the predominant shallow and deep water ecomorphs since a previous lake trout MHC study at the same locale (c. 1990s data). This result is consistent with the reverse speciation hypothesis, although adaptive MHC polymorphisms persist along an ecological gradient. Finally, results suggested that the lake trout have multiple copies of the MHC II locus consistent with a historic genomic duplication event. Our findings indicated that conservation approaches for this species could focus on managing various ecological habitats by depth, in addition to regulating the fisheries specific to ecomorphs.
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Abstract
Primary sclerosing cholangitis (PSC) is a chronic disease leading to fibrotic scarring of the intrahepatic and extrahepatic bile ducts, causing considerable morbidity and mortality via the development of cholestatic liver cirrhosis, concurrent IBD and a high risk of bile duct cancer. Expectations have been high that genetic studies would determine key factors in PSC pathogenesis to support the development of effective medical therapies. Through the application of genome-wide association studies, a large number of disease susceptibility genes have been identified. The overall genetic architecture of PSC shares features with both autoimmune diseases and IBD. Strong human leukocyte antigen gene associations, along with several susceptibility genes that are critically involved in T-cell function, support the involvement of adaptive immune responses in disease pathogenesis, and position PSC as an autoimmune disease. In this Review, we survey the developments that have led to these gene discoveries. We also elaborate relevant interpretations of individual gene findings in the context of established disease models in PSC, and propose relevant translational research efforts to pursue novel insights.
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169
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017. [PMID: 28449694 DOI: 10.1186/s13059-017-1207-1.] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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170
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Matzaraki V, Kumar V, Wijmenga C, Zhernakova A. The MHC locus and genetic susceptibility to autoimmune and infectious diseases. Genome Biol 2017; 18:76. [PMID: 28449694 PMCID: PMC5406920 DOI: 10.1186/s13059-017-1207-1] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past 50 years, variants in the major histocompatibility complex (MHC) locus, also known as the human leukocyte antigen (HLA), have been reported as major risk factors for complex diseases. Recent advances, including large genetic screens, imputation, and analyses of non-additive and epistatic effects, have contributed to a better understanding of the shared and specific roles of MHC variants in different diseases. We review these advances and discuss the relationships between MHC variants involved in autoimmune and infectious diseases. Further work in this area will help to distinguish between alternative hypotheses for the role of pathogens in autoimmune disease development.
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Affiliation(s)
- Vasiliki Matzaraki
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Vinod Kumar
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands. .,Department of Immunology, KG Jebsen Coeliac Disease Research Centre, University of Oslo, PO Box 4950 Nydalen, 0424, Oslo, Norway.
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB, Groningen, The Netherlands
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Analysis of the human monocyte-derived macrophage transcriptome and response to lipopolysaccharide provides new insights into genetic aetiology of inflammatory bowel disease. PLoS Genet 2017; 13:e1006641. [PMID: 28263993 PMCID: PMC5358891 DOI: 10.1371/journal.pgen.1006641] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 03/20/2017] [Accepted: 02/17/2017] [Indexed: 12/15/2022] Open
Abstract
The FANTOM5 consortium utilised cap analysis of gene expression (CAGE) to provide an unprecedented insight into transcriptional regulation in human cells and tissues. In the current study, we have used CAGE-based transcriptional profiling on an extended dense time course of the response of human monocyte-derived macrophages grown in macrophage colony-stimulating factor (CSF1) to bacterial lipopolysaccharide (LPS). We propose that this system provides a model for the differentiation and adaptation of monocytes entering the intestinal lamina propria. The response to LPS is shown to be a cascade of successive waves of transient gene expression extending over at least 48 hours, with hundreds of positive and negative regulatory loops. Promoter analysis using motif activity response analysis (MARA) identified some of the transcription factors likely to be responsible for the temporal profile of transcriptional activation. Each LPS-inducible locus was associated with multiple inducible enhancers, and in each case, transient eRNA transcription at multiple sites detected by CAGE preceded the appearance of promoter-associated transcripts. LPS-inducible long non-coding RNAs were commonly associated with clusters of inducible enhancers. We used these data to re-examine the hundreds of loci associated with susceptibility to inflammatory bowel disease (IBD) in genome-wide association studies. Loci associated with IBD were strongly and specifically (relative to rheumatoid arthritis and unrelated traits) enriched for promoters that were regulated in monocyte differentiation or activation. Amongst previously-identified IBD susceptibility loci, the vast majority contained at least one promoter that was regulated in CSF1-dependent monocyte-macrophage transitions and/or in response to LPS. On this basis, we concluded that IBD loci are strongly-enriched for monocyte-specific genes, and identified at least 134 additional candidate genes associated with IBD susceptibility from reanalysis of published GWA studies. We propose that dysregulation of monocyte adaptation to the environment of the gastrointestinal mucosa is the key process leading to inflammatory bowel disease. Macrophages are immune cells that form the first line of defense against pathogens, but also mediate tissue damage in inflammatory disease. Macrophages initiate inflammation by recognising and responding to components of bacterial cells. Macrophages of the wall of the gut are constantly replenished from the blood. Upon entering the intestine, newly-arrived cells modulate their response to stimuli derived from the bacteria in the wall of the gut. This process fails in chronic inflammatory bowel diseases (IBD). Both the major forms of IBD, Crohn’s disease and ulcerative colitis, run in families. The inheritance is complex, involving more than 200 different regions of the genome. We hypothesised that the genetic risk of IBD is associated specifically with altered regulation of genes that control the development of macrophages. In this study, we used the comprehensive transcriptome dataset produced by the FANTOM5 consortium to identify the sets of promoters and enhancers that are involved in adaptation of macrophages to the gut wall, their response to bacterial stimuli, and how their functions are integrated. A reanalysis of published genome-wide association data based upon regulated genes in monocytes as candidates strongly supports the view that susceptibility to IBD arises from a primary defect in macrophage differentiation.
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172
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Cesarini M, Collins GS, Rönnblom A, Santos A, Wang LM, Sjöberg D, Parkes M, Keshav S, Travis SPL. Predicting the Individual Risk of Acute Severe Colitis at Diagnosis. J Crohns Colitis 2017; 11:335-341. [PMID: 27647858 PMCID: PMC5881607 DOI: 10.1093/ecco-jcc/jjw159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/17/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Acute severe colitis [ASC] is associated with major morbidity. We aimed to develop and externally validate an index that predicted ASC within 3 years of diagnosis. METHODS The development cohort included patients aged 16-89 years, diagnosed with ulcerative colitis [UC] in Oxford and followed for 3 years. Primary outcome was hospitalization for ASC, excluding patients admitted within 1 month of diagnosis. Multivariable logistic regression examined the adjusted association of seven risk factors with ASC. Backwards elimination produced a parsimonious model that was simplified to create an easy-to-use index. External validation occurred in separate cohorts from Cambridge, UK, and Uppsala, Sweden. RESULTS The development cohort [Oxford] included 34/111 patients who developed ASC within a median 14 months [range 1-29]. The final model applied the sum of 1 point each for extensive disease, C-reactive protein [CRP] > 10mg/l, or haemoglobin < 12g/dl F or < 14g/dl M at diagnosis, to give a score from 0/3 to 3/3. This predicted a 70% risk of developing ASC within 3 years [score 3/3]. Validation cohorts included different proportions with ASC [Cambridge = 25/96; Uppsala = 18/298]. Of those scoring 3/3 at diagnosis, 18/18 [Cambridge] and 12/13 [Uppsala] subsequently developed ASC. Discriminant ability [c-index, where 1.0 = perfect discrimination] was 0.81 [Oxford], 0.95 [Cambridge], 0.97 [Uppsala]. Internal validation using bootstrapping showed good calibration, with similar predicted risk across all cohorts. A nomogram predicted individual risk. CONCLUSIONS An index applied at diagnosis reliably predicts the risk of ASC within 3 years in different populations. Patients with a score 3/3 at diagnosis may merit early immunomodulator therapy.
