101
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Niehrs A, Altfeld M. Regulation of NK-Cell Function by HLA Class II. Front Cell Infect Microbiol 2020; 10:55. [PMID: 32133304 PMCID: PMC7040486 DOI: 10.3389/fcimb.2020.00055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 01/31/2020] [Indexed: 12/11/2022] Open
Abstract
Natural Killer (NK) cells were initially described as part of the innate immune system and characterized by their ability to lyse malignant and virus-infected cells. The cytolytic function of NK cells is tightly controlled by activating and inhibitory receptors expressed on the cell surface. Ligands that interact with a variety of NK-cell receptors include the human leukocyte antigen (HLA) molecules, and the regulation of NK-cell function by HLA class I molecules is well-established. Earlier studies also suggested a role of HLA class II molecules in regulating NK cell activity; yet, interactions between HLA class II molecules and NK cell receptors have not been well-characterized. We recently identified a subset of HLA-DP molecules that can serve as ligands for the natural cytotoxicity receptor NKp44 and activate NK cells. This novel receptor-ligand interaction provides a potential mechanism to explain the strong associations of HLA-DP molecules with HBV infection outcomes, graft-vs.-host disease and inflammatory bowel disease. Furthermore, it adds a new mechanism for NK-cell crosstalk with immune cells expressing HLA class II molecules. In this perspective article, we discuss the potential implications of NK cell receptor interactions with HLA class II molecules for the regulation of immune responses.
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Affiliation(s)
- Annika Niehrs
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.,Institute for Immunology, Universitätsklinikum Hamburg Eppendorf, Hamburg, Germany
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102
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Lindholm CR, Siegel CA. Are We Ready to Include Prognostic Factors in Inflammatory Bowel Disease Trials? Curr Pharm Des 2020; 25:64-68. [PMID: 30864506 DOI: 10.2174/1381612825666190312113935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/06/2019] [Indexed: 12/24/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease characterized by periodic episodes of flares and remission. Treatment is aimed at healing the bowel, to ultimately decrease hospitalization rates, need for surgeries and overall disability. In more recent years, treatment has transitioned from a reactive approach to a more proactive approach focusing on treating disease earlier and preventing complications. The challenge lies in identifying patients who need more intensive treatment early and trying to determine who will respond to which medications. Biomarkers and clinical activity scoring systems can be used to help guide treatment decisions. However, IBDs are very heterogeneous and the significance of these biomarkers can be difficult to discern on an individual basis. Recently, prognostic tools have been developed to aid in determining a patient's prognosis as well as their likelihood to respond to different therapies. Despite this progress, clinical trials have not routinely adopted this approach in their study design. Tools for stratification of disease severity and to personalize treatment choices have the potential to improve our studies both by enriching the patient population and further guiding clinical decision making in practice. This review aims to discuss biomarkers, current prognosticating tools, tools that determine response to therapy and how incorporating these into clinical trials will be beneficial.
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Affiliation(s)
- Christopher R Lindholm
- Dartmouth Hitchcock Medical Center, Department of Medicine, Lebanon, NH 03766, United States
| | - Corey A Siegel
- Dartmouth Hitchcock Medical Center, Section of Gastroenterology and Hepatology, Lebanon, NH 03756, United States
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103
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Degenhardt F, Wendorff M, Wittig M, Ellinghaus E, Datta LW, Schembri J, Ng SC, Rosati E, Hübenthal M, Ellinghaus D, Jung ES, Lieb W, Abedian S, Malekzadeh R, Cheon JH, Ellul P, Sood A, Midha V, Thelma BK, Wong SH, Schreiber S, Yamazaki K, Kubo M, Boucher G, Rioux JD, Lenz TL, Brant SR, Franke A. Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles. Hum Mol Genet 2020; 28:2078-2092. [PMID: 30590525 PMCID: PMC6548229 DOI: 10.1093/hmg/ddy443] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/16/2022] Open
Abstract
Genotype imputation of the human leukocyte antigen (HLA) region is a cost-effective means to infer classical HLA alleles from inexpensive and dense SNP array data. In the research setting, imputation helps avoid costs for wet lab-based HLA typing and thus renders association analyses of the HLA in large cohorts feasible. Yet, most HLA imputation reference panels target Caucasian ethnicities and multi-ethnic panels are scarce. We compiled a high-quality multi-ethnic reference panel based on genotypes measured with Illumina’s Immunochip genotyping array and HLA types established using a high-resolution next generation sequencing approach. Our reference panel includes more than 1,300 samples from Germany, Malta, China, India, Iran, Japan and Korea and samples of African American ancestry for all classical HLA class I and II alleles including HLA-DRB3/4/5. Applying extensive cross-validation, we benchmarked the imputation using the HLA imputation tool HIBAG, our multi-ethnic reference and an independent, previously published data set compiled of subpopulations of the 1000 Genomes project. We achieved average imputation accuracies higher than 0.924 for the commonly studied HLA-A, -B, -C, -DQB1 and -DRB1 genes across all ethnicities. We investigated allele-specific imputation challenges in regard to geographic origin of the samples using sensitivity and specificity measurements as well as allele frequencies and identified HLA alleles that are challenging to impute for each of the populations separately. In conclusion, our new multi-ethnic reference data set allows for high resolution HLA imputation of genotypes at all classical HLA class I and II genes including the HLA-DRB3/4/5 loci based on diverse ancestry populations.
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Affiliation(s)
- Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Wittig
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eva Ellinghaus
- K.G. Jebsen Inflammation Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Lisa W Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John Schembri
- Division of Gastroenterology, Mater Dei Hospital, Msida MSD, Malta
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Elisa Rosati
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Eun Suk Jung
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Wolfgang Lieb
- Biobank PopGen and Institute of Epidemiology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Shifteh Abedian
- Department of Epidemiology, University Medical Center Groningen, RB Groningen, The Netherlands.,Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Jae Hee Cheon
- Department of Internal Medicine and Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Pierre Ellul
- Division of Gastroenterology, Mater Dei Hospital, Msida MSD, Malta
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - Vandana Midha
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, Punjab, India.,Department of Medicine, Dayanand Medical College and Hospital, Ludhiana, Punjab, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Sunny H Wong
- Department of Medicine and Therapeutics, Institute of Digestive Disease, LKS Institute of Health Science, State Key Laboratory of Digestive Disease, The Chinese University of Hong Kong, Hong Kong, China
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.,Department of Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN Yokohama Institute, Yokohama, Japan.,Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - John D Rioux
- Montreal Heart Institute, Research Center, Montréal, Québec, Canada.,Université de Montréal Department of Medicine, Montréal, Québec, Canada
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Steven R Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Medicine, Rutgers Robert Wood Johnson Medical School and Department of Genetics, Rutgers University, New Brunswick and Piscataway, NJ, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
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104
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Zorro MM, Aguirre-Gamboa R, Mayassi T, Ciszewski C, Barisani D, Hu S, Weersma RK, Withoff S, Li Y, Wijmenga C, Jabri B, Jonkers IH. Tissue alarmins and adaptive cytokine induce dynamic and distinct transcriptional responses in tissue-resident intraepithelial cytotoxic T lymphocytes. J Autoimmun 2020; 108:102422. [PMID: 32033836 PMCID: PMC7049906 DOI: 10.1016/j.jaut.2020.102422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
The respective effects of tissue alarmins interleukin (IL)-15 and interferon beta (IFNβ), and IL-21 produced by T cells on the reprogramming of cytotoxic T lymphocytes (CTLs) that cause tissue destruction in celiac disease is poorly understood. Transcriptomic and epigenetic profiling of primary intestinal CTLs showed massive and distinct temporal transcriptional changes in response to tissue alarmins, while the impact of IL-21 was limited. Only anti-viral pathways were induced in response to all the three stimuli, albeit with differences in dynamics and strength. Moreover, changes in gene expression were primarily independent of changes in H3K27ac, suggesting that other regulatory mechanisms drive the robust transcriptional response. Finally, we found that IL-15/IFNβ/IL-21 transcriptional signatures could be linked to transcriptional alterations in risk loci for complex immune diseases. Together these results provide new insights into molecular mechanisms that fuel the activation of CTLs under conditions that emulate the inflammatory environment in patients with autoimmune diseases.
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Affiliation(s)
- Maria Magdalena Zorro
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Raul Aguirre-Gamboa
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Toufic Mayassi
- Department of Medicine, University of Chicago, Chicago, USA; Committee on Immunology, University of Chicago, Chicago, USA
| | | | | | - Shixian Hu
- Department of Gastroenterology and Hepatology, University Medical Center, Groningen, University of Groningen, Groningen, the Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University Medical Center, Groningen, University of Groningen, Groningen, the Netherlands
| | - Sebo Withoff
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Yang Li
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands; Department of Computational Biology for Individualised Infection Medicine, Centre for Individualised Infection Medicine, Helmholtz Centre for Infection Research, Hannover Medical School. Hannover, Germany
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway
| | - Bana Jabri
- Department of Medicine, University of Chicago, Chicago, USA; Committee on Immunology, University of Chicago, Chicago, USA.
| | - Iris H Jonkers
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands; K.G. Jebsen Coeliac Disease Research Centre, Department of Immunology, University of Oslo, Oslo, Norway.
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105
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Graham DB, Xavier RJ. Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature 2020; 578:527-539. [PMID: 32103191 PMCID: PMC7871366 DOI: 10.1038/s41586-020-2025-2] [Citation(s) in RCA: 363] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022]
Abstract
Inflammatory bowel disease (IBD) is a complex genetic disease that is instigated and amplified by the confluence of multiple genetic and environmental variables that perturb the immune-microbiome axis. The challenge of dissecting pathological mechanisms underlying IBD has led to the development of transformative approaches in human genetics and functional genomics. Here we describe IBD as a model disease in the context of leveraging human genetics to dissect interactions in cellular and molecular pathways that regulate homeostasis of the mucosal immune system. Finally, we synthesize emerging insights from multiple experimental approaches into pathway paradigms and discuss future prospects for disease-subtype classification and therapeutic intervention.
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Affiliation(s)
- Daniel B. Graham
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Corresponding authors. ,
| | - Ramnik J. Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Department of Molecular Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA, USA.,Corresponding authors. ,
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106
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Okabayashi S, Kobayashi T, Hibi T. Inflammatory Bowel Disease in Japan-Is It Similar to or Different from Westerns? J Anus Rectum Colon 2020; 4:1-13. [PMID: 32002471 PMCID: PMC6989123 DOI: 10.23922/jarc.2019-003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 07/08/2019] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis and Crohn's disease, the most common types of inflammatory bowel disease, are idiopathic, intractable disease characterized by chronic inflammation in the intestine. In recent years, studies elucidating the clinical characteristics of these diseases and basic researches have suggested that the diseases are induced by the immunological abnormalities through the involvement of environmental factors with their predisposition. In Japan, significant progress of basic and epidemiological researches has been developed for these diseases and the clinical guidelines have been established. However, no fundamental treatment for these diseases has been established yet. The current number of patients in Japan continues to increase, with at least 180,000 patients suffering from ulcerative colitis and 40,000 suffering from Crohn's disease. Thus, further studies are required to understand these diseases and improve medical treatments.
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Affiliation(s)
- Shinji Okabayashi
- Center for Advanced IBD Research and Treatment, Kitasato Institute Hospital, Kitasato University, Tokyo, Japan
| | - Taku Kobayashi
- Center for Advanced IBD Research and Treatment, Kitasato Institute Hospital, Kitasato University, Tokyo, Japan
| | - Toshifumi Hibi
- Center for Advanced IBD Research and Treatment, Kitasato Institute Hospital, Kitasato University, Tokyo, Japan
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107
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Abstract
PURPOSE OF REVIEW This article aims to review recent literature linking epithelial barrier inflammation and arthritis in spondyloarthritis (SpA), with a critical view on how they are bound by genetic, immunological and environmental ties. RECENT FINDINGS The epithelia-joint axis has become an intense area of both basic and clinical SpA research. The penultimate goal is to understand the immunopathologic links between epithelial inflammation and arthritis in SpA. Inflammatory bowel disease (IBD) and psoriasis (PsO) have strong links to SpA at several levels. Clinically, there is a strong association of IBD, PsO and SpA. Genetically, there are many shared risk factors; however, there are also distinct differences in the genetics of the respective diseases. Immunologically, type 3 immunity, especially interleukin (IL)-17 and IL-23 dysregulation, has been shown to play a central role in IBD, PsO and SpA. Environmentally, a microbial dysbiosis has been noted in each of these diseases, but whether the microbial signature is similar between diseases is not clear, nor is the effect of dysbiosis on the immune response known. SUMMARY It will be crucial to determine whether the relationship between epithelia inflammation and SpA is truly causal for both the understanding of pathogenesis and for future treatment strategies.
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108
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Sazonovs A, Kennedy NA, Moutsianas L, Heap GA, Rice DL, Reppell M, Bewshea CM, Chanchlani N, Walker GJ, Perry MH, McDonald TJ, Lees CW, Cummings JRF, Parkes M, Mansfield JC, Irving PM, Barrett JC, McGovern D, Goodhand JR, Anderson CA, Ahmad T. HLA-DQA1*05 Carriage Associated With Development of Anti-Drug Antibodies to Infliximab and Adalimumab in Patients With Crohn's Disease. Gastroenterology 2020; 158:189-199. [PMID: 31600487 DOI: 10.1053/j.gastro.2019.09.041] [Citation(s) in RCA: 232] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/24/2019] [Accepted: 09/29/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Anti-tumor necrosis factor (anti-TNF) therapies are the most widely used biologic drugs for treating immune-mediated diseases, but repeated administration can induce the formation of anti-drug antibodies. The ability to identify patients at increased risk for development of anti-drug antibodies would facilitate selection of therapy and use of preventative strategies. METHODS We performed a genome-wide association study to identify variants associated with time to development of anti-drug antibodies in a discovery cohort of 1240 biologic-naïve patients with Crohn's disease starting infliximab or adalimumab therapy. Immunogenicity was defined as an anti-drug antibody titer ≥10 AU/mL using a drug-tolerant enzyme-linked immunosorbent assay. Significant association signals were confirmed in a replication cohort of 178 patients with inflammatory bowel disease. RESULTS The HLA-DQA1*05 allele, carried by approximately 40% of Europeans, significantly increased the rate of immunogenicity (hazard ratio [HR], 1.90; 95% confidence interval [CI], 1.60-2.25; P = 5.88 × 10-13). The highest rates of immunogenicity, 92% at 1 year, were observed in patients treated with infliximab monotherapy who carried HLA-DQA1*05; conversely the lowest rates of immunogenicity, 10% at 1 year, were observed in patients treated with adalimumab combination therapy who did not carry HLA-DQA1*05. We confirmed this finding in the replication cohort (HR, 2.00; 95% CI, 1.35-2.98; P = 6.60 × 10-4). This association was consistent for patients treated with adalimumab (HR, 1.89; 95% CI, 1.32-2.70) or infliximab (HR, 1.92; 95% CI, 1.57-2.33), and for patients treated with anti-TNF therapy alone (HR, 1.75; 95% CI, 1.37-2.22) or in combination with an immunomodulator (HR, 2.01; 95% CI, 1.57-2.58). CONCLUSIONS In an observational study, we found a genome-wide significant association between HLA-DQA1*05 and the development of antibodies against anti-TNF agents. A randomized controlled biomarker trial is required to determine whether pretreatment testing for HLA-DQA1*05 improves patient outcomes by helping physicians select anti-TNF and combination therapies. ClinicalTrials.gov ID: NCT03088449.
