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Xu J, Xu HM, Yang MF, Liang YJ, Peng QZ, Zhang Y, Tian CM, Wang LS, Yao J, Nie YQ, Li DF. New Insights Into the Epigenetic Regulation of Inflammatory Bowel Disease. Front Pharmacol 2022; 13:813659. [PMID: 35173618 PMCID: PMC8841592 DOI: 10.3389/fphar.2022.813659] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 01/10/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the colonic mucosa. Environmental factors, genetics, intestinal microbiota, and the immune system are all involved in the pathophysiology of IBD. Lately, accumulating evidence has shown that abnormal epigenetic changes in DNA methylation, histone markers, and non-coding RNA expression greatly contribute to the development of the entire disease. Epigenetics regulates many functions, such as maintaining the homeostasis of the intestinal epithelium and regulating the immune system of the immune cells. In the present study, we systematically summarized the latest advances in epigenetic modification of IBD and how epigenetics reveals new mechanisms of IBD. Our present review provided new insights into the pathophysiology of IBD. Moreover, exploring the patterns of DNA methylation and histone modification through epigenetics can not only be used as biomarkers of IBD but also as a new target for therapeutic intervention in IBD patients.
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Affiliation(s)
- Jing Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Hao-ming Xu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Mei-feng Yang
- Department of Hematology, Yantian District People’s Hospital, Shenzhen, China
| | | | - Quan-zhou Peng
- Department of Pathology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Yuan Zhang
- Department of Medical Administration, Huizhou Institute of Occupational Diseases Control and Prevention, Huizhou, China
| | - Cheng-mei Tian
- Department of Emergency, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Li-sheng Wang
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - Jun Yao
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - Yu-qiang Nie
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
| | - De-feng Li
- Department of Gastroenterology, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- *Correspondence: De-feng Li, ; Li-sheng Wang, ; Jun Yao, ; Yu-qiang Nie,
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2
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Wahida A, Müller M, Hiergeist A, Popper B, Steiger K, Branca C, Tschurtschenthaler M, Engleitner T, Donakonda S, De Coninck J, Öllinger R, Pfautsch MK, Müller N, Silva M, Usluer S, Thiele Orberg E, Böttcher JP, Pfarr N, Anton M, Slotta-Huspenina JB, Nerlich AG, Madl T, Basic M, Bleich A, Berx G, Ruland J, Knolle PA, Rad R, Adolph TE, Vandenabeele P, Kanegane H, Gessner A, Jost PJ, Yabal M. XIAP restrains TNF-driven intestinal inflammation and dysbiosis by promoting innate immune responses of Paneth and dendritic cells. Sci Immunol 2021; 6:eabf7235. [PMID: 34739338 DOI: 10.1126/sciimmunol.abf7235] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deficiency in X-linked inhibitor of apoptosis protein (XIAP) is the cause for X-linked lymphoproliferative syndrome 2 (XLP2). About one-third of these patients suffer from severe and therapy-refractory inflammatory bowel disease (IBD), but the exact cause of this pathogenesis remains undefined. Here, we used XIAP-deficient mice to characterize the mechanisms underlying intestinal inflammation. In Xiap−/− mice, we observed spontaneous terminal ileitis and microbial dysbiosis characterized by a reduction of Clostridia species. We showed that in inflamed mice, both TNF receptor 1 and 2 (TNFR1/2) cooperated in promoting ileitis by targeting TLR5-expressing Paneth cells (PCs) or dendritic cells (DCs). Using intestinal organoids and in vivo modeling, we demonstrated that TLR5 signaling triggered TNF production, which induced PC dysfunction mediated by TNFR1. TNFR2 acted upon lamina propria immune cells. scRNA-seq identified a DC population expressing TLR5, in which Tnfr2 expression was also elevated. Thus, the combined activity of TLR5 and TNFR2 signaling may be responsible for DC loss in lamina propria of Xiap−/− mice. Consequently, both Tnfr1−/−Xiap−/− and Tnfr2−/−Xiap−/− mice were rescued from dysbiosis and intestinal inflammation. Furthermore, RNA-seq of ileal crypts revealed that in inflamed Xiap−/− mice, TLR5 signaling was abrogated, linking aberrant TNF responses with the development of a dysbiosis. Evidence for TNFR2 signaling driving intestinal inflammation was detected in XLP2 patient samples. Together, these data point toward a key role of XIAP in mediating resilience of TLR5-expressing PCs and intestinal DCs, allowing them to maintain tissue integrity and microbiota homeostasis.