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Affiliation(s)
- Monica Cesarini
- Translational Gastroenterology Unit, Oxford University Hospitals, Oxford, UK,Dipartimento di Medicina Interna e Specialità Mediche, ‘Sapienza’, University of Rome, Rome, Italy
| | - Gary S. Collins
- Centre for Statistics in Medicine, University of Oxford, Oxford, UK
| | - Anders Rönnblom
- Department of Medical Sciences, Gastroenterology, Uppsala University, Uppsala, Sweden
| | - Antonieta Santos
- Gastroenterology Unit, Cambridge University Hospitals, Cambridge, UK,Gastroenterology Unit, Hospital Amato Lusitano, Castelo Branco, Portugal
| | - Lai Mun Wang
- Department of Cellular Pathology, Oxford University Hospitals, Oxford, UK
| | - Daniel Sjöberg
- Department of Medical Sciences, Gastroenterology, Uppsala University, Uppsala, Sweden
| | - Miles Parkes
- Gastroenterology Unit, Cambridge University Hospitals, Cambridge, UK
| | - Satish Keshav
- Translational Gastroenterology Unit, Oxford University Hospitals, Oxford, UK
| | - Simon P. L. Travis
- Translational Gastroenterology Unit, Oxford University Hospitals, Oxford, UK
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173
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Westerlind H, Mellander MR, Bresso F, Munch A, Bonfiglio F, Assadi G, Rafter J, Hübenthal M, Lieb W, Källberg H, Brynedal B, Padyukov L, Halfvarson J, Törkvist L, Bjork J, Andreasson A, Agreus L, Almer S, Miehlke S, Madisch A, Ohlsson B, Löfberg R, Hultcrantz R, Franke A, D'Amato M. Dense genotyping of immune-related loci identifies HLA variants associated with increased risk of collagenous colitis. Gut 2017; 66:421-428. [PMID: 26525574 DOI: 10.1136/gutjnl-2015-309934] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 10/11/2015] [Accepted: 10/12/2015] [Indexed: 12/27/2022]
Abstract
OBJECTIVE Collagenous colitis (CC) is a major cause of chronic non-bloody diarrhoea, particularly in the elderly female population. The aetiology of CC is unknown, and still poor is the understanding of its pathogenesis. This possibly involves dysregulated inflammation and immune-mediated reactions in genetically predisposed individuals, but the contribution of genetic factors to CC is underinvestigated. We systematically tested immune-related genes known to impact the risk of several autoimmune diseases for their potential CC-predisposing role. DESIGN Three independent cohorts of histologically confirmed CC cases (N=314) and controls (N=4299) from Sweden and Germany were included in a 2-step association analysis. Immunochip and targeted single nucleotide polymorphism (SNP) genotype data were produced, respectively, for discovery and replication purposes. Classical human leucocyte antigen (HLA) variants at 2-digit and 4-digit resolution were obtained via imputation from single marker genotypes. SNPs and HLA variants passing quality control filters were tested for association with CC with logistic regression adjusting for age, sex and country of origin. RESULTS Forty-two markers gave rise to genome-wide significant association signals, all contained within the HLA region on chromosome 6 (best p=4.2×10-10 for SNP rs4143332). Among the HLA variants, most pronounced risk effects were observed for 8.1 haplotype alleles including DQ2.5, which was targeted and confirmed in the replication data set (p=2.3×10-11; OR=2.06; 95% CI (1.67 to 2.55) in the combined analysis). CONCLUSIONS HLA genotype associates with CC, thus implicating HLA-related immune mechanisms in its pathogenesis.
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Affiliation(s)
- Helga Westerlind
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Marie-Rose Mellander
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Francesca Bresso
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Andreas Munch
- Department of Clinical and Experimental Medicine, Faculty of Health Science, Linköpings University, Linköping, Sweden
| | - Ferdinando Bonfiglio
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Ghazaleh Assadi
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Joseph Rafter
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank POPGEN, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Henrik Källberg
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Boel Brynedal
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Leonid Padyukov
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Leif Törkvist
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Jan Bjork
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Andreasson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Lars Agreus
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Sven Almer
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Gastrocentrum, Karolinska University Hospital, Stockholm, Sweden
| | - Stephan Miehlke
- Center for Digestive Diseases, Internal Medicine Center Eppendorf, Hamburg, Germany
| | - Ahmed Madisch
- Clinic for Gastroenterology, Endoscopy and Interventional Diabetology, Siloah Hospital, Hannover, Germany
| | - Bodil Ohlsson
- Department of Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Robert Löfberg
- Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Sophiahemmet Hospital, Stockholm, Sweden
| | - Rolf Hultcrantz
- Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Mauro D'Amato
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- BioCruces Health Research Institute and IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
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Hov JR, Boberg KM, Taraldsrud E, Vesterhus M, Boyadzhieva M, Solberg IC, Schrumpf E, Vatn MH, Lie BA, Molberg Ø, Karlsen TH. Antineutrophil antibodies define clinical and genetic subgroups in primary sclerosing cholangitis. Liver Int 2017; 37:458-465. [PMID: 27558072 DOI: 10.1111/liv.13238] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/18/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS The strongest genetic risk factors in primary sclerosing cholangitis (PSC) are encoded in the HLA complex. Antineutrophil cytoplasmic antibodies (ANCA) have been reported in up to 94% of PSC patients, but their clinical significance and immunogenetic basis are ill defined. We aimed to characterize clinical and genetic associations of ANCA in PSC. METHODS Antineutrophil cytoplasmic antibodies were analysed with indirect immunofluorescence in 241 Norwegian PSC patients. HLA-B and HLA-DRB1 genotyping was performed in the patients and in 368 healthy controls. Data on perinuclear ANCA (pANCA) and HLA-DRB1 were available from 274 ulcerative colitis (UC) patients without known liver disease. RESULTS Antineutrophil cytoplasmic antibodies were found in 193 (80%) of the PSC patients, with pANCA in 169 (70%). ANCA-positive patients were younger than ANCA negative at diagnosis of PSC and had a lower frequency of biliary cancer (9% vs 19%, P=.047). There were no differences between PSC patients with and without inflammatory bowel disease. Genetically, the strong PSC risk factors HLA-B*08 (frequency in healthy 13%) and DRB1*03 (14%) were more prevalent in ANCA-positive than -negative patients (43% vs 25%, P=.0012 and 43% vs 25%, P=.0015 respectively). The results were similar when restricting the analysis to pANCA-positive patients. In UC patients without liver disease, HLA-DRB1*03 was more prevalent in pANCA-positive compared with -negative patients (P=.03). CONCLUSIONS Antineutrophil cytoplasmic antibodies identified PSC patients with particular clinical and genetic characteristics, suggesting that ANCA may mark a clinically relevant pathogenetic subgroup in the PSC-UC disease spectrum.
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Affiliation(s)
- Johannes R Hov
- Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Division of Surgery, Inflammatory Medicine and Transplantation, Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Inflammation Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kirsten M Boberg
- Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Eli Taraldsrud
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K.G.Jebsen Inflammation Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Mette Vesterhus
- Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway.,National Centre for Ultrasound in Gastroenterology, Haukeland University Hospital, Bergen, Norway
| | - Maria Boyadzhieva
- Clinical Center of Endocrinology, Medical University Sofia, Sofia, Bulgaria
| | - Inger Camilla Solberg
- Division of Medicine, Department of Gastroenterology, Oslo University Hospital Ullevål, Oslo, Norway
| | - Erik Schrumpf
- Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Morten H Vatn
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,EpiGen Institute, Campus AHUS, Akershus University Hospital, Nordbyhagen, Norway
| | - Benedicte A Lie
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K.G.Jebsen Inflammation Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Øyvind Molberg
- Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Rheumatology Unit, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Tom H Karlsen
- Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Section of Gastroenterology, Division of Surgery, Department of Transplantation Medicine, Inflammatory Medicine and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway.,Division of Surgery, Inflammatory Medicine and Transplantation, Research Institute of Internal Medicine, Oslo University Hospital, Oslo, Norway.,K.G.Jebsen Inflammation Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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175
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Genetics of inflammatory bowel disease: beyond NOD2. Lancet Gastroenterol Hepatol 2017; 2:224-234. [PMID: 28404137 DOI: 10.1016/s2468-1253(16)30111-x] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/02/2016] [Accepted: 09/02/2016] [Indexed: 01/11/2023]
Abstract
The study of the genetic underpinnings of inflammatory bowel disease has made great progress since the identification of NOD2 as a major susceptibility gene. Novel genotyping and sequencing technologies have led to the discovery of 242 common susceptibility loci, 45 of which have been fine-mapped to statistically conclusive causal variants; 50 genes associated with very-early-onset inflammatory disease have been identified. The evolving genetic architecture of inflammatory bowel disease has deepened our understanding of its pathogenesis through identification of major disease associated pathways-knowledge that has the potential to indicate novel drug targets or markers for personalised medicine. However, many causal variants have yet to be identified, and a large proportion of missing heritability still needs to be accounted for. In addition, the medical and scientific communities are probably not yet fully harnessing the power of these genetic discoveries.