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Affiliation(s)
| | - Nicholas A Kennedy
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | | | - Graham A Heap
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; AbbVie Inc, North Chicago, Illinois
| | - Daniel L Rice
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Claire M Bewshea
- Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Neil Chanchlani
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Gareth J Walker
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Mandy H Perry
- Department of Blood Science, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK
| | - Timothy J McDonald
- Department of Blood Science, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK
| | - Charlie W Lees
- Department of Gastroenterology, Western General Hospital, National Health Service Lothian, Edinburgh, UK
| | - J R Fraser Cummings
- Department of Gastroenterology, University Hospital Southampton National Health Service Foundation Trust, Southampton, UK; Faculty of Experimental Medicine, University of Southampton, Southampton, UK
| | - Miles Parkes
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - John C Mansfield
- Department of Gastroenterology, Newcastle Upon Tyne Hospitals National Health Service Foundation Trust, Newcastle upon Tyne, UK
| | - Peter M Irving
- Department of Gastroenterology, Guy's and St Thomas' NHS Foundation, Trust, London, UK
| | | | - Dermot McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - James R Goodhand
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK
| | - Carl A Anderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Tariq Ahmad
- Department of Gastroenterology, Royal Devon and Exeter Hospital National Health Service Foundation Trust, Exeter, UK; Exeter Inflammatory Bowel Disease and Pharmacogenetics Research Group, University of Exeter, Exeter, UK.
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109
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HLA and autoantibodies define scleroderma subtypes and risk in African and European Americans and suggest a role for molecular mimicry. Proc Natl Acad Sci U S A 2019; 117:552-562. [PMID: 31871193 PMCID: PMC6955366 DOI: 10.1073/pnas.1906593116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Systemic sclerosis (SSc) is a clinically heterogeneous autoimmune disease characterized by mutually exclusive autoantibodies directed against distinct nuclear antigens. We examined HLA associations in SSc and its autoantibody subsets in a large, newly recruited African American (AA) cohort and among European Americans (EA). In the AA population, the African ancestry-predominant HLA-DRB1*08:04 and HLA-DRB1*11:02 alleles were associated with overall SSc risk, and the HLA-DRB1*08:04 allele was strongly associated with the severe antifibrillarin (AFA) antibody subset of SSc (odds ratio = 7.4). These African ancestry-predominant alleles may help explain the increased frequency and severity of SSc among the AA population. In the EA population, the HLA-DPB1*13:01 and HLA-DRB1*07:01 alleles were more strongly associated with antitopoisomerase (ATA) and anticentromere antibody-positive subsets of SSc, respectively, than with overall SSc risk, emphasizing the importance of HLA in defining autoantibody subtypes. The association of the HLA-DPB1*13:01 allele with the ATA+ subset of SSc in both AA and EA patients demonstrated a transancestry effect. A direct correlation between SSc prevalence and HLA-DPB1*13:01 allele frequency in multiple populations was observed (r = 0.98, P = 3 × 10-6). Conditional analysis in the autoantibody subsets of SSc revealed several associated amino acid residues, mostly in the peptide-binding groove of the class II HLA molecules. Using HLA α/β allelic heterodimers, we bioinformatically predicted immunodominant peptides of topoisomerase 1, fibrillarin, and centromere protein A and discovered that they are homologous to viral protein sequences from the Mimiviridae and Phycodnaviridae families. Taken together, these data suggest a possible link between HLA alleles, autoantibodies, and environmental triggers in the pathogenesis of SSc.
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110
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Abstract
The epidemiology of inflammatory bowel disease has changed over the past 4 decades. The incidence is rising dramatically and the age of onset has become younger. This changing landscape of inflammatory bowel disease reflects the new recognition that the youngest children with inflammatory bowel disease are enriched in cases with underlying primary immunodeficiency and monogenic causes. The management of these cases can be quite different, with specific genetic etiologies supporting unique interventions and some requiring hematopoietic cell transplantation for effective treatment.
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Affiliation(s)
- Judith R Kelsen
- Division of Gastroenterology, Hepatology and Nutrition, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Pierre Russo
- Department of Pathology, Division of Allergy Immunology, The Children's Hospital of Philadelphia, ARC 1216-I, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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111
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Watad A, Bragazzi NL, Adawi M, Shoenfeld Y, Comaneshter D, Cohen AD, McGonagle D, Amital H. FMF Is Associated With a Wide Spectrum of MHC Class I- and Allied SpA Disorders but Not With Classical MHC Class II-Associated Autoimmune Disease: Insights From a Large Cohort Study. Front Immunol 2019; 10:2733. [PMID: 31849945 PMCID: PMC6901995 DOI: 10.3389/fimmu.2019.02733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022] Open
Abstract
Objectives: To test the hypothesis that familial Mediterranean fever (FMF)-associated autoinflammation may exaggerate the tendency toward adaptive immunopathology or spondyloarthritis (SpA)-associated disorders including major histocompatibility complex (MHC) class I associated disorders but not classical MHC class II-associated disorders that exhibit transplacental autoimmunity including myasthenia gravis and pemphigus. Methods: Seven thousand seven hundred forty-seven FMF patients and 10,080 age- and sex-matched controls in the Clalit Health Services medical database were identified and compared in terms of prevalence of SpA-associated disorders. We also evaluated four classical and strong MHC class II-associated disorders, namely, pemphigus vulgaris, myasthenia gravis, sarcoidosis, and pernicious anemia, to ascertain whether such associations with SpA-spectrum disease were specific or merely reflected the non-specific consequences of innate immune system activation on driving divergent types of immunity. The diagnosis of FMF was based on the medical records and not genetically proven. Results: FMF showed a strong association with MHC class I-related diseases: odds ratio (OR) of 28.58 [95% confidence interval (95% CI), 6.93–117.87; p < 0.0001] for Behçet's disease, OR of 10.33 (95% CI, 4.09–26.09; p < 0.0001) for ankylosing spondylitis, and OR of 1.67 (95% CI, 1.19–2.33; p = 0.0029) for psoriasis. For weakly MHC class I-linked diseases, an OR of 3.76 (95% CI, 2.48–5.69; p < 0.0001) for Crohn's disease and OR of 2.64 (95% CI, 1.52–4.56; p = 0.0005) for ulcerative colitis were found. No association was found between FMF and the four MHC class II-associated autoimmune disorders. Conclusion: FMF patients are associated with increased risk of SpA-related disease diagnosis including MHC-I-opathies but not MHC-II-associated autoimmune diseases, suggesting that tissue-specific dysregulation of innate immunity share between FMF and SpA spectrum disorders may drive adaptive immune MHC class I-associated conditions.
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Affiliation(s)
- Abdulla Watad
- Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Section of Musculoskeletal Disease, NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Institute of Molecular Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, United Kingdom
| | - Nicola Luigi Bragazzi
- Department of Health Sciences (DISSAL), Postgraduate School of Public Health, University of Genoa, Genoa, Italy.,Laboratory for Industrial and Applied Mathematics, Department of Mathematics and Statistics, York University, Toronto, ON, Canada
| | - Mohammad Adawi
- Azrieli Faculty of Medicine, Padeh and Ziv Hospitals, Bar-Ilan University, Ramat Gan, Israel
| | - Yehuda Shoenfeld
- Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow, Russia
| | | | - Arnon D Cohen
- Chief Physician's Office, Clalit Health Services, Tel-Aviv, Israel.,Faculty of Health Sciences, Siaal Research Center for Family Medicine and Primary Care, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Dennis McGonagle
- Section of Musculoskeletal Disease, NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Institute of Molecular Medicine, University of Leeds, Chapel Allerton Hospital, Leeds, United Kingdom
| | - Howard Amital
- Department of Medicine B and Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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112
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Cleynen I, Linsen L, Verstockt S, Verstockt B, Ballet V, Vandeput E, Van Assche G, Ferrante M, Van Landuyt K, Vermeire S, Ectors N. Inflammatory Bowel Disease (IBD)-A Textbook Case for Multi-Centric Banking of Human Biological Materials. Front Med (Lausanne) 2019; 6:230. [PMID: 31681784 PMCID: PMC6813565 DOI: 10.3389/fmed.2019.00230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition affecting mainly the gastro-intestinal tract with two main entities: Crohn's disease (CD) and ulcerative colitis (UC). Although the exact mechanisms underlying the initial development of IBD are not fully understood, it is believed that an abnormal immune response is elicited against the intestinal microbiota in genetically predisposed individuals. Crucial elements of the etiopathogenesis have been elucidated by research using human biological materials. The estimated prevalence of IBD is 0.5% in the Western world. Although incidence rates are increasing, both conditions are not "common" in general terms mandating a multicentric approach. Biological material from numerous Belgian patients have been collected over time in a number of university hospitals in Belgium (UH Ghent: 800 CD patients, 350 UC patients, 600 normal controls; UH Leuven: 2,600 CD patients, 1,380 UC patients, 98 IC/IBDU patients, 6,260 normal controls). Within the setting of the Flemish Center Medical Innovation (CMI) initiative and later on the Flemish biobank network a prospective study was set-up across three Belgian IBD centers (University Hospitals Brussels, Ghent, and Leuven). Human biological materials and data have been collected prospectively from newly diagnosed CD and UC patients. The analyses hereof have generated new insights which have been published in the most renowned journals. The approach of well-thought off, multi-centric, structured, and systematic biobanking has proven to be a success-story and thus a textbook case for multi-centric banking of human biological materials. This story is being told in this article.
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Affiliation(s)
- Isabelle Cleynen
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Loes Linsen
- Activity Center Biobanking, University Hospitals Leuven, Leuven, Belgium
| | - Sare Verstockt
- Laboratory for Complex Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Bram Verstockt
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Vera Ballet
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Eline Vandeput
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Gert Van Assche
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Marc Ferrante
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | | | - Séverine Vermeire
- Department of Chronic Diseases, Metabolism and Ageing (CHROMETA), Translational Research Center for Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Nadine Ectors
- Activity Center Biobanking, University Hospitals Leuven, Leuven, Belgium
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113
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Pouget JG, Han B, Wu Y, Mignot E, Ollila HM, Barker J, Spain S, Dand N, Trembath R, Martin J, Mayes MD, Bossini-Castillo L, López-Isac E, Jin Y, Santorico SA, Spritz RA, Hakonarson H, Polychronakos C, Raychaudhuri S, Knight J. Cross-disorder analysis of schizophrenia and 19 immune-mediated diseases identifies shared genetic risk. Hum Mol Genet 2019; 28:3498-3513. [PMID: 31211845 PMCID: PMC6891073 DOI: 10.1093/hmg/ddz145] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/24/2019] [Accepted: 06/13/2019] [Indexed: 01/01/2023] Open
Abstract
Many immune diseases occur at different rates among people with schizophrenia compared to the general population. Here, we evaluated whether this phenomenon might be explained by shared genetic risk factors. We used data from large genome-wide association studies to compare the genetic architecture of schizophrenia to 19 immune diseases. First, we evaluated the association with schizophrenia of 581 variants previously reported to be associated with immune diseases at genome-wide significance. We identified five variants with potentially pleiotropic effects. While colocalization analyses were inconclusive, functional characterization of these variants provided the strongest evidence for a model in which genetic variation at rs1734907 modulates risk of schizophrenia and Crohn's disease via altered methylation and expression of EPHB4-a gene whose protein product guides the migration of neuronal axons in the brain and the migration of lymphocytes towards infected cells in the immune system. Next, we investigated genome-wide sharing of common variants between schizophrenia and immune diseases using cross-trait LD score regression. Of the 11 immune diseases with available genome-wide summary statistics, we observed genetic correlation between six immune diseases and schizophrenia: inflammatory bowel disease (rg = 0.12 ± 0.03, P = 2.49 × 10-4), Crohn's disease (rg = 0.097 ± 0.06, P = 3.27 × 10-3), ulcerative colitis (rg = 0.11 ± 0.04, P = 4.05 × 10-3), primary biliary cirrhosis (rg = 0.13 ± 0.05, P = 3.98 × 10-3), psoriasis (rg = 0.18 ± 0.07, P = 7.78 × 10-3) and systemic lupus erythematosus (rg = 0.13 ± 0.05, P = 3.76 × 10-3). With the exception of ulcerative colitis, the degree and direction of these genetic correlations were consistent with the expected phenotypic correlation based on epidemiological data. Our findings suggest shared genetic risk factors contribute to the epidemiological association of certain immune diseases and schizophrenia.
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Affiliation(s)
- Jennie G Pouget
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON M5T 1R8, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Buhm Han
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yang Wu
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Emmanuel Mignot
- Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, School of Medicine, Palo Alto, CA, USA
| | - Hanna M Ollila
- Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Sciences, Stanford University, School of Medicine, Palo Alto, CA, USA
- Finnish Institute for Molecular Medicine, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA and Broad Institute, Cambridge, MA, USA
| | - Jonathan Barker
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
- St. John’s Institute of Dermatology, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Sarah Spain
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Nick Dand
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
| | - Richard Trembath
- School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Queen Mary University of London, Barts and the London School of Medicine and Dentistry, London, UK
| | - Javier Martin
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Maureen D Mayes
- The University of Texas Health Science Center–Houston, Houston, USA
| | - Lara Bossini-Castillo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Elena López-Isac
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Ying Jin
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora 80045, CO, USA
| | - Stephanie A Santorico
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, CO, USA
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, CO, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora 80045, CO, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Constantin Polychronakos
- Endocrine Genetics Laboratory, Department of Pediatrics and the Child Health Program of the Research Institute, McGill University Health Centre, Montreal, QC, Canada
| | - Soumya Raychaudhuri
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Jo Knight
- Lancaster Medical School and Data Science Institute, Lancaster University, Lancaster, UK
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114
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Lee HS, Kim K, Jung S, Hong M, Kim BM, Yoo DS, Moon JW, Baek J, Hwang SW, Park SH, Yang SK, Han B, Song K, Ye BD. Effects of smoking on the association of human leukocyte antigen with ulcerative colitis. J Gastroenterol Hepatol 2019; 34:1777-1783. [PMID: 31038770 DOI: 10.1111/jgh.14695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIM Tobacco smoking is a risk factor for gastrointestinal disorders, causing mucosal damage and impairing immune responses. However, smoking has been found to be protective against ulcerative colitis (UC). Human leukocyte antigen (HLA) is a major susceptibility locus for UC, and HLA-DRB1*15:02 has the strongest effect in Asians. This study investigated the effects of smoking on the association between HLA and UC. METHODS The study enrolled 882 patients with UC, including 526 never, 151 current, and 205 former smokers, and 3091 healthy controls, including 2124 never, 502 current, and 465 former smokers. Smoking-stratified analyses of HLA data were performed using a case-control approach. RESULTS In a case-control approach, HLA-DRB1*15:02 was associated with UC in never smokers (ORnever smokers = 3.20, Pnever smokers = 7.88 × 10-23 ) but not in current or former smokers (Pcurrent smokers = 0.72 and Pformer smokers = 0.33, respectively). In current smokers, HLA-DQB1*06 was associated with UC (ORcurrent smokers = 2.59, Pcurrent smokers = 6.39 × 10-12 ). No variants reached genome-wide significance in former smokers. CONCLUSIONS An association between UC and HLA-DRB1*15:02 was limited to never smokers. Our findings highlight that tobacco smoking modifies the effects of HLA on the risk of UC.
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Affiliation(s)
- Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea.,Stem Cell Immunomodulation Research Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Kihyun Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Byoung Mok Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dae-Sung Yoo
- Division of Veterinary Epidemiology, Animal and Plant Quarantine Agency, Ministry of Agriculture Food and Rural Affair, Gimcheon, Republic of Korea
| | - Jung Won Moon
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sung Wook Hwang
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Sang Hyoung Park
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
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115
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Cornillet M, Jansson H, Schaffer M, Hertwig L, Berglin L, Zimmer CL, Johansson H, Ellis E, Isaksson B, Gonzalez-Galarza FF, Middleton D, Malmberg KJ, Sparrelid E, Björkström NK. Imbalance of Genes Encoding Natural Killer Immunoglobulin-Like Receptors and Human Leukocyte Antigen in Patients With Biliary Cancer. Gastroenterology 2019; 157:1067-1080.e9. [PMID: 31229495 DOI: 10.1053/j.gastro.2019.06.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 06/03/2019] [Accepted: 06/16/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND & AIMS Bile duct tumors are rare and have poor prognoses. Natural killer (NK) cells are frequent in human liver and infiltrate these tumors but do not control their progression. Responses of NK cells are regulated by NK immunoglobulin-like receptors (KIRs), which interact with HLA class I ligands. We aimed to characterize the features of the KIR gene loci and their ligands in patients with bile duct cancer (BDC). METHODS We performed combined multidimensional characterization of genes that encode KIRs and their ligands in blood samples from patients with BDC from Sweden, followed for up to 8 years after diagnosis (n = 148), in 2 geographically matched cohorts of healthy individuals from Northern Europe (n = 204 and n = 900), and in healthy individuals from 6 geographically unrelated populations (n = 2917). We used real-time polymerase chain reaction, RNA sequencing, immunohistochemistry, and flow cytometry to evaluate NK-cell presence, as well as KIR and KIR-ligand expression in bile duct tumors and control tissues. RESULTS Patients with bile duct tumors had multiple alterations at the KIR gene loci. KIR loci are grouped into genotypes that encode more inhibitory (group A) and more activating (group B) receptors, which can be subdivided into centromeric and telomeric fragments. Patients with BDC had a lower prevalence of KIR2DL3, which was linked to disequilibrium in centromeric A/B and B/B genotypes, compared with control individuals. The associations between KIRs and KIR ligands differed between patients with BDC and control individuals; patients had an altered balance between activating and inhibitory KIRs. KIR-positive NK cells infiltrated biliary tumors that expressed matched KIR ligands. CONCLUSIONS In a multidimensional analysis of DNA from blood samples of patients with BDC in Europe, we found patients to have multiple alterations at the KIR and HLA gene loci compared with control individuals. These alterations might affect NK-cell tumor surveillance. NK cells from bile duct tumors expressed KIRs and were found in tumors that expressed cognate ligands. This should be considered in development of immune-based therapies for BDC.
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Affiliation(s)
- Martin Cornillet
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
| | - Hannes Jansson
- Division of Surgery, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Marie Schaffer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Laura Hertwig
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lena Berglin
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christine L Zimmer
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Helene Johansson
- Department of Clinical Science, Intervention and Technology, Division of Transplantation Surgery, Karolinska Institutet, and Department of Transplantation, Karolinska University Hospital, Stockholm, Sweden
| | - Ewa Ellis
- Department of Clinical Science, Intervention and Technology, Division of Transplantation Surgery, Karolinska Institutet, and Department of Transplantation, Karolinska University Hospital, Stockholm, Sweden
| | - Bengt Isaksson
- Division of Surgery, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Faviel F Gonzalez-Galarza
- Center for Biomedical Research, Faculty of Medicine, Autonomous University of Coahuila, Torreon, Mexico
| | - Derek Middleton
- Transplant Immunology Laboratory, Royal Liverpool University Hospital, Liverpool, UK
| | - Karl-Johan Malmberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Ernesto Sparrelid
- Division of Surgery, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
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116
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Ashton JJ, Latham K, Beattie RM, Ennis S. Review article: the genetics of the human leucocyte antigen region in inflammatory bowel disease. Aliment Pharmacol Ther 2019; 50:885-900. [PMID: 31518029 DOI: 10.1111/apt.15485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/05/2019] [Accepted: 08/10/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND The human leucocyte antigen (HLA) complex, located at chromosome 6p21.3 is a highly polymorphic region containing the classical class I and II HLA genes. The region is highly associated with inflammatory bowel disease (IBD), largely through genome-wide association studies (GWAS). AIMS To review the role of HLA in immune function, summarise data on risk/protective HLA genotypes for IBD, discuss the role of HLA in IBD pathogenesis, treatment and examine limitations that might be addressed by future research. METHODS An organised search strategy was used to collate articles describing HLA genes in IBD, including Crohn's disease and ulcerative colitis. RESULTS All classical HLA genes with variation (including HLA-A, B, C, DRB1, DQA1, DQB1, DPA1 and DPB1) harbour IBD-associated genotypes. The most implicated gene is HLA-DRB1, with HLA-DRB1*03:01 the most associated risk allele in both Crohn's disease and ulcerative colitis. Elucidating precise disease associations is challenging due to high linkage disequilibrium between HLA genotypes. The mechanisms by which risk alleles cause disease are multifactorial, with the best evidence indicating structural and electrostatic alteration impacting antigen binding and downstream signalling. Adverse medication events have been associated with HLA genotypes including with thiopurines (pancreatitis) and anti-TNF agents (antibody formation). CONCLUSIONS The HLA complex is associated with multiple risk/protective alleles for IBD. Future research utilising long-read technology, ascertainment of zygosity and integration in disease modelling will improve the functional understanding and clinical translation of genetic findings.
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Affiliation(s)
- James J Ashton
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK.,Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Katy Latham
- Anthony Nolan Research Institute, University College London, London, UK
| | - Robert Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, UK
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117
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Wang FY, Chi CC. Association of rosacea with inflammatory bowel disease: A MOOSE-compliant meta-analysis. Medicine (Baltimore) 2019; 98:e16448. [PMID: 31593075 PMCID: PMC6799824 DOI: 10.1097/md.0000000000016448] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/21/2019] [Accepted: 06/13/2019] [Indexed: 01/04/2023] Open
Abstract
Rosacea has been reported with several systemic comorbidities, but its relationship with inflammatory bowel disease (IBD) is unclear. Thus, our objective is to conduct a meta-analysis on the association of rosacea with IBD.We conduct a meta-analysis and searched MEDLINE, CENTRAL, and Embase databases for case-controlled and cohort studies that assessed the association of rosacea with IBD from inception to July 2nd, 2018. Two authors independently selected studies, extracted data, and assessed the risk of bias of included studies. Disagreement was resolved by discussion. We performed random-effects model meta-analysis to obtain the pooled risk estimates for Crohn disease (CD) and ulcerative colitis (UC) in patients with rosacea.We included three case-control and three cohort studies. The risk of bias of included studies was generally low. The meta-analysis on case-control studies showed marginally increased odds of CD (pooled odds ratio (OR) 1.30, 95% confidence interval (CI) 0.99-1.69) and a significantly increased odds of UC (pooled OR 1.64, 95% CI 1.43-1.89) in patients with rosacea. The meta-analysis on cohort studies demonstrated significant increased risk of CD (pooled hazard ratio (HR) 1.58, 95% CI 1.14-2.20) and UC (pooled HR 1.18, 95% CI 1.01-1.37) in patients with rosacea.The evidence indicates an association of rosacea with IBD. If patients with rosacea suffer from prolonged abdominal pain, diarrhea, and bloody stool, referral to gastroenterologists may be considered.
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Affiliation(s)
- Fang-Ying Wang
- Department of Dermatology, Chang Gung Memorial Hospital, Linkou
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ching-Chi Chi
- Department of Dermatology, Chang Gung Memorial Hospital, Linkou
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
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118
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Chaparro M, Aterido A, Guerra I, Iborra M, Cabriada JL, Bujanda L, Taxonera C, García-Sánchez V, Marín-Jiménez I, Barreiro-de Acosta M, Vera I, Martín-Arranz MD, Hernández-Breijo B, Mesonero F, Sempere L, Gomollón F, Hinojosa J, Bermejo F, Beltrán B, Rodríguez-Pescador A, Banales JM, Olivares D, Aguilar-Melero P, Menchén L, Ferreiro-Iglesias R, Blazquez Gómez I, Benitez García B, Guijarro LG, Marin AC, Bernardo D, Marsal S, Julia A, Gisbert JP. Functional rare variants influence the clinical response to anti-TNF therapy in Crohn's disease. Therap Adv Gastroenterol 2019; 12:1756284819867848. [PMID: 31598133 PMCID: PMC6764039 DOI: 10.1177/1756284819867848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/28/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The effect of low-frequency functional variation on anti-tumor necrosis factor alpha (TNF) response in Crohn's disease (CD) patients remains unexplored. The objective of this study was to investigate the impact of functional rare variants in clinical response to anti-TNF therapy in CD. METHODS CD anti-TNF naïve patients starting anti-TNF treatment due to active disease [Crohn's Disease Activity Index (CDAI > 150)] were included. The whole genome was sequenced using the Illumina Hiseq4000 platform. Clinical response was defined as a CDAI score <150 at week 14 of anti-TNF treatment. Low-frequency variants were annotated and classified according to their damaging potential. The whole genome of CD patients was screened to identify homozygous loss-of-function (LoF) variants. The TNF signaling pathway was tested for overabundance of damaging variants using the SKAT-O method. Functional implication of the associated rare variation was evaluated using cell-type epigenetic enrichment analyses. RESULTS A total of 41 consecutive CD patients were included; 3250 functional rare variants were identified (2682 damaging and 568 LoF variants). Two homozygous LoF mutations were found in HLA-B and HLA-DRB1 genes associated with lack of response and remission, respectively. Genome-wide LoF variants were enriched in epigenetic marks specific for the gastrointestinal tissue (colon, p = 4.11e-4; duodenum, p = 0.011). The burden of damaging variation in the TNF signaling pathway was associated with response to anti-TNF therapy (p = 0.016); damaging variants were enriched in epigenetic marks from CD8+ (p = 6.01e-4) and CD4+ (p = 0.032) T cells. CONCLUSIONS Functional rare variants are involved in the response to anti-TNF therapy in CD. Cell-type enrichment analysis suggests that the gut mucosa and CD8+ T cells are the main mediators of this response.
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Affiliation(s)
| | | | - Iván Guerra
- Gastroenterology Unit, Hospital Universitario de
Fuenlabrada, Instituto de Investigación de Hospital La Paz (IdiPaz), Madrid,
Spain
| | | | - Jose Luis Cabriada
- Gastroenterology Unit, Hospital Universitario de
Galdakano, Vizcaya, Spain
| | | | - Carlos Taxonera
- Gastroenterology Unit, Hospital Universitario
Clínico San Carlos and IdISSC, Madrid, Spain
| | | | - Ignacio Marín-Jiménez
- Gastroenterology Unit, Hospital Universitario
Gregorio Marañón e IiSGM, Madrid, Spain
| | | | - Isabel Vera
- Gastroenterology Unit, Hospital Universitario
Puerta de Hierro Majadahonda, Madrid, Spain
| | | | - Borja Hernández-Breijo
- Universidad de Alcalá, Alcalá de Henares,
Spain,Immuno-Rheumatology Research Group. IdiPaz.
Hospital Universitario La Paz, Madrid, Spain
| | - Francisco Mesonero
- Gastroenterology Unit, Hospital Universitario
Ramón y Cajal, Madrid, Spain
| | - Laura Sempere
- Gastroenterology Unit, Hospital Universitario
Alicante, Alicante, Spain
| | | | - Joaquín Hinojosa
- Gastroenterology Unit, Hospital Universitario
Manises, Valencia, Spain
| | - Fernando Bermejo
- Gastroenterology Unit, Hospital Universitario
de Fuenlabrada, Instituto de Investigación de Hospital La Paz (IdiPaz),
Madrid, Spain
| | | | | | | | - David Olivares
- Gastroenterology Unit, Hospital Universitario
Clínico San Carlos and IdISSC, Madrid, Spain
| | - Patricia Aguilar-Melero
- Gastroenterology Unit, Instituto Maimónides de
Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina
Sofía/Universidad de Córdoba, Spain
| | - Luis Menchén
- Gastroenterology Unit, Hospital Universitario
Gregorio Marañón e IiSGM, Madrid, Spain
| | - Rocío Ferreiro-Iglesias
- Gastroenterology Unit, Hospital Universitario
Clínico de Santiago, Santiago de Compostela, Spain
| | - Isabel Blazquez Gómez
- Gastroenterology Unit, Hospital Universitario
Puerta de Hierro Majadahonda, Madrid, Spain
| | | | | | | | | | - Sara Marsal
- Rheumatology Research Group, Vall d’Hebron
Research Institute, Barcelona, Spain
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119
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Vidotti MS, Lyra DH, Morosini JS, Granato ÍSC, Quecine MC, de Azevedo JL, Fritsche-Neto R. Additive and heterozygous (dis)advantage GWAS models reveal candidate genes involved in the genotypic variation of maize hybrids to Azospirillum brasilense. PLoS One 2019; 14:e0222788. [PMID: 31536609 PMCID: PMC6752820 DOI: 10.1371/journal.pone.0222788] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/07/2019] [Indexed: 11/18/2022] Open
Abstract
Maize genotypes can show different responsiveness to inoculation with Azospirillum brasilense and an intriguing issue is which genes of the plant are involved in the recognition and growth promotion by these Plant Growth-Promoting Bacteria (PGPB). We conducted Genome-Wide Association Studies (GWAS) using additive and heterozygous (dis)advantage models to find candidate genes for root and shoot traits under nitrogen (N) stress and N stress plus A. brasilense. A total of 52,215 Single Nucleotide Polymorphism (SNP) markers were used for GWAS analyses. For the six root traits with significant inoculation effect, the GWAS analyses revealed 25 significant SNPs for the N stress plus A. brasilense treatment, in which only two were overlapped with the 22 found for N stress only. Most were found by the heterozygous (dis)advantage model and were more related to exclusive gene ontology terms. Interestingly, the candidate genes around the significant SNPs found for the maize-A. brasilense association were involved in different functions previously described for PGPB in plants (e.g. signaling pathways of the plant's defense system and phytohormone biosynthesis). Our findings are a benchmark in the understanding of the genetic variation among maize hybrids for the association with A. brasilense and reveal the potential for further enhancement of maize through this association.
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Affiliation(s)
- Miriam Suzane Vidotti
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Júlia Silva Morosini
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | | | - Maria Carolina Quecine
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - João Lúcio de Azevedo
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Roberto Fritsche-Neto
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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120
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Tavakolpour S, Darvishi M, Ghasemiadl M. Pharmacogenetics: A strategy for personalized medicine for autoimmune diseases. Clin Genet 2019; 93:481-497. [PMID: 29194620 DOI: 10.1111/cge.13186] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 11/24/2017] [Accepted: 11/24/2017] [Indexed: 12/12/2022]
Abstract
For many years, a considerable number of patients with autoimmune diseases (ADs) have suffered from a lack of drug response and drug-related toxicity. Despite the emergence of new therapeutic options such as biological agents, patients continue to struggle with these problems. Unfortunately, new challenges, including the paradoxical effects of biological drugs, have complicated the situation. In recent decades, efforts have been made to predict drug response as well as drug-related side effects. Thanks to the many advances in genetics, evaluation of markers to predict drug response/toxicity before the initiation of treatment may be an avenue toward personalizing treatments. Implementing pharmacogenetics and pharmacogenomics in the clinic could improve clinical care; however, obstacles remain to effective personalized medicine for ADs. The present study attempted to clarify the concept of pharmacogenetics/pharmacogenomics for ADs. After an overview on the pathogenesis of the most common types of treatments, this paper focuses on pharmacogenetic studies related to the selected ADs. Bridging the gap between pharmacogenetics and personalized medicine is also discussed. Moreover, the advantages, disadvantages and recommendations related to making personalized medicine practical for ADs have been addressed.
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Affiliation(s)
- S Tavakolpour
- Genomic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
| | - M Darvishi
- Infectious Diseases and Tropical Medicine Research Center (IDTMRC), Department of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - M Ghasemiadl
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran
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121
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Niehrs A, Garcia-Beltran WF, Norman PJ, Watson GM, Hölzemer A, Chapel A, Richert L, Pommerening-Röser A, Körner C, Ozawa M, Martrus G, Rossjohn J, Lee JH, Berry R, Carrington M, Altfeld M. A subset of HLA-DP molecules serve as ligands for the natural cytotoxicity receptor NKp44. Nat Immunol 2019; 20:1129-1137. [PMID: 31358998 PMCID: PMC8370669 DOI: 10.1038/s41590-019-0448-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 06/06/2019] [Indexed: 01/25/2023]
Abstract
Natural killer (NK) cells can recognize virus-infected and stressed cells1 using activating and inhibitory receptors, many of which interact with HLA class I. Although early studies also suggested a functional impact of HLA class II on NK cell activity2,3, the NK cell receptors that specifically recognize HLA class II molecules have never been identified. We investigated whether two major families of NK cell receptors, killer-cell immunoglobulin-like receptors (KIRs) and natural cytotoxicity receptors (NCRs), contained receptors that bound to HLA class II, and identified a direct interaction between the NK cell receptor NKp44 and a subset of HLA-DP molecules, including HLA-DP401, one of the most frequent class II allotypes in white populations4. Using NKp44ζ+ reporter cells and primary human NKp44+ NK cells, we demonstrated that interactions between NKp44 and HLA-DP401 trigger functional NK cell responses. This interaction between a subset of HLA-DP molecules and NKp44 implicates HLA class II as a component of the innate immune response, much like HLA class I. It also provides a potential mechanism for the described associations between HLA-DP subtypes and several disease outcomes, including hepatitis B virus infection5-7, graft-versus-host disease8 and inflammatory bowel disease9,10.