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176
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Ylinen E, Salmela L, Peräsaari J, Jaatinen T, Tenca A, Vapalahti O, Färkkilä M, Jalanko H, Kolho K. Human leucocyte antigens B*08, DRB1*03 and DRB1*13 are significantly associated with autoimmune liver and biliary diseases in Finnish children. Acta Paediatr 2017; 106:322-326. [PMID: 27759901 DOI: 10.1111/apa.13641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/05/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022]
Abstract
AIM The human leucocyte antigen (HLA) allele and haplotype frequencies of the Finnish population are unique because of the restricted and homogenous gene population. There are no published data on HLA genotype associations in paediatric autoimmune liver diseases in Scandinavia. This study characterised the HLA genotypes of children with autoimmune liver or biliary disease in Finland. METHODS The study cohort comprised 19 paediatric patients (13 female) aged three years to 15 years treated for autoimmune liver or biliary disease at the Children's Hospital, Helsinki University Hospital, between 2000 and 2011, and followed up for four years and three months to 14.6 years. We genotyped HLA-B and HLA-DRB1 in the children, and the HLA antigen frequencies were compared with 19 807 records from the Finnish Bone Marrow Donor Registry. RESULTS All paediatric patients with autoimmune liver or biliary disease had either autoimmune HLA haplotype B*08;DRB1*03 or DRB1*13. These were significantly more common among patients with autoimmune hepatitis, primary sclerosing cholangitis and autoimmune hepatitis/primary sclerosing cholangitis overlap syndrome than the Finnish control population. HLA RB1*04 was not found in the study cohort. CONCLUSION Our study found that B*08, DRB1*03 and DRB1*13 were significantly associated with autoimmune liver and biliary diseases in Finnish paediatric patients.
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Affiliation(s)
- E Ylinen
- Department of Paediatric Nephrology and Transplantation Children's Hospital University of Helsinki Helsinki University Hospital Helsinki Finland
- Department of Gastroenterology Children's Hospital University of Helsinki Helsinki University Hospital Helsinki Finland
| | - L Salmela
- Medical School University of Helsinki Helsinki Finland
| | - J Peräsaari
- Clinical Laboratory Finnish Red Cross Blood Service Helsinki Finland
| | - T Jaatinen
- Clinical Laboratory Finnish Red Cross Blood Service Helsinki Finland
| | - A Tenca
- Clinic of Gastroenterology University of Helsinki Helsinki University Hospital Helsinki Finland
| | - O Vapalahti
- Department of Virology and Immunology HUSLAB Hospital District of Helsinki and Uusimaa Helsinki Finland
| | - M Färkkilä
- Clinic of Gastroenterology University of Helsinki Helsinki University Hospital Helsinki Finland
| | - H Jalanko
- Department of Paediatric Nephrology and Transplantation Children's Hospital University of Helsinki Helsinki University Hospital Helsinki Finland
| | - K‐L Kolho
- Department of Gastroenterology Children's Hospital University of Helsinki Helsinki University Hospital Helsinki Finland
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177
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Lee JC, Biasci D, Roberts R, Gearry RB, Mansfield JC, Ahmad T, Prescott NJ, Satsangi J, Wilson DC, Jostins L, Anderson CA, Traherne JA, Lyons PA, Parkes M, Smith KG. Genome-wide association study identifies distinct genetic contributions to prognosis and susceptibility in Crohn's disease. Nat Genet 2017; 49:262-268. [PMID: 28067912 PMCID: PMC5730041 DOI: 10.1038/ng.3755] [Citation(s) in RCA: 176] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
For most immune-mediated diseases, the main determinant of patient well-being is not the diagnosis itself but instead the course that the disease takes over time (prognosis). Prognosis may vary substantially between patients for reasons that are poorly understood. Familial studies support a genetic contribution to prognosis, but little evidence has been found for a proposed association between prognosis and the burden of susceptibility variants. To better characterize how genetic variation influences disease prognosis, we performed a within-cases genome-wide association study in two cohorts of patients with Crohn's disease. We identified four genome-wide significant loci, none of which showed any association with disease susceptibility. Conversely, the aggregated effect of all 170 disease susceptibility loci was not associated with disease prognosis. Together, these data suggest that the genetic contribution to prognosis in Crohn's disease is largely independent of the contribution to disease susceptibility and point to a biology of prognosis that could provide new therapeutic opportunities.
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Affiliation(s)
- James C. Lee
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Daniele Biasci
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Rebecca Roberts
- University of Otago, Department of Medicine, Christchurch, New Zealand
| | - Richard B. Gearry
- University of Otago, Department of Medicine, Christchurch, New Zealand
| | | | - Tariq Ahmad
- University of Exeter Medical School, Exeter, UK
| | - Natalie J. Prescott
- Department of Medical and Molecular Genetics, Faculty of Life Science and Medicine, King’s College London, 8th Floor Guy’s Tower, Guy’s Hospital, London, UK
| | - Jack Satsangi
- Gastrointestinal Unit, Division of Medical Sciences, School of Molecular and Clinical Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - David C. Wilson
- Paediatric Gastroenterology and Nutrition, Child Life and Health, College of Medicine and Veterinary Medicine, University of Edinburgh, Royal Hospital for Sick Children, Edinburgh, UK
| | - Luke Jostins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Headington, UK
| | - Carl A. Anderson
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | | | - Paul A. Lyons
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Miles Parkes
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - Kenneth G.C. Smith
- Department of Medicine, University of Cambridge School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
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178
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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: 193] [Impact Index Per Article: 27.6] [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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179
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Jansen PLM, Ghallab A, Vartak N, Reif R, Schaap FG, Hampe J, Hengstler JG. The ascending pathophysiology of cholestatic liver disease. Hepatology 2017; 65:722-738. [PMID: 27981592 DOI: 10.1002/hep.28965] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/26/2016] [Accepted: 11/17/2016] [Indexed: 02/06/2023]
Abstract
In this review we develop the argument that cholestatic liver diseases, particularly primary biliary cholangitis and primary sclerosing cholangitis (PSC), evolve over time with anatomically an ascending course of the disease process. The first and early lesions are in "downstream" bile ducts. This eventually leads to cholestasis, and this causes bile salt (BS)-mediated toxic injury of the "upstream" liver parenchyma. BS are toxic in high concentration. These concentrations are present in the canalicular network, bile ducts, and gallbladder. Leakage of bile from this network and ducts could be an important driver of toxicity. The liver has a great capacity to adapt to cholestasis, and this may contribute to a variable symptom-poor interval that is often observed. Current trials with drugs that target BS toxicity are effective in only about 50%-60% of primary biliary cholangitis patients, with no effective therapy in PSC. This motivated us to develop and propose a new view on the pathophysiology of primary biliary cholangitis and PSC in the hope that these new drugs can be used more effectively. These views may lead to better stratification of these diseases and to recommendations on a more "tailored" use of the new therapeutic agents that are currently tested in clinical trials. Apical sodium-dependent BS transporter inhibitors that reduce intestinal BS absorption lower the BS load and are best used in cholestatic patients. The effectiveness of BS synthesis-suppressing drugs, such as farnesoid X receptor agonists, is greatest when optimal adaptation is not yet established. By the time cytochrome P450 7A1 expression is reduced these drugs may be less effective. Anti-inflammatory agents are probably most effective in early disease, while drugs that antagonize BS toxicity, such as ursodeoxycholic acid and nor-ursodeoxycholic acid, may be effective at all disease stages. Endoscopic stenting in PSC should be reserved for situations of intercurrent cholestasis and cholangitis, not for cholestasis in end-stage disease. These are arguments to consider a step-wise pathophysiology for these diseases, with therapy adjusted to disease stage. An obstacle in such an approach is that disease stage-defining biomarkers are still lacking. This review is meant to serve as a call to prioritize the development of biomarkers that help to obtain a better stratification of these diseases. (Hepatology 2017;65:722-738).