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Affiliation(s)
- Annika Niehrs
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Wilfredo F Garcia-Beltran
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Paul J Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA
- Department of Microbiology and Immunology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Gabrielle M Watson
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Angelique Hölzemer
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
- First Department of Internal Medicine, University Medical Center Eppendorf, Hamburg, Germany
| | - Anaïs Chapel
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Unité HIV Inflammation et Persistance, Institut Pasteur, Paris, France
| | - Laura Richert
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- Inserm Inria SISTM Bordeaux Population Health Research Center UMR 1219, Univ. Bordeaux, Bordeaux, France
| | | | - Christian Körner
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | | | - Glòria Martrus
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Jamie Rossjohn
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
- Institute of Infection and Immunity, Cardiff University School of Medicine, Cardiff, UK
| | | | - Richard Berry
- Infection and Immunity Program and The Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Mary Carrington
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
- Basic Science Program, HLA Immunogenetics Section, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Marcus Altfeld
- Research Department Virus Immunology, Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
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122
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Cohen LJ, Cho JH, Gevers D, Chu H. Genetic Factors and the Intestinal Microbiome Guide Development of Microbe-Based Therapies for Inflammatory Bowel Diseases. Gastroenterology 2019; 156:2174-2189. [PMID: 30880022 PMCID: PMC6568267 DOI: 10.1053/j.gastro.2019.03.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 02/28/2019] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
The intestinal microbiota is a dynamic community of bacteria, fungi, and viruses that mediates mucosal homeostasis and physiology. Imbalances in the microbiome and aberrant immune responses to gut bacteria can disrupt homeostasis and are associated with inflammatory bowel diseases (IBDs) in humans and colitis in mice. We review genetic variants associated with IBD and their effects on the intestinal microbiome, the immune response, and disease pathogenesis. The intestinal microbiome, which includes microbial antigens, adjuvants, and metabolic products, affects the development and function of the intestinal mucosa, influencing inflammatory responses in the gut. Therefore, strategies to manipulate the microbiome might be used in treatment of IBD. We review microbe-based therapies for IBD and the potential to engineer patients' intestinal microbiota. We discuss how studies of patients with IBD and mouse models have advanced our understanding of the interactions between genetic factors and the gut microbiome, and challenges to the development of microbe-based therapies for IBD.
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Affiliation(s)
- Louis J. Cohen
- Division of Gastroenterology, Department of Medicine, Icahn
School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Correspondence:
(L.J.C.),
(H.C.)
| | - Judy H. Cho
- Division of Gastroenterology, Department of Medicine, Icahn
School of Medicine at Mount Sinai, New York, New York, 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School
of Medicine at Mount Sinai; The Charles Bronfman Institute for Personalized
Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, 10029,
USA
| | - Dirk Gevers
- Janssen Human Microbiome Institute, Janssen Research &
Development, Cambridge, MA, 02142, USA
| | - Hiutung Chu
- Department of Pathology, University of California-San Diego, La Jolla, California; Chiba University and University of California-San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, California.
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123
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Does MHC heterozygosity influence microbiota form and function? PLoS One 2019; 14:e0215946. [PMID: 31095603 PMCID: PMC6522005 DOI: 10.1371/journal.pone.0215946] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 04/11/2019] [Indexed: 12/14/2022] Open
Abstract
MHC molecules are essential for the adaptive immune response, and they are the most polymorphic genetic loci in vertebrates. Extreme genetic variation at these loci is paradoxical given their central importance to host health. Classic models of MHC gene evolution center on antagonistic host-pathogen interactions to promote gene diversification and allelic diversity in host populations. However, all multicellular organisms are persistently colonized by their microbiota that perform essential metabolic functions for their host and protect from infection. Here, we provide data to support the hypothesis that MHC heterozygote advantage (a main force of selection thought to drive MHC gene evolution), may operate by enhancing fitness advantages conferred by the host’s microbiome. We utilized fecal 16S rRNA gene sequences and their predicted metagenome datasets collected from multiple MHC congenic homozygote and heterozygote mouse strains to describe the influence of MHC heterozygosity on microbiome form and function. We find that in contrast to homozygosity at MHC loci, MHC heterozygosity promotes functional diversification of the microbiome, enhances microbial network connectivity, and results in enrichment for a variety of microbial functions that are positively associated with host fitness. We demonstrate that taxonomic and functional diversity of the microbiome is positively correlated in MHC heterozygote but not homozygote animals, suggesting that heterozygote microbiomes are more functionally adaptive under similar environmental conditions than homozygote microbiomes. Our data complement previous observations on the role of MHC polymorphism in sculpting microbiota composition, but also provide functional insights into how MHC heterozygosity may enhance host health by modulating microbiome form and function. We also provide evidence to support that MHC heterozygosity limits functional redundancy among commensal microbes and may enhance the metabolic versatility of their microbiome. Results from our analyses yield multiple testable predictions regarding the role of MHC heterozygosity on the microbiome that will help guide future research in the area of MHC-microbiome interactions.
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124
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Han B, Akiyama M, Kim KK, Oh H, Choi H, Lee CH, Jung S, Lee HS, Kim EE, Cook S, Haritunians T, Yamazaki K, Park SH, Ye BD, McGovern DPB, Esaki M, Kawaguchi T, Khor SS, Taylor KD, Rotter JI, Suzuki Y, Matsui T, Motoya S, Bang SY, Kim TH, Momozawa Y, Kamatani Y, Tokunaga K, Kubo M, Okada Y, Yang SK, Song K. Amino acid position 37 of HLA-DRβ1 affects susceptibility to Crohn's disease in Asians. Hum Mol Genet 2019; 27:3901-3910. [PMID: 30084967 DOI: 10.1093/hmg/ddy285] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/24/2018] [Indexed: 12/19/2022] Open
Abstract
Crohn's disease (CD) and ulcerative colitis (UC) are the major types of chronic inflammatory bowel disease (IBD) characterized by recurring episodes of inflammation of the gastrointestinal tract. Although it is well established that human leukocyte antigen (HLA) is a major risk factor for IBD, it is yet to be determined which HLA alleles or amino acids drive the risks of CD and UC in Asians. To define the roles of HLA for IBD in Asians, we fine-mapped HLA in 12 568 individuals from Korea and Japan (3294 patients with CD, 1522 patients with UC and 7752 controls). We identified that the amino acid position 37 of HLA-DRβ1 plays a key role in the susceptibility to CD (presence of serine being protective, P = 3.6 × 10-67, OR = 0.48 [0.45-0.52]). For UC, we confirmed the known association of the haplotype spanning HLA-C*12:02, HLA-B*52:01 and HLA-DRB1*1502 (P = 1.2 × 10-28, OR = 4.01 [3.14-5.12]).
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Affiliation(s)
- Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kyung-Kon Kim
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea.,Convergence Medicine Research Center and Biomedical Research Center, AILS, Asan Medical Center, Seoul, Korea
| | - Hyunjung Oh
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunchul Choi
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Cue Hyunkyu Lee
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Emma E Kim
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea.,Department of Chemistry, Seoul National University, Seoul, Korea
| | - Seungho Cook
- Department of Medicine, Seoul National University College of Medicine, Seoul, Korea.,Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Talin Haritunians
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Keiko Yamazaki
- Division of Genomic Epidemiology and Clinical Trials, Clinical Trials Research Center, Nihon University School of Medicine, Tokyo, Japan.,Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dermot P B McGovern
- The F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takaaki Kawaguchi
- Division of Gastroenterology, Department of Medicine, TokyoYamate Medical Center, Tokyo, Japan.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Seik-Soon Khor
- Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences,Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical CenterTorrance, CA, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences,Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor-UCLA Medical CenterTorrance, CA, USA
| | - Yasuo Suzuki
- Department of Internal Medicine, Faculty of Medicine, Toho University, Chiba, Japan
| | - Toshiyuki Matsui
- Department of Gastroenterology, Fukuoka University,Chikushi Hospital, Fukuoka, Japan
| | - Satoshi Motoya
- Department of Gastroenterology, Sapporo-Kosei General Hospital, Sapporo, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine,Sakyo-ku, Kyoto, Japan
| | - Katsushi Tokunaga
- Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukinori Okada
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Osaka, Japan
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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125
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Lawrenson K, Song F, Hazelett DJ, Kar SP, Tyrer J, Phelan CM, Corona RI, Rodríguez-Malavé NI, Seo JH, Adler E, Coetzee SG, Segato F, Fonseca MAS, Amos CI, Carney ME, Chenevix-Trench G, Choi J, Doherty JA, Jia W, Jin GJ, Kim BG, Le ND, Lee J, Li L, Lim BK, Adenan NA, Mizuno M, Park B, Pearce CL, Shan K, Shi Y, Shu XO, Sieh W, Thompson PJ, Wilkens LR, Wei Q, Woo YL, Yan L, Karlan BY, Freedman ML, Noushmehr H, Goode EL, Berchuck A, Sellers TA, Teo SH, Zheng W, Matsuo K, Park S, Chen K, Pharoah PDP, Gayther SA, Goodman MT. Genome-wide association studies identify susceptibility loci for epithelial ovarian cancer in east Asian women. Gynecol Oncol 2019; 153:343-355. [PMID: 30898391 PMCID: PMC6754211 DOI: 10.1016/j.ygyno.2019.02.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/20/2019] [Accepted: 02/21/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Genome-wide association studies (GWASs) for epithelial ovarian cancer (EOC) have focused largely on populations of European ancestry. We aimed to identify common germline variants associated with EOC risk in Asian women. METHODS Genotyping was performed as part of the OncoArray project. Samples with >60% Asian ancestry were included in the analysis. Genotyping was performed on 533,631 SNPs in 3238 Asian subjects diagnosed with invasive or borderline EOC and 4083 unaffected controls. After imputation, genotypes were available for 11,595,112 SNPs to identify associations. RESULTS At chromosome 6p25.2, SNP rs7748275 was associated with risk of serous EOC (odds ratio [OR] = 1.34, P = 8.7 × 10-9) and high-grade serous EOC (HGSOC) (OR = 1.34, P = 4.3 × 10-9). SNP rs6902488 at 6p25.2 (r2 = 0.97 with rs7748275) lies in an active enhancer and is predicted to impact binding of STAT3, P300 and ELF1. We identified additional risk loci with low Bayesian false discovery probability (BFDP) scores, indicating they are likely to be true risk associations (BFDP <10%). At chromosome 20q11.22, rs74272064 was associated with HGSOC risk (OR = 1.27, P = 9.0 × 10-8). Overall EOC risk was associated with rs10260419 at chromosome 7p21.3 (OR = 1.33, P = 1.2 × 10-7) and rs74917072 at chromosome 2q37.3 (OR = 1.25, P = 4.7 × 10-7). At 2q37.3, expression quantitative trait locus analysis in 404 HGSOC tissues identified ESPNL as a putative candidate susceptibility gene (P = 1.2 × 10-7). CONCLUSION While some risk loci were shared between East Asian and European populations, others were population-specific, indicating that the landscape of EOC risk in Asian women has both shared and unique features compared to women of European ancestry.
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Affiliation(s)
- Kate Lawrenson
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Fengju Song
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Dennis J Hazelett
- Center for Bioinformatics and Functional Genomics, Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Siddhartha P Kar
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Jonathan Tyrer
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK
| | - Catherine M Phelan
- Department of Gynecologic Oncology, Moffitt Cancer Center, Tampa, FL, USA; Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Rosario I Corona
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Norma I Rodríguez-Malavé
- Center for Bioinformatics and Functional Genomics, Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ji-Hei Seo
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Emily Adler
- Department of Preventive Medicine, University of Southern California, Keck School of Medicine, 1450 Biggy Street, Los Angeles, CA, USA
| | - Simon G Coetzee
- Center for Bioinformatics and Functional Genomics, Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Felipe Segato
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Brazil
| | - Marcos A S Fonseca
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Brazil
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Department of Medicine, Baylor School of Medicine, Houston,TX, USA
| | - Michael E Carney
- Department of Obstetrics and Gynecology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Georgia Chenevix-Trench
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD 4006, Australia
| | - Jiyeob Choi
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Biomedical Science, Graduate School, Seoul National University, Seoul, Republic of Korea
| | - Jennifer A Doherty
- Jon M. and Karen Huntsman Endowed Associate Professor in Cancer Research Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, USA
| | - Weihua Jia
- State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-sen University, Guangzhou, Guangdong 510060, China
| | - Gang J Jin
- ShanghaiBio Corporation, Shanghai, China; CloudHealth Genomics Ltd, Shanghai, China
| | - Byoung-Gie Kim
- Department of Obstetrics and Gynecology, Samsung Medical Center, Sungkyunkwan University, School of Medicine, Republic of Korea
| | - Nhu D Le
- Cancer Control Research, BC Cancer Agency, Vancouver, BC, Canada
| | - Juyeon Lee
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Biomedical Science, Graduate School, Seoul National University, 103 Daehak-ro, Jongno-gu, Seoul 110-799, Republic of Korea
| | - Lian Li
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Boon K Lim
- The Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Noor A Adenan
- The Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Mika Mizuno
- Department of Gynecological Oncology, Aichi Cancer Center Hospital, Japan
| | - Boyoung Park
- Department of Preventive Medicine, College of Medicine, Hanyang, Seoul, Republic of Korea
| | - Celeste L Pearce
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kang Shan
- Department of Obstetrics and Gynaecology,Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Weiva Sieh
- Department of Population Health Science and Policy, Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pamela J Thompson
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lynne R Wilkens
- Cancer Epidemiology Program, University of Hawaii Cancer Center, HI, USA
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Yin L Woo
- The Department of Obstetrics and Gynaecology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Li Yan
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Beth Y Karlan
- Women's Cancer Program at the Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Suite 290W, Los Angeles, CA, USA
| | - Matthew L Freedman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Houtan Noushmehr
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, 14049-900, Brazil; Department of Neurosurgery, Henry Ford Health System, Detroit, MI, USA
| | - Ellen L Goode
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA
| | - Andrew Berchuck
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Thomas A Sellers
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Soo-Hwang Teo
- Cancer Research Initiatives Foundation, Subang Jaya, Selangor, Malaysia
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Keitaro Matsuo
- Division of Molecular and Clinical Epidemiology, Aichi Cancer Center Research Institute, Japan
| | - Sue Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Biomedical Science, Graduate School, Seoul National University, Seoul, Republic of Korea
| | - Kexin Chen
- National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China; Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Paul D P Pharoah
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Strangeways Research Laboratory, Cambridge, UK; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratory, Worts Causeway, Cambridge, UK
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics, Cedars Sinai Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Marc T Goodman
- Cancer Prevention and Control, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Community and Population Health Research Institute, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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Genetic Studies of Inflammatory Bowel Disease-Focusing on Asian Patients. Cells 2019; 8:cells8050404. [PMID: 31052430 PMCID: PMC6563043 DOI: 10.3390/cells8050404] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/19/2019] [Accepted: 04/26/2019] [Indexed: 12/25/2022] Open
Abstract
The pathogenesis of inflammatory bowel disease (IBD) is not well-understood; however, increased and persistent intestinal inflammation, due to inappropriate immune responses that are caused by interactions between genetic factors, gut microbiota, and environmental factors, are thought to lead to IBD. Various studies have identified more than 240 genetic variants related to IBD. These genetic variants are involved in innate and adaptive immunity, autophagy, defective bacterial handing, interleukin-23 and 10 signaling, and so on. According to several epidemiological and clinical studies, the phenotypes and clinical course of IBD differ between Asians and Europeans. Although the risk loci for IBD typically overlap between Asians and Westerners, genetic heterogeneity has been detected in many loci/genes, such as NOD2/CARD15, TNFSF15 and human leukocyte antigen, contributing to the risk of IBD. Thus, although common pathways exist between Westerners and Asians in the development of IBD, their significance may differ for individual pathways. Although genetic studies are not universally applicable in the clinical field, they may be useful for diagnosing and categorizing IBD, predicting therapeutic responses and toxicity to drugs, and assessing prognosis by risk modeling, thereby enabling precision medicine for individual patients.