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Affiliation(s)
- Peter L M Jansen
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands.,Department of Surgery, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands.,Research Network of Liver Systems Medicine, Freiburg, Germany
| | - Ahmed Ghallab
- Research Network of Liver Systems Medicine, Freiburg, Germany.,Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany.,Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Nachiket Vartak
- Research Network of Liver Systems Medicine, Freiburg, Germany.,Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Raymond Reif
- Research Network of Liver Systems Medicine, Freiburg, Germany.,Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
| | - Frank G Schaap
- Department of Surgery, NUTRIM School for Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands
| | - Jochen Hampe
- Research Network of Liver Systems Medicine, Freiburg, Germany.,Department of Medicine 1, Technical University Dresden, Dresden, Germany
| | - Jan G Hengstler
- Research Network of Liver Systems Medicine, Freiburg, Germany.,Leibniz Research Centre for Working Environment and Human Factors at the Technical University Dortmund, Dortmund, Germany
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180
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Paziewska A, Habior A, Rogowska A, Zych W, Goryca K, Karczmarski J, Dabrowska M, Ambrozkiewicz F, Walewska-Zielecka B, Krawczyk M, Cichoz-Lach H, Milkiewicz P, Kowalik A, Mucha K, Raczynska J, Musialik J, Boryczka G, Wasilewicz M, Ciecko-Michalska I, Ferenc M, Janiak M, Kanikowska A, Stankiewicz R, Hartleb M, Mach T, Grzymislawski M, Raszeja-Wyszomirska J, Wunsch E, Bobinski T, Mikula M, Ostrowski J. A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients. BMC Med Genomics 2017; 10:2. [PMID: 28056976 PMCID: PMC5217265 DOI: 10.1186/s12920-016-0239-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 12/15/2016] [Indexed: 01/28/2023] Open
Abstract
Background Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are forms of hepatic autoimmunity, and risk for both diseases has a strong genetic component. This study aimed to define the genetic architecture of PBC and PSC within the Polish population. Methods Subjects were 443 women with PBC, 120 patients with PSC, and 934 healthy controls recruited from Gastroenterology Departments in various Polish hospitals. Allelotyping employed a pooled-DNA sample-based genome-wide association study (GWAS) approach, using Illumina Human Omni2.5-Exome BeadChips and the following novel selection criteria for risk loci: blocks of at least 10 single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium, where the distance between each adjacent SNP pair in the block was less than 30 kb, and each SNP was associated with disease at a significance level of P < 0.005. A selected index SNP from each block was validated using TaqMan SNP genotyping assays. Results Nineteen and twenty-one SNPs were verified as associated with PBC and PSC, respectively, by individual genotyping; 19 (10/9, PBC/PSC) SNPs reached a stringent (corrected) significance threshold and a further 21 (9/12, PBC/PSC) reached a nominal level of significance (P < 0.05 with odds ratio (OR) > 1.2 or < 0.83), providing suggestive evidence of association. The SNPs mapped to seven (1p31.3, 3q13, 6p21, 7q32.1, 11q23.3, 17q12, 19q13.33) and one (6p21) chromosome region previously associated with PBC and PSC, respectively. The SNP, rs35730843, mapping to the POLR2G gene promoter (P = 1.2 × 10-5, OR = 0.39) demonstrated the highest effect size, and was protective for PBC, whereas for PSC respective SNPs were: rs13191240 in the intron of ADGRB3 gene (P = 0.0095, OR = 0.2) and rs3822659 (P = 0.0051, OR = 0.236) along with rs9686714 (P = 0.00077, OR = 0.2), both located in the WWC1 gene. Conclusions Our cost-effective GWAS approach followed by individual genotyping confirmed several previously identified associations and discovered new susceptibility loci associated with PBC and/or PSC in Polish patients. However, further functional studies are warranted to understand the roles of these newly identified variants in the development of the two disorders. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0239-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Andrzej Habior
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Rogowska
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Włodzimierz Zych
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Bozena Walewska-Zielecka
- Department of Public Health, Faculty of Health Sciences, Medical University of Warsaw, Warsaw, Poland
| | - Marek Krawczyk
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | | | - Piotr Milkiewicz
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland.,Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Raczynska
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Musialik
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Grzegorz Boryczka
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Michal Wasilewicz
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Irena Ciecko-Michalska
- Department of Gastroenterology and Infectious Diseases, Collegium Medicum Jagiellonian University, Krakow, Poland
| | - Malgorzata Ferenc
- Department of Gastroenterology, Provincial Hospital, Olsztyn, Poland
| | - Maria Janiak
- Department of Gastroenterology and Hepatology, Medical University of Gdansk, Gdansk, Poland
| | - Alina Kanikowska
- Department of Internal and Metabolic Diseases and Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Rafal Stankiewicz
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Marek Hartleb
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Tomasz Mach
- Department of Gastroenterology and Infectious Diseases, Collegium Medicum Jagiellonian University, Krakow, Poland
| | - Marian Grzymislawski
- Department of Internal and Metabolic Diseases and Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Raszeja-Wyszomirska
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Wunsch
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Bobinski
- Department of Gastroenterology, Provincial Hospital, Ostroleka, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
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181
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Marcussen M, Bødker JS, Christensen HS, Johansen P, Nielsen S, Christiansen I, Bergmann OJ, Bøgsted M, Dybkær K, Vyberg M, Johnsen HE. Molecular Characteristics of High-Dose Melphalan Associated Oral Mucositis in Patients with Multiple Myeloma: A Gene Expression Study on Human Mucosa. PLoS One 2017; 12:e0169286. [PMID: 28052121 PMCID: PMC5215401 DOI: 10.1371/journal.pone.0169286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 12/14/2016] [Indexed: 11/19/2022] Open
Abstract
Background Toxicity of the oral and gastrointestinal mucosa induced by high-dose melphalan is a clinical challenge with no documented prophylactic interventions or predictive tests. The aim of this study was to describe molecular changes in human oral mucosa and to identify biomarkers correlated with the grade of clinical mucositis. Methods and Findings Ten patients with multiple myeloma (MM) were included. For each patient, we acquired three buccal biopsies, one before, one at 2 days, and one at 20 days after high-dose melphalan administration. We also acquired buccal biopsies from 10 healthy individuals that served as controls. We analyzed the biopsies for global gene expression and performed an immunohistochemical analysis to determine HLA-DRB5 expression. We evaluated associations between clinical mucositis and gene expression profiles. Compared to gene expression levels before and 20 days after therapy, at two days after melphalan treatment, we found gene regulation in the p53 and TNF pathways (MDM2, INPPD5, TIGAR), which favored anti-apoptotic defense, and upregulation of immunoregulatory genes (TREM2, LAMP3) in mucosal dendritic cells. This upregulation was independent of clinical mucositis. HLA-DRB1 and HLA-DRB5 (surface receptors on dendritic cells) were expressed at low levels in all patients with MM, in the subgroup of patients with ulcerative mucositis (UM), and in controls; in contrast, the subgroup with low-grade mucositis (NM) displayed 5–6 fold increases in HLA-DRB1 and HLA-DRB5 expression in the first two biopsies, independent of melphalan treatment. Moreover, different splice variants of HLA-DRB1 were expressed in the UM and NM subgroups. Conclusions Our results revealed that, among patients with MM, immunoregulatory genes and genes involved in defense against apoptosis were affected immediately after melphalan administration, independent of the presence of clinical mucositis. Furthermore, our results suggested that the expression levels of HLA-DRB1 and HLA-DRB5 may serve as potential predictive biomarkers for mucositis severity.