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Molineros JE, Looger LL, Kim K, Okada Y, Terao C, Sun C, Zhou XJ, Raj P, Kochi Y, Suzuki A, Akizuki S, Nakabo S, Bang SY, Lee HS, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Lee SS, Zuo X, Yamamoto K, Li QZ, Shen N, Porter LL, Harley JB, Chua KH, Zhang H, Wakeland EK, Tsao BP, Bae SC, Nath SK. Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians. PLoS Genet 2019; 15:e1008092. [PMID: 31022184 PMCID: PMC6504188 DOI: 10.1371/journal.pgen.1008092] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/07/2019] [Accepted: 03/13/2019] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology. The Human leukocyte antigen (HLA) region is a key genetic factor conferring risk of systemic lupus erythematosus (SLE). In spite of multiple SLE association signals identified in the HLA region, only amino-acid residues within HLA-DRB1 have been specifically described previously. In this study, we performed an imputation-based analysis on individuals with East Asian ancestry, and characterized SLE risk within the HLA region for all involved independent genes (HLA-DRB1, HLA-DPB1, HLA-DQB1, HLA-A, and HLA-B). Furthermore, we identified a characteristic SLE risk residue signature as well as a pattern of specific nRNP and Ro/La autoantibody residues located in the peptide-binding grooves, suggesting their key involvement in autoantibody production.
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Affiliation(s)
- Julio E. Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Chikashi Terao
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Xu-jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuichiro Nakabo
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Young Mo Kang
- School of Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University Hospital, Suwon, Korea
| | - Won Tae Chung
- Dong-A University Hospital, Department of Internal Medicine, Busan, Korea
| | - Yong-Beom Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Yoon Choe
- Department of Rheumatology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Seung-Cheol Shim
- Daejeon Rheumatoid & Degenerative Arthritis Center, Chungnam National University Hospital, Daejeon, Korea
| | - Shin-Seok Lee
- Department of Rheumatology, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nan Shen
- Department of Rheumatology and Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Lauren L. Porter
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Betty P. Tsao
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- * E-mail: (SCB); (SKN)
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail: (SCB); (SKN)
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Cheng B, Liang X, Wen Y, Li P, Zhang L, Ma M, Cheng S, Du Y, Liu L, Ding M, Zhao Y, Zhang F. Integrative analysis of transcriptome‐wide association study data and messenger RNA expression profiles identified candidate genes and pathways for inflammatory bowel disease. J Cell Biochem 2019; 120:14831-14837. [DOI: 10.1002/jcb.28744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 03/17/2019] [Accepted: 03/22/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Xiao Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Yanan Du
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Miao Ding
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Yan Zhao
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, Key Laboratory of Environment and Genes Related to Diseases of Ministry of Education, Collaborative Innovation Center of Endemic Diseases and Health Promotion in Silk Road Region, School of Public Health, Health Science Center Xi'an Jiaotong University Xi'an Shaanxi P.R. China
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Zhang J, Wei Z, Cardinale CJ, Gusareva ES, Van Steen K, Sleiman P, Hakonarson H. Multiple Epistasis Interactions Within MHC Are Associated With Ulcerative Colitis. Front Genet 2019; 10:257. [PMID: 31001315 PMCID: PMC6456704 DOI: 10.3389/fgene.2019.00257] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/08/2019] [Indexed: 12/20/2022] Open
Abstract
Successful searching for epistasis is much challenging, which generally requires very large sample sizes and/or very dense marker information. We exploited the largest Crohn's disease (CD) dataset (18,000 cases + 34,000 controls) and ulcerative colitis (UC) dataset (14,000 cases + 34,000 controls) to date. Leveraging its dense marker information and the large sample size of this IBD dataset, we employed a two-step approach to exhaustively search for epistasis. We detected abundant genome-wide significant (p < 1 × 10-13) epistatic signals, all within the MHC region. These signals were reduced substantially when conditional on the additive background, but still nine pairs remained significant at the Immunochip-wide level (P < 1.1 × 10-8) in conditional tests for UC. All these nine epistatic interactions come from the MHC region, and each explains on average 0.15% of the phenotypic variance. Eight of them were replicated in a replication cohort. There are multiple but relatively weak interactions independent of the additive effects within the MHC region for UC. Our promising results warrant the search for epistasis in large data sets with dense markers, exploiting dependencies between markers.
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Affiliation(s)
- Jie Zhang
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, United States.,Adobe Inc., San Jose, CA, United States
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, United States
| | - Christopher J Cardinale
- The Children's Hospital of Philadelphia, Center for Applied Genomics, Philadelphia, PA, United States
| | - Elena S Gusareva
- GIGA-R Medical Genomics - BIO3, University of Liege, Avenue de l'Hôpital 11, Liège, Belgium
| | - Kristel Van Steen
- GIGA-R Medical Genomics - BIO3, University of Liege, Avenue de l'Hôpital 11, Liège, Belgium.,WELBIO-Walloon Excellence in Life Sciences and BIOtechnology, Liège, Belgium
| | - Patrick Sleiman
- The Children's Hospital of Philadelphia, Center for Applied Genomics, Philadelphia, PA, United States.,Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Hakon Hakonarson
- The Children's Hospital of Philadelphia, Center for Applied Genomics, Philadelphia, PA, United States.,Division of Human Genetics, Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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130
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Rasmussen NF, Rubin KH, Stougaard M, Tjønneland A, Stenager E, Lund Hetland M, Glintborg B, Bygum A, Andersen V. Impact of red meat, processed meat and fibre intake on risk of late-onset chronic inflammatory diseases: prospective cohort study on lifestyle factors using the Danish 'Diet, Cancer and Health' cohort (PROCID-DCH): protocol. BMJ Open 2019; 9:e024555. [PMID: 30928934 PMCID: PMC6475359 DOI: 10.1136/bmjopen-2018-024555] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/08/2018] [Accepted: 02/18/2019] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Chronic inflammatory diseases (CIDs) (Crohn's disease, ulcerative colitis, psoriasis, psoriatic arthritis, rheumatoid arthritis and multiple sclerosis) are diseases of the immune system that have some shared genetic and environmental predisposing factors, but still few studies have investigated the effects of lifestyle on disease risk of several CIDs. The primary aim of this prospective cohort study is to investigate the impact of fibre, red meat and processed meat on risk of late-onset CID, with the perspective that results of this study can contribute in supporting future diet recommendations for effective personalised prevention. METHODS AND ANALYSIS The study will use data from 57 053 persons from the prospective Danish cohort study 'Diet, Cancer and Health' together with National Health Registry data. The follow-up period is from December 1993 to December 2018. Questionnaire data on diet and lifestyle were collected at entry to the Diet, Cancer and Health study. The outcome CID is defined as having a diagnosis of one of the CIDs registered in the National Patient Registry or, for multiple sclerosis, in the Danish Multiple Sclerosis Registry during follow-up and being treated with a drug used for the specific disease. The major outcome of the analyses will be to detect variability in risk of late onset of any CID and, if power allows, disease risk of late onset of each CID diagnosis between persons with different fibre and red meat, and processed meat intake. The outcome will be adjusted for age, sex, body mass index, physical activity, energy, alcohol, fermented dairy products, education, smoking status, hormone replacement therapy and comorbidity. ETHICS AND DISSEMINATION The study is approved by the Danish Data Protection Agency (2012-58-0018). The core study is an open register-based cohort study. The study does not need approval from the Ethics committee or Institutional Review Board by Danish law. Study findings will be disseminated through peer-reviewed journals, patient associations and presentations at international conferences. TRIAL REGISTRATION NUMBER NCT03456206; Post-results.
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Affiliation(s)
- Nathalie Fogh Rasmussen
- Faculty of Health Sciences, Aarhus University, Aarhus, Denmark
- Focused Research Unit for Molecular Diagnostic and Clinical Research, IRS-Center Sonderjylland, Hospital of Southern Jutland, Aabenraa, Denmark
| | - Katrine Hass Rubin
- OPEN - Odense Patient Data Explorative Network, Department of Clinical Research, University of Southern Denmark, and Odense University Hospital, Odense, Denmark
| | - Maria Stougaard
- OPEN - Odense Patient Data Explorative Network, Department of Clinical Research, University of Southern Denmark, and Odense University Hospital, Odense, Denmark
| | - Anne Tjønneland
- Diet, Genes and Environment, Danish Cancer Society Research Center, Copenhagen Ø, Denmark/Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Egon Stenager
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
- The Multiple Sclerosis Clinic of Southern Jutland (Sonderborg, Kolding, Esbjerg), Department of Neurology, Hospital of Southern Jutland, Sonderborg, Denmark
| | - Merete Lund Hetland
- DANBIO Registry/Copenhagen Center for Arthritis Research (COPECARE), Center for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Rigshospitalet Glostrup, Glostrup, Denmark
| | - Bente Glintborg
- DANBIO Registry/Copenhagen Center for Arthritis Research (COPECARE), Center for Rheumatology and Spine Diseases, Centre of Head and Orthopaedics, Rigshospitalet Glostrup, Glostrup, Denmark
- Department of Rheumatology, Gentofte Hospital, Hellerup, Hovedstaden, Denmark
| | - Anette Bygum
- Department of Dermatology and Allergy Centre, Odense Universitetshospital, Odense, Denmark
| | - Vibeke Andersen
- Focused Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- institute og molecular medicine, Syddansk Universitet Det Sundhedsvidenskabelige Fakultet, Odense, Denmark
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Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vich Vila A, Collij V, Spekhorst LM, der Sloot KWJ V, Peters V, Van Dullemen HM, Visschedijk MC, EAM F, Swertz MA, Dijkstra G, Weersma RK. The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. BMC Gastroenterol 2019; 19:5. [PMID: 30621600 PMCID: PMC6325838 DOI: 10.1186/s12876-018-0917-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 12/06/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data generated from the same IBD patients. CONSTRUCTION AND CONTENT We initiated the 1000IBD project ( https://1000ibd.org ) to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1215 participants have been enrolled in the project and enrolment is on-going. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing. UTILITY AND DISCUSSION All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive ( https://ega-archive.org , accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models. CONCLUSIONS We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets.
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Affiliation(s)
- Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - K. J. Van der Velde
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Barbieri
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - R. Alberts
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. D. Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - A. Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - V. Collij
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - L. M. Spekhorst
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Van der Sloot KWJ
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - V. Peters
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - H. M. Van Dullemen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - M. C. Visschedijk
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - Festen EAM
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - M. A. Swertz
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - G. Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
| | - R. K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, PO Box 30.001, 9700RB Groningen, the Netherlands
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Weimers P, Halfvarson J, Sachs MC, Saunders-Pullman R, Ludvigsson JF, Peter I, Burisch J, Olén O. Inflammatory Bowel Disease and Parkinson's Disease: A Nationwide Swedish Cohort Study. Inflamm Bowel Dis 2019; 25:111-123. [PMID: 29788069 DOI: 10.1093/ibd/izy190] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Few studies have examined the association between inflammatory bowel disease (IBD) and Parkinson's disease (PD). METHODS To estimate the incidence and relative risk of PD development in a cohort of adult IBD, we included all incident IBD patients (n = 39,652) in the Swedish National Patient Register (NPR) between 2002 and 2014 (ulcerative colitis [UC]: n = 24,422; Crohn's disease [CD]: n = 11,418; IBD-unclassified [IBD-U]: n = 3812). Each IBD patient was matched for sex, age, year, and place of residence with up to 10 reference individuals (n = 396,520). In a cohort design, all incident PD occurring after the index date was included from the NPR. In a case-control design, all incident PD occurring before the index date was included. The association between IBD and PD and vice versa was investigated by multivariable Cox and logistic regression. RESULTS In IBD, there were 103 cases of incident PD, resulting in hazard ratios (HRs) for PD of 1.3 (95% confidence interval [CI], 1.0-1.7; P = 0.04) in UC, 1.1 (95% CI, 0.7-1.7) in CD, and 1.7 (95% CI, 0.8-3.0) in IBD-U. However, these effects disappeared when adjusting for number of medical visits during follow-up to minimize potential surveillance bias. In a case-control analysis, IBD patients were more likely to have prevalent PD at the time of IBD diagnosis than matched controls, with odds ratios of 1.4 (95% CI, 1.2-1.8) in all IBD patients, 1.4 (95% CI, 1.1-1.9) for UC, and 1.6 (95% CI, 1.1-2.3) for CD patients alone. CONCLUSIONS IBD is associated with an increased risk of PD, but some of this association might be explained by surveillance bias. 10.1093/ibd/izy190_video1izy190.video15785623138001.
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Affiliation(s)
- Petra Weimers
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Jonas Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Michael C Sachs
- Unit of Biostatistics, Institute of Environmental Medicine, Stockholm, Sweden
| | | | - Jonas F Ludvigsson
- Department Medical Epidemiology and Biostatistics, Stockholm, Sweden.,Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund, Denmark
| | - Ola Olén
- Clinical Epidemiology Unit, Department of Medicine Solna, Stockholm, Sweden.,Department of Pediatric gastroenterology and nutrition, Sachs' Children and Youth Hospital, Stockholm, Sweden.,Department of Clinical Science and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
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133
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Reveille JD, Zhou X, Lee M, Weisman MH, Yi L, Gensler LS, Zou H, Ward MM, Ishimori ML, Learch TJ, He D, Rahbar MH, Wang J, Brown MA. HLA class I and II alleles in susceptibility to ankylosing spondylitis. Ann Rheum Dis 2019; 78:66-73. [PMID: 30341055 PMCID: PMC6982366 DOI: 10.1136/annrheumdis-2018-213779] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 08/12/2018] [Accepted: 08/21/2018] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To examine associations of HLA class I and class II alleles with ankylosing spondylitis (AS) in three cohorts of patients of European, Asian and African ancestry. METHODS HLA-A, HLA-B, HLA-C, HLA-DRB1, HLA-DQB1 and HLA-DPB1 alleles were genotyped in 1948 unrelated white and 67 African-American patients with AS from the Prospective Study of Outcomes in Ankylosing Spondylitis cohort, the North American Spondylitis Consortium and Australo-Anglo-American Spondyloarthritis Consortium, 990 white and 245 African-American Controls and HLA-B alleles in 442 Han Chinese patients with AS and 346 controls from Shanghai and Gansu, China. In addition to the case:control analyses, HLA-B*27-negative patients with AS were analysed separately, and logistic regression and 'relative predispositional effects' (RPE) analyses were carried out to control for the major effect of HLA-B*27 on disease susceptibility. RESULTS Although numerous associations were seen between HLA alleles and AS in whites, among HLA-B*27-negative patients with AS , positive associations were seen with HLA-A*29, B*38, B*49, B*52, DRB1*11 and DPB1*03:01 and negative associations with HLA-B*07, HLA-B*57, HLA-DRB1*15:01, HLA-DQB1*02:01 and HLA-DQB1*06:02. Additional associations with HLA-B*14 and B*40 (B60) were observed via RPE analysis, which excludes the HLA-B*27 alleles. The increased frequency of HLA-B*40:01 and decreased frequency of HLA-B*07 was also seen in Han Chinese and African-Americans with AS. HLA-B*08 was decreased in whites with acute anterior uveitis. CONCLUSIONS These data, analysing the largest number of patients with AS examined to date in three ethnic groups, confirm that other HLA class I and II alleles other than HLA-B*27 to be operative in AS predisposition.
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Affiliation(s)
- John D Reveille
- Division of Rheumatology and Clinical Immunogenetics, McGovern Medical School at The University of Texas Health Science Center, Houston, Texas, USA
| | - Xiaodong Zhou
- Division of Rheumatology and Clinical Immunogenetics, McGovern Medical School at The University of Texas Health Science Center, Houston, Texas, USA
| | - MinJae Lee
- Division of Clinical and Translational Sciences, McGovern Medical School at The University of Texas Health Science Center, Houston, Texas, USA
| | - Michael H Weisman
- Department of Radiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lin Yi
- Division of Rheumatology, Gansu College of Traditional Chinese Medicine, Gansu, China
| | - Lianne S Gensler
- Division of Rheumatology, The University of California, San Francisco, California, USA
| | - Hejian Zou
- Huashan Hospital, Fudan University, Shanghai, China
| | - Michael M Ward
- Division of Rheumatology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, Maryland, USA
| | - Mariko L Ishimori
- Department of Radiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Thomas J Learch
- Department of Radiology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dongyi He
- Division of Rheumatology, Shanghai Guanghua Hospital, Shanghai, China
| | - Mohammad H Rahbar
- Division of Clinical and Translational Sciences, McGovern Medical School at The University of Texas Health Science Center, Houston, Texas, USA
| | - Jiucun Wang
- Huashan Hospital, Fudan University, Shanghai, China
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Translational Research Institute, Princess Alexandra Hospital, Brisbane, Queensland, Australia
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Darlay R, Ayers KL, Mells GF, Hall LS, Liu JZ, Almarri MA, Alexander GJ, Jones DE, Sandford RN, Anderson CA, Cordell HJ. Amino acid residues in five separate HLA genes can explain most of the known associations between the MHC and primary biliary cholangitis. PLoS Genet 2018; 14:e1007833. [PMID: 30507971 PMCID: PMC6292650 DOI: 10.1371/journal.pgen.1007833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 12/13/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022] Open
Abstract
Primary Biliary Cholangitis (PBC) is a chronic autoimmune liver disease characterised by progressive destruction of intrahepatic bile ducts. The strongest genetic association is with HLA-DQA1*04:01, but at least three additional independent HLA haplotypes contribute to susceptibility. We used dense single nucleotide polymorphism (SNP) data in 2861 PBC cases and 8514 controls to impute classical HLA alleles and amino acid polymorphisms using state-of-the-art methodologies. We then demonstrated through stepwise regression that association in the HLA region can be largely explained by variation at five separate amino acid positions. Three-dimensional modelling of protein structures and calculation of electrostatic potentials for the implicated HLA alleles/amino acid substitutions demonstrated a correlation between the electrostatic potential of pocket P6 in HLA-DP molecules and the HLA-DPB1 alleles/amino acid substitutions conferring PBC susceptibility/protection, highlighting potential new avenues for future functional investigation. Primary Biliary Cholangitis (PBC) is a chronic autoimmune liver disease that exhibits strong genetic associations, especially with variants in the human leukocyte antigen (HLA) gene region. Here we use dense single nucleotide polymorphism (SNP) data from the largest PBC study to date (2861 cases, 8514 controls) to investigate the likely underlying causes of this association, via performing imputation of HLA classical alleles and amino acids. We show that the HLA association can be largely explained by variation at five separate amino acid positions, one of which shows functional relevance to electrostatic potentials of HLA-DP molecules.
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Affiliation(s)
- Rebecca Darlay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kristin L. Ayers
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - George F. Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Lynsey S. Hall
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Jimmy Z. Liu
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Mohamed A. Almarri
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
- Department of Forensic Science and Criminology, Dubai Police HQ, Dubai, United Arab Emirates
| | - Graeme J. Alexander
- Department of Hepatology, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - David E. Jones
- Institute of Cellular Medicine, Medical School, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Carl A. Anderson
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, United Kingdom
| | - Heather J. Cordell
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
- * E-mail:
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Hasan Ali O, Berner F, Bomze D, Fässler M, Diem S, Cozzio A, Jörger M, Früh M, Driessen C, Lenz TL, Flatz L. Human leukocyte antigen variation is associated with adverse events of checkpoint inhibitors. Eur J Cancer 2018; 107:8-14. [PMID: 30529903 DOI: 10.1016/j.ejca.2018.11.009] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/01/2018] [Indexed: 01/31/2023]
Abstract
BACKGROUND Checkpoint inhibitors (CIs) are highly effective but can induce severe immune-related adverse events (irAEs), which cannot be predicted. We investigated whether human leukocyte antigen (HLA) genes predispose to developing of irAEs during therapy and thus hold a predictive role. METHODS We established a prospective observational single-centre study and collected data from patients with either metastatic non-small cell lung cancer (NSCLC) or metastatic melanoma, who were treated with anti-PD-1 (programmed cell death receptor 1), anti-CTLA4 (cytotoxic T-lymphocyte-associated protein 4) or both CIs combined. Data include irAEs and ranges from 15th July 2016 until 10th May 2018. In addition, we performed HLA typing via next generation sequencing. RESULTS We enrolled 102 patients (median [range] age, 68 [62-74] years) with metastatic cancer in our study who received CI therapy. Of these patients, 59 (58%) developed one or more irAEs, among which pruritus (n = 32 (54%)) and rash (n = 24 (41%)) had the highest rates. We did not find evidence for a single HLA gene being associated with all irAEs (all P > .05). When assessing each irAE individually, we found a significant association between HLA-DRB1*11:01 and pruritus (OR = 4.53, X21,95 = 9.45, P < .01) as well as a nominally significant additive association between HLA-DQB1*03:01 and colitis (OR = 3.94, X21,95 = 5.67, P = .017). CONCLUSIONS The presence of two HLA alleles that are known to predispose to autoimmune diseases were associated with the development of pruritus or colitis during therapy, suggesting a genetic aetiology of irAEs. Larger genome-wide association studies should be performed to confirm our findings.
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Affiliation(s)
- Omar Hasan Ali
- Department of Dermatology, University Hospital of Zürich, CH-8091, Zürich, Switzerland; Institute of Immunobiology, Kantonsspital St.Gallen, CH-9007, St. Gallen, Switzerland
| | - Fiamma Berner
- Institute of Immunobiology, Kantonsspital St.Gallen, CH-9007, St. Gallen, Switzerland
| | - David Bomze
- Institute of Immunobiology, Kantonsspital St.Gallen, CH-9007, St. Gallen, Switzerland
| | - Mirjam Fässler
- Institute of Immunobiology, Kantonsspital St.Gallen, CH-9007, St. Gallen, Switzerland
| | - Stefan Diem
- Department of Oncology and Hematology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland; Department of Oncology and Hematology, Hospital of Grabs, CH-9472, Grabs, Switzerland
| | - Antonio Cozzio
- Department of Dermatology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland
| | - Markus Jörger
- Department of Oncology and Hematology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland
| | - Martin Früh
- Department of Oncology and Hematology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland
| | - Christoph Driessen
- Department of Oncology and Hematology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, D-24306, Plön, Germany
| | - Lukas Flatz
- Department of Dermatology, University Hospital of Zürich, CH-8091, Zürich, Switzerland; Institute of Immunobiology, Kantonsspital St.Gallen, CH-9007, St. Gallen, Switzerland; Department of Oncology and Hematology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland; Department of Dermatology, Kantonsspital St. Gallen, CH-9007, St. Gallen, Switzerland.
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136
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Mallon DH, Kling C, Robb M, Ellinghaus E, Bradley JA, Taylor CJ, Kabelitz D, Kosmoliaptsis V. Predicting Humoral Alloimmunity from Differences in Donor and Recipient HLA Surface Electrostatic Potential. THE JOURNAL OF IMMUNOLOGY 2018; 201:3780-3792. [PMID: 30429288 PMCID: PMC6287104 DOI: 10.4049/jimmunol.1800683] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 10/02/2018] [Indexed: 11/27/2022]
Abstract
In transplantation, development of humoral alloimmunity against donor HLA is a major cause of organ transplant failure, but our ability to assess the immunological risk associated with a potential donor–recipient HLA combination is limited. We hypothesized that the capacity of donor HLA to induce a specific alloantibody response depends on their structural and physicochemical dissimilarity compared with recipient HLA. To test this hypothesis, we first developed a novel computational scoring system that enables quantitative assessment of surface electrostatic potential differences between donor and recipient HLA molecules at the tertiary structure level [three-dimensional electrostatic mismatch score (EMS-3D)]. We then examined humoral alloimmune responses in healthy females subjected to a standardized injection of donor lymphocytes from their male partner. This analysis showed a strong association between the EMS-3D of donor HLA and donor-specific alloantibody development; this relationship was strongest for HLA-DQ alloantigens. In the clinical transplantation setting, the immunogenic potential of HLA-DRB1 and -DQ mismatches expressed on donor kidneys, as assessed by their EMS-3D, was an independent predictor of development of donor-specific alloantibody after graft failure. Collectively, these findings demonstrate the translational potential of our approach to improve immunological risk assessment and to decrease the burden of humoral alloimmunity in organ transplantation.
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Affiliation(s)
- Dermot H Mallon
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom.,National Institute for Health Research Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge CB2 0QQ, United Kingdom.,National Institute of Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, United Kingdom
| | - Christiane Kling
- Institute for Immunology, University Medical Centre Schleswig-Holstein, Kiel University, 24105 Kiel, Germany
| | - Matthew Robb
- Statistics and Clinical Studies Unit, National Health Service Blood and Transplant, Bristol BS34 7QH, United Kingdom
| | - Eva Ellinghaus
- Institute of Clinical Molecular Biology, University Medical Centre Schleswig-Holstein, Kiel University, 24105 Kiel, Germany; and
| | - J Andrew Bradley
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom.,National Institute for Health Research Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge CB2 0QQ, United Kingdom.,National Institute of Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, United Kingdom
| | - Craig J Taylor
- National Institute of Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, United Kingdom.,Tissue Typing Laboratory, Cambridge University Hospitals National Health Service Foundation Trust, Cambridge CB2 0QQ, United Kingdom
| | - Dieter Kabelitz
- Institute for Immunology, University Medical Centre Schleswig-Holstein, Kiel University, 24105 Kiel, Germany
| | - Vasilis Kosmoliaptsis
- Department of Surgery, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 0QQ, United Kingdom; .,National Institute for Health Research Blood and Transplant Research Unit in Organ Donation and Transplantation, University of Cambridge, Cambridge CB2 0QQ, United Kingdom.,National Institute of Health Research Cambridge Biomedical Research Centre, Cambridge CB2 0QQ, United Kingdom
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138
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Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med 2018; 24:1762-1772. [PMID: 30349087 DOI: 10.1038/s41591-018-0203-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/20/2018] [Indexed: 01/01/2023]
Abstract
Identifying immunodominant T cell epitopes remains a significant challenge in the context of infectious disease, autoimmunity, and immuno-oncology. To address the challenge of antigen discovery, we developed a quantitative proteomic approach that enabled unbiased identification of major histocompatibility complex class II (MHCII)-associated peptide epitopes and biochemical features of antigenicity. On the basis of these data, we trained a deep neural network model for genome-scale predictions of immunodominant MHCII-restricted epitopes. We named this model bacteria originated T cell antigen (BOTA) predictor. In validation studies, BOTA accurately predicted novel CD4 T cell epitopes derived from the model pathogen Listeria monocytogenes and the commensal microorganism Muribaculum intestinale. To conclusively define immunodominant T cell epitopes predicted by BOTA, we developed a high-throughput approach to screen DNA-encoded peptide-MHCII libraries for functional recognition by T cell receptors identified from single-cell RNA sequencing. Collectively, these studies provide a framework for defining the immunodominance landscape across a broad range of immune pathologies.
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139
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Spatial analyzes of HLA data in Rio Grande do Sul, south Brazil: genetic structure and possible correlation with autoimmune diseases. Int J Health Geogr 2018; 17:34. [PMID: 30217207 PMCID: PMC6137739 DOI: 10.1186/s12942-018-0154-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023] Open
Abstract
Background HLA genes are the most polymorphic of the human genome and have distinct allelic frequencies in populations of different geographical regions of the world, serving as genetic markers in ancestry studies. In addition, specific HLA alleles may be associated with various autoimmune and infectious diseases. The bone marrow donor registry in Brazil is the third largest in the world, and it counts with genetic typing of HLA-A, -B, and -DRB1. Since 1991 Brazil has maintained the DATASUS database, a system fed with epidemiological and health data from compulsory registration throughout the country. Methods In this work, we perform spatial analysis and georeferencing of HLA genetic data from more than 86,000 bone marrow donors from Rio Grande do Sul (RS) and data of hospitalization for rheumatoid arthritis, multiple sclerosis and Crohn’s disease in RS, comprising the period from 1995 to 2016 obtained through the DATASUS system. The allele frequencies were georeferenced using Empirical Bayesian Kriging; the diseases prevalence were georeferenced using Inverse Distance Weighted and cluster analysis for both allele and disease were performed using Getis-Ord Gi* method. Spearman’s test was used to test the correlation between each allele and disease. Results The results indicate a HLA genetic structure compatible with the history of RS colonization, where it is possible to observe differentiation between regions that underwent different colonization processes. Spatial analyzes of autoimmune disease hospitalization data were performed revealing clusters for different regions of the state for each disease analyzed. The correlation test between allelic frequency and the occurrence of autoimmune diseases indicated a significant correlation between the HLA-B*08 allele and rheumatoid arthritis. Conclusions Genetic mapping of populations and the spatial analyzes such as those performed in this work have great economic relevance and can be very useful in the formulation of public health campaigns and policies, contributing to the planning and adjustment of clinical actions, as well as informing and educating professionals and the population. Electronic supplementary material The online version of this article (10.1186/s12942-018-0154-8) contains supplementary material, which is available to authorized users.
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140
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Expanded TCRβ CDR3 clonotypes distinguish Crohn's disease and ulcerative colitis patients. Mucosal Immunol 2018; 11:1487-1495. [PMID: 29988119 DOI: 10.1038/s41385-018-0046-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/26/2018] [Accepted: 04/30/2018] [Indexed: 02/04/2023]
Abstract
We aimed to determine whether the TCR repertoires of Crohn's disease (CD) patients contain highly prevalent disease-specific T-cell clonotypes reflective of the characteristic and highly shared aberrant serum antibody reactivity to gut commensal flagellin antigens. The CD4 TCRβ CDR3 sequence repertoires from active CD (n = 20) and ulcerative colitis (UC) (n = 10) patients were significantly more diverse, and individual sequences over-represented, compared to healthy controls (HC) (n = 97). While a very small number of expanded public CDR3 sequences are highly shared between active CD and UC, the majority of significantly expanded TCRβ CDR3 clonotypes are private to CD and UC patients with equivalent prevalence among IBD patients. Further defining TCR clonotypes by Vβ-CDR3 linkage showed significant differences in the TCR repertoires between UC and CD. Flagellin antigen exposure induced expansion of several TCRβ CDR3 sequences in CD4 cells from a flagellin-seropositive subject including sequences highly shared by or relatively private to CD (and UC) patients. These data suggest that flagellin-reactivity contributes to the expansion of a small number of CD4 clonotypes but does not support flagellin antigens as predominantly driving CD4 cell proliferation in CD. Disease-specific expanded TCRβ CDR3 clonotypes characterize CD and UC and the shared exposure to the gamut of gut microbial antigens.