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Affiliation(s)
- Mette Marcussen
- Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
- * E-mail:
| | - Julie Støve Bødker
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
| | - Heidi Søgaard Christensen
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
| | - Preben Johansen
- Department of Pathology, Aalborg University Hospital, Ladegaardsgade 3, Denmark
| | - Søren Nielsen
- Department of Pathology, Aalborg University Hospital, Ladegaardsgade 3, Denmark
| | - Ilse Christiansen
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
| | - Olav Jonas Bergmann
- School of Dentistry, Faculty of Health Science, Aarhus University; Vennelyst Boulevard 9, Aarhus, Denmark
| | - Martin Bøgsted
- Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
| | - Karen Dybkær
- Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
| | - Mogens Vyberg
- Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Pathology, Aalborg University Hospital, Ladegaardsgade 3, Denmark
| | - Hans Erik Johnsen
- Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Sdr. Skovvej 15, Aalborg, Denmark
- Department of Haematology, Aalborg University Hospital, Hobrovej 18–22, Aalborg, Denmark
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182
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Inflammatory bowel disease is associated with an increased risk of inflammatory skin diseases: A population-based cross-sectional study. J Am Acad Dermatol 2017; 76:40-48. [DOI: 10.1016/j.jaad.2016.08.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 08/09/2016] [Accepted: 08/10/2016] [Indexed: 01/18/2023]
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183
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DPB, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:206-217.e2. [PMID: 27693347 PMCID: PMC5164948 DOI: 10.1053/j.gastro.2016.09.032] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10-8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10-6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B,PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David T Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Claire L Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee; Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan P Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Lisa W Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Antonio J Quiros
- Department of Pediatrics, Medical University of South Carolina, Pediatric Center for Inflammatory Bowel Disorders, Summerville, South Carolina
| | - Jenifer Seminerio
- Department of Gastroenterology, Medical University of South Carolina Digestive Disease Center, Charleston, South Carolina
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan S Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | - Robert N Baldassano
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine & Nursing, Baltimore, Maryland
| | - Raymond K Cross
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Lee A Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Tanvi A Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gerald W Dryden
- Department of Medicine, University of Louisville, Louisville, Kentucky
| | - John S Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, North Carolina
| | - Jason K Hou
- Department of Medicine, Baylor College of Medicine; Veterans Affairs Health Services Research and Development Service, Center for Innovations in Quality Effectiveness and Safety; Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Sunny Z Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, Louisiana
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, Connecticut
| | - Kim L Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Michael D Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, Ohio
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Barbara S Kirschner
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, Illinois
| | - John F Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, Virginia
| | - John H Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, New York
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | | | - Ashish S Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shehzad A Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida, Jacksonville, Florida
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan
| | - John D Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, Quebec, Canada
| | - Richard H Duerr
- Department of Medicine and Clinical and Translational Science Institute, School of Medicine and Department of Human Genetics, Graduate School of Public Health; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, Canada
| | - Judy H Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Personalized Medicine, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.
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184
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Franke A. Inflammatory Bowel Disease: A Global Disease That Needs a Broader Ensemble of Populations. Gastroenterology 2017; 152:14-16. [PMID: 27888668 DOI: 10.1053/j.gastro.2016.11.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany.
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185
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Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population. Sci Rep 2016; 6:39831. [PMID: 28008999 PMCID: PMC5180213 DOI: 10.1038/srep39831] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022] Open
Abstract
Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10−11 and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
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186
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Rico Y, Ethier DM, Davy CM, Sayers J, Weir RD, Swanson BJ, Nocera JJ, Kyle CJ. Spatial patterns of immunogenetic and neutral variation underscore the conservation value of small, isolated American badger populations. Evol Appl 2016; 9:1271-1284. [PMID: 27877205 PMCID: PMC5108218 DOI: 10.1111/eva.12410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 07/14/2016] [Indexed: 12/29/2022] Open
Abstract
Small and isolated populations often exhibit low genetic diversity due to drift and inbreeding, but may simultaneously harbour adaptive variation. We investigate spatial distributions of immunogenetic variation in American badger subspecies (Taxidea taxus), as a proxy for evaluating their evolutionary potential across the northern extent of the species' range. We compared genetic structure of 20 microsatellites and the major histocompatibility complex (MHC DRB exon 2) to evaluate whether small, isolated populations show low adaptive polymorphism relative to large and well-connected populations. Our results suggest that gene flow plays a prominent role in shaping MHC polymorphism across large spatial scales, while the interplay between gene flow and selection was stronger towards the northern peripheries. The similarity of MHC alleles within subspecies relative to their neutral genetic differentiation suggests that adaptive divergence among subspecies can be maintained despite ongoing gene flow along subspecies boundaries. Neutral genetic diversity was low in small relative to large populations, but MHC diversity within individuals was high in small populations. Despite reduced neutral genetic variation, small and isolated populations harbour functional variation that likely contribute to the species evolutionary potential at the northern range. Our findings suggest that conservation approaches should focus on managing adaptive variation across the species range rather than protecting subspecies per se.
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Affiliation(s)
- Yessica Rico
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
- Present address: CONACYTInstituto de Ecología A.C.Centro Regional del BajíoAvenida Lázaro Cárdenas 253PátzcuaroMichoacán61600México
| | - Danielle M. Ethier
- Ontario Badger ProjectGuelphONCanada
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Christina M. Davy
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
| | | | - Richard D. Weir
- Ecosystems Protection & Sustainability BranchMinistry of EnvironmentVictoriaBCCanada
| | | | - Joseph J. Nocera
- Wildlife Research and Monitoring SectionMinistry of Natural Resources & ForestryPeterboroughONCanada
| | - Christopher J. Kyle
- Forensic Science DepartmentTrent UniversityPeterboroughONCanada
- Natural Resources DNA Profiling and Forensics CentreTrent UniversityPeterboroughONCanada
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187
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Lichtenstein GR, McGovern DPB. Using Markers in IBD to Predict Disease and Treatment Outcomes: Rationale and a Review of Current Status. ACTA ACUST UNITED AC 2016. [DOI: 10.1038/ajgsup.2016.17] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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188
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189
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Egeberg A, Weinstock LB, Thyssen EP, Gislason GH, Thyssen JP. Rosacea and gastrointestinal disorders: a population-based cohort study. Br J Dermatol 2016; 176:100-106. [PMID: 27501017 DOI: 10.1111/bjd.14930] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND Rosacea is a common inflammatory facial skin condition. Recent genetic and epidemiological studies have suggested pathogenic links between rosacea and gastrointestinal disorders, but data are limited. OBJECTIVES The objective was to investigate the association between rosacea and coeliac disease (CeD), Crohn disease (CD), ulcerative colitis (UC), Helicobacter pylori infection (HPI), small intestinal bacterial overgrowth (SIBO) and irritable bowel syndrome (IBS), respectively. METHODS We performed a nationwide cohort study. A total of 49 475 patients with rosacea and 4 312 213 general population controls were identified using nationwide administrative registers. We established the prevalence of the aforementioned disorders, and used Cox regression analysis to obtain hazard ratios (HRs) of the risk of new-onset CeD, CD, UC, HPI, SIBO and IBS, respectively, in patients with rosacea. RESULTS The prevalence of CeD, CD, UC, HPI, SIBO and IBS, respectively, was higher among patients with rosacea when compared with the control subjects. Adjusted HRs revealed significant associations between rosacea and CeD (HR 1·46, 1·11-1·93), CD (HR 1·45, 1·19-1·77), UC (HR 1·19, 1·02-1·39), and IBS (HR 1·34, 1·19-1·50), respectively, but not HPI (HR 1·04, 0·96-1·13) or SIBO (HR 0·71, 0·18-1·86). CONCLUSIONS Rosacea is associated with certain gastrointestinal diseases, but the possible pathogenic link is unknown. Gastrointestinal complaints in patients with rosacea should warrant clinical suspicion of disease.