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141
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Lee HS, Yang SK, Hong M, Jung S, Kim BM, Moon JW, Park SH, Ye BD, Oh SH, Kim KM, Yoon YS, Yu CS, Baek J, Lee CH, Han B, Liu J, Haritunians T, McGovern DPB, Song K. An Intergenic Variant rs9268877 Between HLA-DRA and HLA-DRB Contributes to the Clinical Course and Long-term Outcome of Ulcerative Colitis. J Crohns Colitis 2018; 12:1113-1121. [PMID: 29905830 DOI: 10.1093/ecco-jcc/jjy080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/30/2018] [Accepted: 06/12/2018] [Indexed: 01/01/2023]
Abstract
BACKGROUND AND AIMS The genetic contribution to the prognosis of ulcerative colitis [UC] is poorly understood, and most currently known susceptibility loci are not associated with prognosis. To identify genetic variants influencing the prognosis of UC, we performed an Immunochip-based study using an extreme phenotype approach. METHODS Based on the finding that the only association, Pdiscovery-meta <1 × 10-4, was located in the human leukocyte antigen [HLA], we focused our analyses on the HLA region. We performed the analysis using HLA imputation data from three independent discovery cohorts of 607 UC patients [243 poor-prognosis and 364 good-prognosis], followed by replication in 274 UC patients [145 poor-prognosis and 129 good-prognosis]. RESULTS We found that rs9268877, located between HLA-DRA and HLA-DRB, was associated with poor-prognosis of UC at genome-wide significance (odds ratio [ORdiscovery] = 1.82; ORreplication = 1.55; ORcombined-meta = 1.72, pcombined-meta = 1.04 × 10-8), with effect size [OR] increasing incrementally according to worsening of prognosis in each of the three independent discovery cohorts and the replication cohort. However, rs9268877 showed no association with UC susceptibility [ORcombined-meta = 1.07, pcombined-meta = 0.135]; rs9268877 influenced 30-year clinical outcomes, and the presence of the rs9268877 risk allele had a sensitivity of 80.0% and specificity of 38.1% for colectomy. CONCLUSIONS Our results provide new insights into prognosis-associated genetic variation in UC, which appears to be distinct from the genetic contribution to disease susceptibility. These findings could be useful in identifying poor-prognosis patients who might benefit from early aggressive therapy.
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Affiliation(s)
- Ho-Su Lee
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Suk-Kyun Yang
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Myunghee Hong
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Seulgi Jung
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Byoung Mok Kim
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Jung Won Moon
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Sang Hyoung Park
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Byong Duk Ye
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seak Hee Oh
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Kyung Mo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Korea
| | - Yong Sik Yoon
- Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Chang Sik Yu
- Colon and Rectal Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Cue Hyunkyu Lee
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Buhm Han
- Department of Convergence Medicine, University of Ulsan College of Medicine & Asan Institute for Life Sciences, Asan Medical Center, Seoul, Korea
| | - Jianjun Liu
- Human Genetics Group, Genome Institute of Singapore, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kyuyoung Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
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Steenland K, Kugathasan S, Barr DB. PFOA and ulcerative colitis. ENVIRONMENTAL RESEARCH 2018; 165:317-321. [PMID: 29777922 PMCID: PMC6358414 DOI: 10.1016/j.envres.2018.05.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/25/2018] [Accepted: 05/08/2018] [Indexed: 05/05/2023]
Abstract
INTRODUCTION PFOA (perfluoroctanoic acid) is a perfluoroalkyl substance (PFAS). Although use in the US has been phased out, PFOA persists indefinitely in the environment, and is present in the serum of virtually all people in industrialized countries. Approximately 6 million Americans drink water comtaminated with PFOA above EPA-recommended levels. In a previous cohort study (n = 32,000), we found a strong positive exposure-response relation between PFOA serum levels and subsequent ulcerative colitis (UC) in a high-exposed population from the mid-Ohio valley, but no association with Crohn's disease. In the present study we aimed to determine if UC cases had higher levels of PFOA than did controls or Crohn's disease patients. METHODS We measured PFOA and three other PFAS in the serum of 114 UC patients, 60 Crohn's disease patients, and 75 controls, within a year of diagnosis. We conducted regression analyses to assess the association of the PFAS with diagnosis. RESULTS The mean age of subjects was 17 years. The mean year of diagnosis was 2007. Mean levels of PFAS were similar to US levels. Mean log PFOA level in UC patients was 38% higher (p = 0.01) than the combined group of Crohn's disease and controls. In contrast, the three other PFASs were significantly higher in controls and Crohn's patients than UC patients. The odds ratio for UC per one unit of log PFOA was 1.60 (95% CI 1.14-2.24), but the trend by quintiles was not monotonic (1, 0.84, 40.98, 33.36, 2.86). CONCLUSION We found higher serum PFOA in UC cases compared to Crohn's disease patients or controls, in contrast to other PFAS. Our research is limited by not knowing if the elevated PFOA preceded UC in this population.
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Affiliation(s)
- Kyle Steenland
- Dept. Environmental Health, Rollins School of Public Health, Emory University, United States.
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Dept of Pediatrics, Emory School of Medicine and Children's Healthcare of Atlanta, United States
| | - Dana Boyd Barr
- Dept. Environmental Health, Rollins School of Public Health, Emory University, United States
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143
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Zhang C, Wiemels JL, Hansen HM, Gonzalez-Maya J, Endicott AA, de Smith AJ, Smirnov IV, Witte JS, Morimoto LM, Metayer C, Walsh KM. Two HLA Class II Gene Variants Are Independently Associated with Pediatric Osteosarcoma Risk. Cancer Epidemiol Biomarkers Prev 2018; 27:1151-1158. [PMID: 30038050 DOI: 10.1158/1055-9965.epi-18-0306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 05/29/2018] [Accepted: 07/09/2018] [Indexed: 12/18/2022] Open
Abstract
Background: The genetic etiology of osteosarcoma remains poorly understood despite the publication of a genome-wide association study. Association between HLA genetic variants and risk of several cancers has been observed, but HLA variation is not well captured by standard SNP arrays.Methods: We genotyped 207 Californian pediatric osteosarcoma cases and 696 controls of European ancestry using a custom genome-wide array supplemented with approximately 6,000 additional probes across the MHC region. We subsequently imputed 4-digit classical HLA alleles using a reference panel of 5,225 individuals who underwent high-resolution HLA typing via next-generation sequencing. Case-control comparisons were adjusted for ancestry-informative principal components, and top associations from the discovery analysis underwent replication in an independent dataset of 657 cases and 1,183 controls.Results: Three highly correlated HLA class II variants (r 2 = 0.33-0.98) were associated with osteosarcoma risk in discovery analyses, including HLA-DRB1*0301 (OR = 0.52; P = 3.2 × 10-3), HLA-DQA1*0501 (OR = 0.74; P = 0.031), and HLA-DQB1*0201 (OR = 0.51; P = 2.7 × 10-3). Similar associations were observed in the replication data (P range = 0.011-0.037). Meta-analysis of the two datasets identified HLA-DRB1*0301 as the most significantly associated variant (ORmeta = 0.62; P meta = 1.5 × 10-4), reaching Bonferroni-corrected statistical significance. The meta-analysis also revealed a second significant independent signal at HLA-DQA1*01:01 (ORmeta = 1.33, P meta = 1.2 × 10-3), and a third suggestive association at HLA-DQB1*0302 (ORmeta = 0.73, P meta = 6.4 × 10-3).Conclusions: Multiple independent HLA class II alleles may influence osteosarcoma risk.Impact: Additional work is needed to extend our observations to other patient populations and to clarify the potential causal mechanisms underlying these associations. Understanding immunologic contributions to the etiology of osteosarcoma may inform rational therapeutic targets. Cancer Epidemiol Biomarkers Prev; 27(10); 1151-8. ©2018 AACR.
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Affiliation(s)
- Chenan Zhang
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Joseph L Wiemels
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California.,Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Helen M Hansen
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Julio Gonzalez-Maya
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Alyson A Endicott
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Ivan V Smirnov
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
| | - Libby M Morimoto
- School of Public Health, University of California, Berkeley, Berkeley, California
| | - Catherine Metayer
- School of Public Health, University of California, Berkeley, Berkeley, California
| | - Kyle M Walsh
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California. .,Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina.,Children's Health and Discovery Institute, Duke University, Durham, North Carolina
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144
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Wang SS, Carrington M, Berndt SI, Slager SL, Bracci PM, Voutsinas J, Cerhan JR, Smedby KE, Hjalgrim H, Vijai J, Morton LM, Vermeulen R, Paltiel O, Vajdic CM, Linet MS, Nieters A, de Sanjose S, Cozen W, Brown EE, Turner J, Spinelli JJ, Zheng T, Birmann BM, Flowers CR, Becker N, Holly EA, Kane E, Weisenburger D, Maynadie M, Cocco P, Albanes D, Weinstein SJ, Teras LR, Diver WR, Lax SJ, Travis RC, Kaaks R, Riboli E, Benavente Y, Brennan P, McKay J, Delfau-Larue MH, Link BK, Magnani C, Ennas MG, Latte G, Feldman AL, Doo NW, Giles GG, Southey MC, Milne RL, Offit K, Musinsky J, Arslan AA, Purdue MP, Adami HO, Melbye M, Glimelius B, Conde L, Camp NJ, Glenn M, Curtin K, Clavel J, Monnereau A, Cox DG, Ghesquières H, Salles G, Bofetta P, Foretova L, Staines A, Davis S, Severson RK, Lan Q, Brooks-Wilson A, Smith MT, Roman E, Kricker A, Zhang Y, Kraft P, Chanock SJ, Rothman N, Hartge P, Skibola CF. HLA Class I and II Diversity Contributes to the Etiologic Heterogeneity of Non-Hodgkin Lymphoma Subtypes. Cancer Res 2018; 78:4086-4096. [PMID: 29735552 PMCID: PMC6065509 DOI: 10.1158/0008-5472.can-17-2900] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 02/07/2018] [Accepted: 04/24/2018] [Indexed: 01/07/2023]
Abstract
A growing number of loci within the human leukocyte antigen (HLA) region have been implicated in non-Hodgkin lymphoma (NHL) etiology. Here, we test a complementary hypothesis of "heterozygote advantage" regarding the role of HLA and NHL, whereby HLA diversity is beneficial and homozygous HLA loci are associated with increased disease risk. HLA alleles at class I and II loci were imputed from genome-wide association studies (GWAS) using SNP2HLA for 3,617 diffuse large B-cell lymphomas (DLBCL), 2,686 follicular lymphomas (FL), 2,878 chronic lymphocytic leukemia/small lymphocytic lymphomas (CLL/SLL), 741 marginal zone lymphomas (MZL), and 8,753 controls of European descent. Both DLBCL and MZL risk were elevated with homozygosity at class I HLA-B and -C loci (OR DLBCL = 1.31, 95% CI = 1.06-1.60; OR MZL = 1.45, 95% CI = 1.12-1.89) and class II HLA-DRB1 locus (OR DLBCL = 2.10, 95% CI = 1.24-3.55; OR MZL = 2.10, 95% CI = 0.99-4.45). Increased FL risk was observed with the overall increase in number of homozygous HLA class II loci (P trend < 0.0001, FDR = 0.0005). These results support a role for HLA zygosity in NHL etiology and suggests that distinct immune pathways may underly the etiology of the different NHL subtypes.Significance: HLA gene diversity reduces risk for non-Hodgkin lymphoma. Cancer Res; 78(14); 4086-96. ©2018 AACR.
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Affiliation(s)
- Sophia S Wang
- Department of Population Sciences, Beckman Research Institute and the City of Hope, Duarte, California.
| | - Mary Carrington
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, and Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Susan L Slager
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, California
| | - Jenna Voutsinas
- Department of Population Sciences, Beckman Research Institute and the City of Hope, Duarte, California
| | - James R Cerhan
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Karin E Smedby
- Department of Medicine Solna, unit of clinical epidemiology, Karolinska Institutet, Stockholm, Sweden
- Hematology Center, Karolinska University Hospital, Stockholm, Sweden
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Hematology, Rishospitalet, Copenhagen, Denmark
| | - Joseph Vijai
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Roel Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Ora Paltiel
- Braun School of Public Health and Community Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Claire M Vajdic
- Centre for Big Data Research in Health, The University of New South Wales, Sydney, New South Wales, Australia
| | - Martha S Linet
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Alexandra Nieters
- Centre for Chronic Immunodeficiency, University Medical Center Freiburg, Freiburg, Baden-Württemberg, Germany
| | - Silvia de Sanjose
- Unit of Infections and Cancer, Cancer Epidemiology Research Programme, Institut Català d' Oncologia, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Wendy Cozen
- Norris Comprehensive Cancer Center, Keck School of Medicine of USC, Departments of Preventive Medicine and Pathology, University of Southern California, Los Angeles, Calfornia
| | - Elizabeth E Brown
- Department of Pathology, School of Medicine and the UAB Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Jennifer Turner
- Department of Histopathology, Douglass Hanly Moir Pathology, Sydney, Australia
- Faculty of Medicine and Health Sciences, Macquarie University, Sydney, Australia
| | - John J Spinelli
- Cancer Control Research, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tongzhang Zheng
- Department of Epidemiology, School of Public Health, Brown University, Providence, Rhode Island
| | - Brenda M Birmann
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher R Flowers
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia
| | - Nikolaus Becker
- Division of Clinical Epidemiology, German Cancer Research Centre, Heidelberg, Baden-Württemberg, Germany
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California-San Francisco, San Francisco, California
| | - Eleanor Kane
- Department of Health Sciences, University of York, York, United Kingdom
| | | | - Marc Maynadie
- Registry of Hematological Malignancies of Cote d'Or, INSERM UMR1231, University of Burgundy and Dijon University Hospital, Dijon, France
| | - Pierluigi Cocco
- Department of Public Health, Clinical and Molecular Medicine, University of Cagliari, Cagliari, Italy
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | | | - Lauren R Teras
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer Society, Atlanta, Georgia
| | - Stephanie J Lax
- Department of Health Sciences, University of York, York, United Kingdom
| | - Ruth C Travis
- Cancer Epidemiology Unit, University of Oxford, Oxford, United Kingdom
| | - Rudolph Kaaks
- Division of Clinical Epidemiology, German Cancer Research Centre, Heidelberg, Baden-Württemberg, Germany
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Yolanda Benavente
- Unit of Infections and Cancer, Cancer Epidemiology Research Programme, Institut Català d' Oncologia, IDIBELL, 08908 L'Hospitalet de Llobregat, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - James McKay
- Department of Immunology, CHU Henri Mondor, Créteil, France
| | - Marie-Hélène Delfau-Larue
- Department of Immunology, CHU Henri Mondor, Créteil, France
- INSERM U 955, CHU Henri Mondor, Créteil, France
| | - Brian K Link
- Department of Internal Medicine, Carver College of Medicine, The University of Iowa, Iowa City, Iowa
| | - Corrado Magnani
- Center of Oncological Prevention (CPO) Piemonte and Unit of Medical Statistics and Epidemiology, Department Translational Medicine, University of Piemonte Orientale, Novara, Italy
| | - Maria Grazia Ennas
- Department of Biomedical Science, University of Cagliari, Monserrato, Cagliari, Italy
| | | | - Andrew L Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Nicole Wong Doo
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Australia
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Pathology, University of Melbourne, Melbourne, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Kenneth Offit
- Department of Hematology, Rishospitalet, Copenhagen, Denmark
| | - Jacob Musinsky
- Department of Hematology, Rishospitalet, Copenhagen, Denmark
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York City, New York
- Department of Environmental Medicine, New York University School of Medicine, New York City, New York
- Perlmutter Cancer Center, NYU Langone Medical Center, New York City, New York
| | - Mark P Purdue
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Hans-Olov Adami
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mads Melbye
- Department of Epidemiology Research, Division of Health Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
- Department of Medicine, Stanford University School of Medicine, Stanford, Calfornia
| | - Bengt Glimelius
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Lucia Conde
- Bill Lyons Informatics Centre, UCL Cancer Institute, University College London, London, United Kingdom
| | - Nicola J Camp
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Martha Glenn
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Karen Curtin
- Department of Internal Medicine, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Jacqueline Clavel
- Epidemiology of Childhood and Adolescent Cancers Group, Inserm, Center of Research in Epidemiology and Statistics Sorbonne Paris Cité (CRESS), Paris, France
- Université Paris Descartes, Paris, France
| | - Alain Monnereau
- Université Paris Descartes, Paris, France
- Université Paris Descartes, Paris, France
- Registre des hémopathies malignes de la Gironde, Institut Bergonié, University of Bordeaux, Inserm, Team EPICENE, UMR 1219, France
| | - David G Cox
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom; Cancer Research Center of Lyon, INSERM UMR1052, Center Léon Bérard, Lyon, France
| | - Hervé Ghesquières
- Université Paris Descartes, Paris, France
- Laboratoire de Biologie Moléculaire de la Cellule UMR 5239, Centre National de la Recherche Scientifique, Pierre benite Cedex, France
| | - Gilles Salles
- Laboratoire de Biologie Moléculaire de la Cellule UMR 5239, Centre National de la Recherche Scientifique, Pierre benite Cedex, France
- Department of Hematology, Hospices Civils De Lyon, Centre Hospitalier Lyon-Sud and Université Claude Bernard, Lyon, France
| | - Paulo Bofetta
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York City, New York
| | - Lenka Foretova
- Department of Cancer Epidemiology and Genetics, Masaryk Memorial Cancer Institute, MF MU, Brno, Czech Republic
| | - Anthony Staines
- School of Nursing and Human Sciences, Dublin City University, Dublin, Ireland
| | - Scott Davis
- Fred Hutchinson Cancer Research Center and School of Public Health and Community Medicine, University of Washington, Seattle, Washington
| | - Richard K Severson
- Department of Family Medicine and Public Health Sciences, Wayne State University, Detroit, Michigan
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Angela Brooks-Wilson
- Department of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia, Canada
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Martyn T Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, California
| | - Eve Roman
- Department of Health Sciences, University of York, York, United Kingdom
| | - Anne Kricker
- Sydney School of Public Health, The University of Sydney, Sydney, Australia
| | - Yawei Zhang
- Department of Surgery, Yale School of Medicine, New Haven, Connecticut
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Christine F Skibola
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia
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145
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Genetic variants at the 16p13 locus confer risk for eosinophilic esophagitis. Genes Immun 2018; 20:281-292. [PMID: 29904099 PMCID: PMC6286696 DOI: 10.1038/s41435-018-0034-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 02/08/2023]
Abstract
Eosinophilic esophagitis (EoE) is a chronic inflammatory disease of the esophagus triggered by immune hypersensitivity to food. Herein, we tested whether genetic risk factors for known, non-allergic, immune-mediated diseases, particularly those involving autoimmunity, were associated with EoE risk. We used the high-density Immunochip platform, encoding 200,000 genetic variants for major auto-immune disease. Accordingly, 1214 subjects with EoE of European ancestry and 3734 population controls were genotyped and assessed using data directly generated or imputed from the previously published GWAS. We found lack of association of EoE with the genetic variants in the major histocompatibility complex (MHC) class I, II, and III genes and nearly all other loci using a highly powered study design with dense genotyping throughout the locus. Importantly, we identified an EoE risk locus at 16p13 with genome-wide significance (Pcombined=2.05 × 10−9, odds ratio = 0.76−0.81). This region is known to encode for the genes CLEC16A, DEXI, and CIITI, which are expressed in immune cells and esophageal epithelial cells. Suggestive EoE risk were also seen 5q23 (intergenic) and 7p15 (JAZF1). Overall, we have identified an additional EoE risk locus at 16p13 and highlight a shared and unique genetic etiology of EoE with a spectrum of immune-associated diseases.