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Affiliation(s)
- A Egeberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Kildegårdsvej 28, 2900, Hellerup, Denmark
| | - L B Weinstock
- Department of Gastroenterology, Washington University School of Medicine, St Louis, MO, U.S.A
| | - E P Thyssen
- Department of Gastroenterology, Washington University School of Medicine, St Louis, MO, U.S.A
| | - G H Gislason
- Department of Cardiology, Herlev and Gentofte Hospital, Kildegårdsvej 28, 2900, Hellerup, Denmark.,The Danish Heart Foundation, DK-1127, Copenhagen, Denmark.,The National Institute of Public Health, University of Southern Denmark, DK-1353, Copenhagen, Denmark
| | - J P Thyssen
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Kildegårdsvej 28, 2900, Hellerup, Denmark
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190
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Ye BD, McGovern DP. Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility. Expert Rev Clin Immunol 2016; 12:1091-107. [PMID: 27156530 PMCID: PMC5083126 DOI: 10.1080/1744666x.2016.1184972] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epidemiological and clinical studies have suggested that the pathogenesis of inflammatory bowel disease (IBD) is strongly influenced by genetic predisposition. Beyond the limitations of linkage analysis, multiple genome-wide association studies, their meta-analyses, and targeted genotyping array techniques have broadened our understanding of the genetic architecture of IBD. Currently, over 200 single nucleotide polymorphisms are known to be associated with susceptibility to IBD and through functional analysis of genes and loci, a substantial proportion of pathophysiologic mechanisms have been revealed. However, because only a modest fraction of predicted heritability can be explained by known genes/loci, additional strategies are needed including the identification of rare variants with large effect sizes to help explain the missing heritability. Considerable progress is also being made on applying outcomes of genetic research in diagnostics, classification, prognostics, and the development of new therapeutics of IBD.
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Affiliation(s)
- Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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191
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Kopylov U, Boucher G, Waterman M, Rivers CR, Patel M, Cho JH, Colombel JF, Duerr RH, Binion D, McGovern DP, Schumm PP, Brant SR, Silverberg MS, Rioux JD, Bitton A. Genetic Predictors of Benign Course of Ulcerative Colitis-A North American Inflammatory Bowel Disease Genetics Consortium Study. Inflamm Bowel Dis 2016; 22:2311-6. [PMID: 27575496 PMCID: PMC5098421 DOI: 10.1097/mib.0000000000000913] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND A subset of patients with ulcerative colitis (UC) have a benign course and an overall favorable prognosis. Early identification of these low-risk patients may allow for a less aggressive therapeutic approach and possible reduction of therapy-associated risks. The aim of this project was to identify the genetic predictors of benign UC phenotype. METHODS UC patients were selected from the National Institute of Diabetes and Digestive and Kidney Diseases Inflammatory Bowel Disease Genetics Consortium. Benign phenotype was defined as no need for immunomodulatory or biological therapy, hospitalizations, or colectomy. The association between benign UC phenotype and known loci linked to the risk of inflammatory bowel disease (IBD) was evaluated. The results for 156 index single-nucleotide polymorphisms (SNPs) from the known IBD loci were extracted for the main analysis. The association of the benign phenotype to a genetic burden score was also evaluated. RESULTS None of the index SNPs from the IBD loci reached the predefined threshold of 1 × 10. In the exploratory analysis of the remaining Immunochip SNPs and imputed major histocompatibility complex data, 5 distinct suggestive association signals are identified (rs1697950, rs2523639, rs17836409, rs11742854, and rs75001121). CONCLUSIONS No SNPs from IBD susceptibility loci were found to be associated (at our predefined threshold of 1 × 10) with a benign UC disease course. The rs11742570 variant on chromosome 5 was the one with the greatest association to benign disease although the association did not reach the predefined significant threshold. Given the modest power of our study, the findings suggested on the exploratory analysis merit extension to larger discovery cohorts.
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Affiliation(s)
- Uri Kopylov
- McGill University Health Centre, Division of Gastroenterology, Montreal, Quebec, Canada
| | - Gabrielle Boucher
- Montreal Heart Institute, Montreal, Quebec, Canada,Université de Montréal, Montreal, Quebec, Canada
| | - Matti Waterman
- Mount Sinai Hospital, Division of Gastroenterology, Toronto, Ontario, Canada
| | - Claudia Ramos Rivers
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Pittsburgh, PA, USA
| | - Mohini Patel
- Yale University, Section of Digestive Diseases, New Haven, CT, USA
| | - Judy H. Cho
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York,Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jean Frederic Colombel
- Department of Medicine, Division of Gastroenterology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Richard H. Duerr
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Pittsburgh, PA, USA
| | - David Binion
- University of Pittsburgh School of Medicine, Division of Gastroenterology, Pittsburgh, PA, USA
| | - Dermot P.B McGovern
- Translational Genomics Group, F. Widjaja Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | | | - Steven R. Brant
- Meyerhoff Inflammatory Bowel Diseases Center, Division of Gastroenterology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Mark S. Silverberg
- Mount Sinai Hospital, Division of Gastroenterology, Toronto, Ontario, Canada
| | - John D. Rioux
- Montreal Heart Institute, Montreal, Quebec, Canada,Université de Montréal, Montreal, Quebec, Canada
| | - Alain Bitton
- McGill University Health Centre, Division of Gastroenterology, Montreal, Quebec, Canada
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Calderón-Gómez E, Bassolas-Molina H, Mora-Buch R, Dotti I, Planell N, Esteller M, Gallego M, Martí M, Garcia-Martín C, Martínez-Torró C, Ordás I, Singh S, Panés J, Benítez-Ribas D, Salas A. Commensal-Specific CD4(+) Cells From Patients With Crohn's Disease Have a T-Helper 17 Inflammatory Profile. Gastroenterology 2016; 151:489-500.e3. [PMID: 27267052 DOI: 10.1053/j.gastro.2016.05.050] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 05/27/2016] [Accepted: 05/29/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Crohn's disease (CD) has been associated with an altered immune response to commensal microbiota, mostly based on increased seroreactivity to microbial proteins. Although T cells are believed to contribute to the development of CD, little is known about the antigens involved. We investigated the antigen-specificity of T cells isolated from patients with CD. METHODS We isolated peripheral blood mononuclear cells from 65 patients with CD and 45 healthy individuals (controls). We investigated T-cell reactivity to commensal microbial antigens using proliferation assays (based on thymidine incorporation and carboxyfluorescein succinimidyl ester dilution). Gene expression patterns were determined using microarray and real-time polymerase chain reaction analyses. Cytokines, chemokines, and antibodies were measured by enzyme-linked immunosorbent assay, flow cytometry, or multiplex cytokine assays. Intestinal crypts were obtained from surgical resection specimens of 7 individuals without inflammatory bowel disease. We examined the effects of commensal-specific CD4(+) T cells on primary intestinal epithelial cells from these samples. RESULTS The bacterial proteins FlaX, A4-fla2, and YidX increased proliferation of CD4(+) T cells isolated from peripheral blood of patients with CD compared with controls. In blood samples from controls, CD4(+) T cells specific for FlaX, A4-fla2, or YidX had a T-helper (Th)1 phenotype; a larger proportion of CD4(+) T cells specific for these proteins in patients with CD had a Th17 phenotype or produced Th1 and Th17 cytokines. When supernatants collected from commensal-specific CD4(+) T cells from patients with CD were applied to healthy intestinal epithelial cells, the epithelial cells increased the expression of the chemokine (C-X-C motif) ligand 1 (CXCL1), CXCL8 and the CC chemokine ligand 20 (CCL20). CONCLUSIONS A larger proportion of commensal-specific CD4(+) T cells from patients with CD have a Th17 phenotype or produce Th1 and Th17 cytokines, compared with T cells from controls; this might contribute to intestinal inflammation in patients with CD. These cells might be targeted for treatment of CD. The transcriptional data of commensal-specific CD4(+) T cells from healthy individuals and CD patients have been deposited in the Gene Expression Omnibus at the National Center for Biotechnology Information (accession no: GSE70469).
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Affiliation(s)
- Elisabeth Calderón-Gómez
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Helena Bassolas-Molina
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Rut Mora-Buch
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Isabella Dotti
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Núria Planell
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain; Bioinformatics Platform, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Míriam Esteller
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Marta Gallego
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Mercè Martí
- Laboratory of Cellular Immunology, Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Carme Garcia-Martín
- Laboratory of Cellular Immunology, Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Carlos Martínez-Torró
- Laboratory of Cellular Immunology, Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, Barcelona, Spain
| | - Ingrid Ordás
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Sharat Singh
- Department of Research and Development, Prometheus Laboratories, San Diego, California
| | - Julian Panés
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Daniel Benítez-Ribas
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Azucena Salas
- Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain.
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193
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Bek S, Nielsen JV, Bojesen AB, Franke A, Bank S, Vogel U, Andersen V. Systematic review: genetic biomarkers associated with anti-TNF treatment response in inflammatory bowel diseases. Aliment Pharmacol Ther 2016; 44:554-67. [PMID: 27417569 PMCID: PMC5113857 DOI: 10.1111/apt.13736] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 03/20/2016] [Accepted: 06/29/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND Personalised medicine, including biomarkers for treatment selection, may provide new algorithms for more effective treatment of patients. Genetic variation may impact drug response and genetic markers could help selecting the best treatment strategy for the individual patient. AIM To identify polymorphisms and candidate genes from the literature that are associated with anti-tumour necrosis factor (TNF) treatment response in patients with inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis. METHODS We performed a PubMed literature search and retrieved studies reporting original data on association between polymorphisms and anti-TNF treatment response and conducted a meta-analysis. RESULTS A functional polymorphism in FCGR3A was significantly associated with anti-TNF treatment response among CD patients using biological response criterion (decrease in C-reactive protein, levels). Meta-analyses showed that polymorphisms in TLR2 (rs3804099, OR (95% CI) = 2.17 (1.35-3.47)], rs11938228 [OR = 0.64 (0.43-0.96)], TLR4 (rs5030728) [OR = 3.18 (1.63-6.21)], TLR9 (rs352139) [OR = 0.43 (0.21-0.88)], TNFRSF1A (rs4149570) [OR = 2.06 (1.02-4.17)], IFNG (rs2430561) [OR = 1.66 (1.05-2.63)], IL6 (rs10499563) [OR = 1.65 (1.04-2.63)] and IL1B (rs4848306) [OR = 1.88 (1.05-3.35)] were significantly associated with response among IBD patients using clinical response criteria. A positive predictive value of 0.96 was achieved by combining five genetic markers in an explorative analysis. CONCLUSIONS There are no genetic markers currently available which are adequately predictive of anti-TNF response for use in the clinic. Genetic markers bear the advantage that they do not change over time. Therefore, hypothesis-free approaches, testing a large number of polymorphisms in large, well-characterised cohorts, are required in order to identify genetic profiles with larger effect sizes, which could be employed as biomarkers for treatment selection in clinical settings.
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Affiliation(s)
- S. Bek
- Molecular and Diagnostic Research UnitHospital of Southern JutlandAabenraaDenmark
| | - J. V. Nielsen
- Molecular and Diagnostic Research UnitHospital of Southern JutlandAabenraaDenmark
| | - A. B. Bojesen
- Research Unit for E‐mental HealthMental Health Services in the Region of Southern OdenseOdenseDenmark
| | - A. Franke
- Institute of Clinical Molecular BiologyChristian‐Albrechts‐University of KielKielGermany
| | - S. Bank
- Molecular and Diagnostic Research UnitHospital of Southern JutlandAabenraaDenmark
| | - U. Vogel
- National Research Centre for the Working EnvironmentCopenhagenDenmark
| | - V. Andersen
- Molecular and Diagnostic Research UnitHospital of Southern JutlandAabenraaDenmark,Institute of Molecular MedicineUniversity of Southern DenmarkOdenseDenmark,Institute of Regional Health ResearchUniversity of Southern DenmarkOdenseDenmark,OPENUniversity of Southern DenmarkOdenseDenmark
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Pouget JG, Gonçalves VF, Spain SL, Finucane HK, Raychaudhuri S, Kennedy JL, Knight J. Genome-Wide Association Studies Suggest Limited Immune Gene Enrichment in Schizophrenia Compared to 5 Autoimmune Diseases. Schizophr Bull 2016; 42:1176-84. [PMID: 27242348 PMCID: PMC4988748 DOI: 10.1093/schbul/sbw059] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
There has been intense debate over the immunological basis of schizophrenia, and the potential utility of adjunct immunotherapies. The major histocompatibility complex is consistently the most powerful region of association in genome-wide association studies (GWASs) of schizophrenia and has been interpreted as strong genetic evidence supporting the immune hypothesis. However, global pathway analyses provide inconsistent evidence of immune involvement in schizophrenia, and it remains unclear whether genetic data support an immune etiology per se. Here we empirically test the hypothesis that variation in immune genes contributes to schizophrenia. We show that there is no enrichment of immune loci outside of the MHC region in the largest genetic study of schizophrenia conducted to date, in contrast to 5 diseases of known immune origin. Among 108 regions of the genome previously associated with schizophrenia, we identify 6 immune candidates (DPP4, HSPD1, EGR1, CLU, ESAM, NFATC3) encoding proteins with alternative, nonimmune roles in the brain. While our findings do not refute evidence that has accumulated in support of the immune hypothesis, they suggest that genetically mediated alterations in immune function may not play a major role in schizophrenia susceptibility. Instead, there may be a role for pleiotropic effects of a small number of immune genes that also regulate brain development and plasticity. Whether immune alterations drive schizophrenia progression is an important question to be addressed by future research, especially in light of the growing interest in applying immunotherapies in schizophrenia.
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Affiliation(s)
- Jennie G. Pouget
- *To whom correspondence should be addressed; Centre for Addiction and Mental Health, 250 College Street, Toronto, Ontario M5T 1R8, Canada; tel: 416-535-8501, fax: 416-979-4666, e-mail:
| | - Vanessa F. Gonçalves
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada;,Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | | | - Sarah L. Spain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK;,Division of Genetics and Molecular Medicine, King’s College London, London, UK
| | - Hilary K. Finucane
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA;,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA
| | | | | | - Jo Knight
- Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada;,Lancaster Medical School and Data Science Institute, Lancaster University, Lancaster, UK
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Anti-Inflammatory Effects of Hyperbaric Oxygenation during DSS-Induced Colitis in BALB/c Mice Include Changes in Gene Expression of HIF-1α, Proinflammatory Cytokines, and Antioxidative Enzymes. Mediators Inflamm 2016; 2016:7141430. [PMID: 27656047 PMCID: PMC5021505 DOI: 10.1155/2016/7141430] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 07/08/2016] [Accepted: 07/12/2016] [Indexed: 12/21/2022] Open
Abstract
Reactive oxygen species (ROS) and nitrogen species have an indispensable role in regulating cell signalling pathways, including transcriptional control via hypoxia inducible factor-1α (HIF-1α). Hyperbaric oxygenation treatment (HBO2) increases tissue oxygen content and leads to enhanced ROS production. In the present study DSS-induced colitis has been employed in BALB/c mice as an experimental model of gut mucosa inflammation to investigate the effects of HBO2 on HIF-1α, antioxidative enzyme, and proinflammatory cytokine genes during the colonic inflammation. Here we report that HBO2 significantly reduces severity of DSS-induced colitis, as evidenced by the clinical features, histological assessment, impaired immune cell expansion and mobilization, and reversal of IL-1β, IL-2, and IL-6 gene expression. Gene expression and antioxidative enzyme activity were changed by the HBO2 and the inflammatory microenvironment in the gut mucosa. Strong correlation of HIF-1α mRNA level to GPx1, SOD1, and IL-6 mRNA expression suggests involvement of HIF-1α in transcriptional regulation of these genes during colonic inflammation and HBO2. This is further confirmed by a strong correlation of HIF-1α with known target genes VEGF and PGK1. Results demonstrate that HBO2 has an anti-inflammatory effect in DSS-induced colitis in mice, and this effect is at least partly dependent on expression of HIF-1α and antioxidative genes.