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146
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Prinz JC. Human Leukocyte Antigen-Class I Alleles and the Autoreactive T Cell Response in Psoriasis Pathogenesis. Front Immunol 2018; 9:954. [PMID: 29760713 PMCID: PMC5936982 DOI: 10.3389/fimmu.2018.00954] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2018] [Indexed: 01/08/2023] Open
Abstract
Psoriasis is a complex immune-mediated inflammatory skin disease characterized by T-cell-driven epidermal hyperplasia. It occurs on a strong genetic predisposition. The human leukocyte antigen (HLA)-class I allele HLA-C*06:02 on psoriasis susceptibility locus 1 (PSORS1 on 6p21.3) is the main psoriasis risk gene. Other HLA-class I alleles encoding HLA molecules presenting overlapping peptide repertoires show associations with psoriasis as well. Outside the major histocompatibility complex region, genome-wide association studies identified more than 60 psoriasis-associated common gene variants exerting only modest individual effects. They mainly refer to innate immune activation and the interleukin-23/Th/c17 pathway. Given their strong risk association, explaining the role of the HLA-risk alleles is essential for elucidating psoriasis pathogenesis. Psoriasis lesions develop upon epidermal infiltration, activation, and expansion of CD8+ T cells. The unbiased analysis of a paradigmatic Vα3S1/Vβ13S1-T-cell receptor from a pathogenic epidermal CD8+ T-cell clone of an HLA-C*06:02+ psoriasis patient had revealed that HLA-C*06:02 directs an autoimmune response against melanocytes through autoantigen presentation, and it identified a peptide form ADAMTS-like protein 5 as an HLA-C*06:02-presented melanocyte autoantigen. These data demonstrate that psoriasis is an autoimmune disease, where the predisposing HLA-class I alleles promote organ-specific inflammation through facilitating a T-cell response against a particular skin-specific cell population. This review discusses the role of HLA-class I alleles in the pathogenic psoriatic T-cell immune response. It concludes that as a principle of T-cell driven HLA-associated inflammatory diseases proinflammatory traits promote autoimmunity in the context of certain HLA molecules that present particular autoantigens.
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Affiliation(s)
- Jörg Christoph Prinz
- Department of Dermatology, University Clinics, Ludwig-Maximilian-University of Munich, Munich, Germany
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147
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Venkateswaran S, Prince J, Cutler DJ, Marigorta UM, Okou DT, Prahalad S, Mack D, Boyle B, Walters T, Griffiths A, Sauer CG, LeLeiko N, Keljo D, Markowitz J, Baker SS, Rosh J, Pfefferkorn M, Heyman MB, Patel A, Otley A, Baldassano R, Noe J, Rufo P, Oliva-Hemker M, Davis S, Zwick ME, Gibson G, Denson LA, Hyams J, Kugathasan S. Enhanced Contribution of HLA in Pediatric Onset Ulcerative Colitis. Inflamm Bowel Dis 2018; 24:829-838. [PMID: 29562276 PMCID: PMC6350448 DOI: 10.1093/ibd/izx084] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND The genetic contributions to pediatric onset ulcerative colitis (UC), characterized by severe disease and extensive colonic involvement, are largely unknown. In adult onset UC, Genome Wide Association Study (GWAS) has identified numerous loci, most of which have a modest susceptibility risk (OR 0.84-1.14), with the exception of the human leukocyte antigen (HLA) region on Chromosome 6 (OR 3.59). METHOD To study the genetic contribution to exclusive pediatric onset UC, a GWAS was performed on 466 cases with 2099 healthy controls using UK Biobank array. SNP2HLA was used to impute classical HLA alleles and their corresponding amino acids, and the results are compared with adult onset UC. RESULTS HLA explained the almost entire association signal, dominated with 191 single nucleotide polymorphisms (SNPs) (p = 5 x 10-8 to 5 x 10-10). Although very small effects, established SNPs in adult onset UC loci had similar direction and magnitude in pediatric onset UC. SNP2HLA imputation identified HLA-DRB1*0103 (odds ratio [OR] = 6.941, p = 1.92*10-13) as the most significant association for pediatric UC compared with adult onset UC (OR = 3.59). Further conditioning showed independent effects for HLA-DRB1*1301 (OR = 2.25, p = 7.92*10-9) and another SNP rs17188113 (OR = 0.48, p = 7.56*10-9). Two HLA-DRB1 causal alleles are shared with adult onset UC, while at least 2 signals are unique to pediatric UC. Subsequent stratified analyses indicated that HLA-DRB1*0103 has stronger association for extensive disease (E4: OR = 8.28, p = 4.66x10-10) and female gender (OR = 8.85, p = 4.82x10-13). CONCLUSION In pediatric onset UC, the HLA explains almost the entire genetic associations. In addition, the HLA association is approximately twice as strong in pediatric UC compared with adults, due to a combination of novel and shared effects. We speculate the paramount importance of antigenic stimulation either by infectious or noninfectious stimuli as a causal event in pediatric UC onset.
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Affiliation(s)
- Suresh Venkateswaran
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, GA
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, GA
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA
| | - David T Okou
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, GA
| | - Sampath Prahalad
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, GA
| | - David Mack
- Department of Pediatrics, Children’s Hospital of Eastern Ontario IBD Centre and University of Ottawa, Ontario, Canada
| | - Brendan Boyle
- Department of Gastroenterology, Nationwide Children’s Hospital Columbus, OH
| | - Thomas Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Cary G Sauer
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, GA
| | - Neal LeLeiko
- Division of Pediatric Gastroenterology, Nutrition, and Liver Diseases, Hasbro Children’s Hospital, Providence, RI
| | - David Keljo
- Gastroenterology, Hepatology and Nutrition Department, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA
| | - James Markowitz
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cohen Children’s Medical Center of NY, New Hyde Park, NY
| | - Susan S Baker
- Department of Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, NY
| | - Joel Rosh
- Department of Pediatrics, Goryeb Children’s Hospital, Morristown, NJ
| | - Marian Pfefferkorn
- Bronson Pediatric Gastroenterology, Bronson Children’s Hospital, Kalamazoo, MI
| | - Melvin B Heyman
- Department of Pediatrics, University of California at San Francisco, San Francisco, CA
| | - Ashish Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Anthony Otley
- Division of Pediatric Gastroenterology and Nutrition, Department of Pediatrics, IWK Health Centre, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Robert Baldassano
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA
| | - Joshua Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI
| | - Paul Rufo
- Division of Gastroenterology and Nutrition, Boston Children’s Hospital, Harvard Medical School, Boston, MA
| | - Maria Oliva-Hemker
- Department of Pediatrics, John Hopkins University School of Medicine, Baltimore, MD
| | - Sonia Davis
- Collaborative Studies Coordinating Center Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Jeffrey Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, CT
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, GA,Address correspondence to: Subra Kugathasan, MD, Division of Pediatric Gastroenterology, Emory University School of Medicine, 1760 Haygood Drive, W427, Atlanta, GA 30322. E-mail: Tel: 404 727 4542; Fax: 404 727 4069
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148
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DNA polymorphisms predict time to progression from uncomplicated to complicated Crohn's disease. Eur J Gastroenterol Hepatol 2018; 30:447-455. [PMID: 29293112 DOI: 10.1097/meg.0000000000001055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Most patients with Crohn's disease (CD) are diagnosed with the uncomplicated inflammatory form of the disease (Montreal stage B1). However, the majority of them will progress to complicated stricturing (B2) and penetrating (B3) CD during their lifetimes. The aim of our study was to identify the genetic factors associated with time to progression from uncomplicated to complicated CD. PATIENTS AND METHODS Patients with an inflammatory phenotype at diagnosis were followed up for 10 years. Genotyping was carried out using Illumina ImmunoChip. After quality control, association analyses, Bonferroni's adjustments, linear and Cox's regression, and Kaplan-Meier analysis were carried out for 111 patients and Manhattan plots were constructed. RESULTS Ten years after diagnosis, 39.1% of the patients still had the inflammatory form and 60.9% progressed to complicated disease, with an average time to progression of 5.91 years. Ileal and ileocolonic locations were associated with the complicated CD (P=1.08E-03). We found that patients with the AA genotype at single-nucleotide polymorphism rs16857259 near the gene CACNA1E progressed to the complicated form later (8.80 years) compared with patients with the AC (5.11 years) or CC (2.00 years) genotypes (P=3.82E-07). In addition, nine single-nucleotide polymorphisms (near the genes RASGRP1, SULF2, XPO1, ZBTB44, HLA DOA/BRD2, HLA DRB1/HLA DQA1, PPARA, PUDP, and KIAA1614) showed a suggestive association with disease progression (P<10). Multivariate Cox's regression analysis on the basis of clinical and genetic data confirmed the association of the selected model with disease progression (P=5.73E-16). CONCLUSION Our study confirmed the association between the locus on chromosome 1 near the gene CACNA1E with time to progression from inflammatory to stricturing or penetrating CD. Predicting the time to progression is useful to the clinician in terms of individualizing patients' management.
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149
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Yang C, Wu J, Zhang X, Wen L, Sun J, Cheng Y, Tang X, Liang B, Chen G, Zhou F, Cui Y, Zhang A, Zhang X, Zheng X, Yang S, Sun L. Fine-mapping analysis of the MHC region for vitiligo based on a new Han-MHC reference panel. Gene 2018; 648:76-81. [DOI: 10.1016/j.gene.2018.01.053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/30/2017] [Accepted: 01/16/2018] [Indexed: 11/26/2022]
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150
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Onoufriadis A, Stone K, Katsiamides A, Amar A, Omar Y, de Lange KM, Taylor K, Barrett JC, Pollok R, Hayee B, Mansfield JC, Sanderson JD, Simpson MA, Mathew CG, Prescott NJ. Exome Sequencing and Genotyping Identify a Rare Variant in NLRP7 Gene Associated With Ulcerative Colitis. J Crohns Colitis 2018; 12:321-326. [PMID: 29211899 PMCID: PMC6290881 DOI: 10.1093/ecco-jcc/jjx157] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND AIMS Although genome-wide association studies [GWAS] in inflammatory bowel disease [IBD] have identified a large number of common disease susceptibility alleles for both Crohn's disease [CD] and ulcerative colitis [UC], a substantial fraction of IBD heritability remains unexplained, suggesting that rare coding genetic variants may also have a role in pathogenesis. We used high-throughput sequencing in families with multiple cases of IBD, followed by genotyping of cases and controls, to investigate whether rare protein-altering genetic variants are associated with susceptibility to IBD. METHODS Whole-exome sequencing was carried out in 10 families in whom three or more individuals were affected with IBD. A stepwise filtering approach was applied to exome variants, to identify potential causal variants. Follow-up genotyping was performed in 6025 IBD cases [2948 CD; 3077 UC] and 7238 controls. RESULTS Our exome variant analysis revealed coding variants in the NLRP7 gene that were present in affected individuals in two distinct families. Genotyping of the two variants, p.S361L and p.R801H, in IBD cases and controls showed that the p.S361L variant was significantly associated with an increased risk of ulcerative colitis [odds ratio 4.79, p = 0.0039] and IBD [odds ratio 3.17, p = 0.037]. A combined analysis of both variants showed suggestive association with an increased risk of IBD [odds ratio 2.77, p = 0.018]. CONCLUSIONS The results suggest that NLRP7 signalling and inflammasome formation may be a significant component in the pathogenesis of IBD.
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Affiliation(s)
| | - Kristina Stone
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | - Antreas Katsiamides
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | - Ariella Amar
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | - Yasmin Omar
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | | | - Kirstin Taylor
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | | | - Richard Pollok
- Department Gastroenterology and Hepatology, St George’s University Hospitals NHS Foundation Trust, London, UK
| | - Bu’Hussain Hayee
- IBD Service, King’s College Hospital NHS Foundation Trust, London, UK
| | - John C Mansfield
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Jeremy D Sanderson
- Department of Gastroenterology, Guy’s and St Thomas’ NHS Foundation Trust, London, UK
| | - Michael A Simpson
- Department of Medical and Molecular Genetics, King’s College London, London, UK
| | - Christopher G Mathew
- Department of Medical and Molecular Genetics, King’s College London, London, UK,Sydney Brenner Institute for Molecular Bioscience, University of Witwatersrand, Johannesburg, South Africa
| | - Natalie J Prescott
- Department of Medical and Molecular Genetics, King’s College London, London, UK,Corresponding author: Natalie J. Prescott, PhD, Department of Medical and Molecular Genetics, Faculty of Life Sciences & Medicine, King’s College London, 7th Floor, Tower Wing, Guy’s Hospital, London, SE1 9RT. E-mail:
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