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196
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Abstract
BACKGROUND Distinct CD8+ T-cell subsets such as interleukin-17-expressing Tc17 and Foxp3-expressing Tcreg are functionally similar to CD4+ T cells. Though CD4+ T cells are dysregulated in patients with inflammatory bowel disease (IBD), CD8+ T cells are not well investigated. Vitamin D is an environmental factor which influences T-cell subsets. We assessed the prevalence of CD8+ T-cell subsets among peripheral blood mononuclear cells (PBMC) and lamina propria mononuclear cells (LPMC) of patients with Crohn's disease, patients with ulcerative colitis, and healthy controls. We then tested the effect of 1α,25-dihydroxyvitamin D3 on CD8+ T-cell subsets. METHODS A total of 73 patients with Crohn's disease, 49 patients with ulcerative colitis, and 47 healthy controls were studied. LPMC or PBMC were isolated and flow cytometry was performed. CD3+ T cells, isolated from PBMC, were cultured with or without 1α,25-dihydroxyvitamin D3, before flow cytometry. RESULTS In LPMC, the prevalence of Tcreg was higher in patients with IBD (P < 0.05), whereas Tc17 were higher in patients with ulcerative colitis compared with patients with Crohn's disease and healthy controls (P < 0.05). In PBMC, both Tcreg and Tc17 were higher in patients with IBD (P < 0.01). Double-expressing interferon-γ+ interleukin-17+ and Foxp3+ interleukin-17+ CD8+ T cells were also identified indicating possible CD8+ plasticity. 1α,25-dihydroxyvitamin D3 decreased interferon-γ-expressing Tc1 (P < 0.05), but had no effect on Tc17 or Tcreg. CONCLUSIONS The prevalence of novel CD8+ T-cell subsets is altered in patients with IBD. Double-expressing cells indicate plasticity and were identified in patients with IBD. Vitamin D may have a limited effect on CD8+ T cells by decreasing interferon-γ expression.
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197
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Verstockt B, Cleynen I. Genetic Influences on the Development of Fibrosis in Crohn's Disease. Front Med (Lausanne) 2016; 3:24. [PMID: 27303667 PMCID: PMC4885006 DOI: 10.3389/fmed.2016.00024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022] Open
Abstract
Fibrostenotic strictures are an important complication in patients with Crohn’s disease (CD), very often necessitating surgery. This fibrotic process develops in a genetically susceptible individual and is influenced by an interplay with environmental, immunological, and disease-related factors. A deeper understanding of the genetic factors driving this fibrostenotic process might help to unravel the pathogenesis, and ultimately lead to development of new, anti-fibrotic therapy. Here, we review the genetic factors that have been associated with the development of fibrosis in patients with CD, as well as their potential pathophysiological mechanism(s). We also hypothesize on clinical implications, if any, and future research directions.
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Affiliation(s)
- Bram Verstockt
- Department of Medicine and Cambridge Institute for Medical Research, University of Cambridge School of Clinical Medicine, Cambridge, UK; Translational Research in Gastrointestinal Disorders (TARGID), Department of Clinical and Experimental Medicine, KU Leuven, Leuven, Belgium
| | - Isabelle Cleynen
- Laboratory of Complex Genetics, Department of Human Genetics, KU Leuven , Leuven , Belgium
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198
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Abstract
We are currently in an exciting time when our understanding of genetic underpinnings of inflammatory bowel disease (IBD) has undergone a revolution, based in large part on novel genotyping and sequencing technologies. With >160 susceptible loci identified for IBD, the goal is now to understand at a fundamental level the function of these susceptibility alleles. Determining the clinical relevance of how these susceptible genes shape the development of IBD is also a high priority. The main challenge is to understand how the environment and microbiome play a role in triggering disease in genetically susceptible individuals, as the interactions may be complex. To advance the field, novel in vitro and mouse models that are designed to interrogate complex genetics and functionally test hypotheses are needed. Ultimately, the goal of genetics studies will be to translate genetics to patients with IBD and improve their care.
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Affiliation(s)
- Ta-Chiang Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110;
| | - Thaddeus S Stappenbeck
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110;
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Wei WH, Bowes J, Plant D, Viatte S, Yarwood A, Massey J, Worthington J, Eyre S. Major histocompatibility complex harbors widespread genotypic variability of non-additive risk of rheumatoid arthritis including epistasis. Sci Rep 2016; 6:25014. [PMID: 27109064 PMCID: PMC4842957 DOI: 10.1038/srep25014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/08/2016] [Indexed: 11/10/2022] Open
Abstract
Genotypic variability based genome-wide association studies (vGWASs) can identify potentially interacting loci without prior knowledge of the interacting factors. We report a two-stage approach to make vGWAS applicable to diseases: firstly using a mixed model approach to partition dichotomous phenotypes into additive risk and non-additive environmental residuals on the liability scale and secondly using the Levene's (Brown-Forsythe) test to assess equality of the residual variances across genotype groups per marker. We found widespread significant (P < 2.5e-05) vGWAS signals within the major histocompatibility complex (MHC) across all three study cohorts of rheumatoid arthritis. We further identified 10 epistatic interactions between the vGWAS signals independent of the MHC additive effects, each with a weak effect but jointly explained 1.9% of phenotypic variance. PTPN22 was also identified in the discovery cohort but replicated in only one independent cohort. Combining the three cohorts boosted power of vGWAS and additionally identified TYK2 and ANKRD55. Both PTPN22 and TYK2 had evidence of interactions reported elsewhere. We conclude that vGWAS can help discover interacting loci for complex diseases but require large samples to find additional signals.
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Affiliation(s)
- Wen-Hua Wei
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - John Bowes
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Darren Plant
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Sebastien Viatte
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Annie Yarwood
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jonathan Massey
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jane Worthington
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Stephen Eyre
- Arthritis Research UK Centre for Genetics and Genomics, Institute of Inflammation and Repair, Faculty of Medical and Human Sciences, Manchester Academic Health Science Centre, University of Manchester, Oxford Road, Manchester M13 9PT, UK.,NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
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Abstract
BACKGROUND A dysregulated mucosal immune response to the intestinal environment in a genetically susceptible host is hypothesized to be critical to the pathogenesis of Crohn's disease (CD). Therefore, we examined CD-susceptibility genes involved in the immune response through a genome-wide association study and consecutive genotyping of human leukocyte antigens (HLAs) and killer cell immunoglobulin-like receptors. METHODS An initial genome-wide association study was performed with 275 CD patients and 2369 controls from a Korean population. To validate the loci identified in the genome-wide association study, replication genotyping was performed in a different cohort of 242 CD patients and 1066 controls. Finally, high-resolution genotyping of HLA and killer cell immunoglobulin-like receptor was performed. RESULTS Four susceptibility loci, a promoter region in tumor necrosis factor (ligand) superfamily member (TNFSF15) and 3 independent regions in HLAs, showed significant associations with CD. Among them, rs114985235 in the intergenic region between HLA-B and HLA-C showed the strongest association, with an increased risk of CD (P = 8.71 × 10; odds ratio, 2.25). HLA typing in this region showed HLA-C*01 to be responsible for the association of CD among 43 HLA-B and HLA-C genotypes identified in the Korean population. However, the interaction of HLA-C with killer cell immunoglobulin-like receptor had little effect on the development of CD. CONCLUSIONS We newly identified HLA-C*01 as a prominent CD-susceptibility HLA allotype in the Korean population. In addition, these results confirm that genetic variations in immune response genes, such as HLAs and TNFSF15, are important host factors for the pathogenesis of CD.
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