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MESH Headings
- Animals
- Dendritic Cells/immunology
- Dysbiosis/immunology
- Humans
- Immunity, Innate/immunology
- Inflammation/immunology
- Intestines/immunology
- Mice
- Mice, Knockout
- Paneth Cells/immunology
- Receptors, Tumor Necrosis Factor, Type I/deficiency
- Receptors, Tumor Necrosis Factor, Type I/immunology
- Receptors, Tumor Necrosis Factor, Type II/deficiency
- Receptors, Tumor Necrosis Factor, Type II/immunology
- Toll-Like Receptor 5/immunology
- X-Linked Inhibitor of Apoptosis Protein/deficiency
- X-Linked Inhibitor of Apoptosis Protein/immunology
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Affiliation(s)
- Adam Wahida
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
| | - Madeleine Müller
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Bastian Popper
- Biomedical Center, Core Facility Animal Models, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Katja Steiger
- Institute of Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
- Comparative Experimental Pathology and Digital Pathology, Institute for Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
| | - Caterina Branca
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
| | - Markus Tschurtschenthaler
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Thomas Engleitner
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Jordy De Coninck
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Rupert Öllinger
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Marie K Pfautsch
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicole Müller
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Miguel Silva
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Sinem Usluer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Erik Thiele Orberg
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
| | - Jan P Böttcher
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
| | - Martina Anton
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia B Slotta-Huspenina
- Institute of Pathology and Pathological Anatomy, Technical University of Munich, Munich, Germany
| | - Andreas G Nerlich
- Institute of Pathology, Academic Clinic Munich-Bogenhausen, Munich, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Medical University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Hannover, Germany
| | - Geert Berx
- Molecular and Cellular Oncology Laboratory, Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Percy A Knolle
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Roland Rad
- TranslaTUM, Center for Translational Cancer Research, Munich, Germany
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, Munich, Germany
| | - Timon E Adolph
- Department of Internal Medicine I for Gastroenterology, Hepatology, and Endocrinology, Medical University of Innsbruck, Innsbruck, Austria
| | - Peter Vandenabeele
- Cell Death and Inflammation Unit, VIB-Center for Inflammation Research (IRC), VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology (DBMB), Ghent University, Ghent, Belgium
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Philipp J Jost
- Medical Department III for Hematology and Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
- Division of Clinical Oncology, Department of Medicine, Medical University of Graz, Graz, Austria
| | - Monica Yabal
- Institute of Molecular Immunology and Experimental Oncology, TUM School of Medicine, Technical University of Munich, Munich, Germany
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3
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Di Narzo AF, Hart A, Kosoy R, Peters L, Stojmirovic A, Cheng H, Zhang Z, Shan M, Cho J, Kasarskis A, Argmann C, Peter I, Schadt EE, Hao K. Polygenic risk score for alcohol drinking behavior improves prediction of inflammatory bowel disease risk. Hum Mol Genet 2021; 30:514-523. [PMID: 33601420 PMCID: PMC8599895 DOI: 10.1093/hmg/ddab045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/23/2021] [Accepted: 02/03/2021] [Indexed: 02/05/2023] Open
Abstract
Epidemiological studies have long recognized risky behaviors as potentially modifiable factors for the onset and flares of inflammatory bowel disease (IBD); yet, the underlying mechanisms are largely unknown. Recently, the genetic susceptibilities to cigarette smoking, alcohol and cannabis use [i.e. substance use (SU)] have been characterized by well-powered genome-wide association studies (GWASs). We aimed to assess the impact of genetic determinants of SU on IBD risk. Using Mount Sinai Crohn's and Colitis Registry (MSCCR) cohort of 1058 IBD cases and 188 healthy controls, we computed the polygenic risk score (PRS) for SU and correlated them with the observed IBD diagnoses, while adjusting for genetic ancestry, PRS for IBD and SU behavior at enrollment. The results were validated in a pediatric cohort with no SU exposure. PRS of alcohol consumption (DrnkWk), smoking cessation and age of smoking initiation, were associated with IBD risk in MSCCR even after adjustment for PRSIBD and actual smoking status. One interquartile range decrease in PRSDrnkWk was significantly associated to higher IBD risk (i.e. inverse association) (with odds ratio = 1.65 and 95% confidence interval: 1.32, 2.06). The association was replicated in a pediatric Crohn's disease cohort. Colocalization analysis identified a locus on chromosome 16 with polymorphisms in IL27, SULT1A2 and SH2B1, which reached genome-wide statistical significance in GWAS (P < 7.7e-9) for both alcohol consumption and IBD risk. This study demonstrated that the genetic predisposition to SU was associated with IBD risk, independent of PRSIBD and in the absence of SU behaviors. Our study may help further stratify individuals at risk of IBD.
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Affiliation(s)
- Antonio F Di Narzo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amy Hart
- Immunology Translational Sciences, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Roman Kosoy
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lauren Peters
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | | | - Haoxiang Cheng
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhongyang Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mingxu Shan
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Statistical Genomics, Sema4, Stamford, CT 06902, USA
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4
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Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn's Disease. Sci Rep 2021; 11:5595. [PMID: 33692434 PMCID: PMC7946957 DOI: 10.1038/s41598-021-84938-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 02/23/2021] [Indexed: 12/14/2022] Open
Abstract
Inflammatory bowel disease (IBD), clinically defined as Crohn’s disease (CD), ulcerative colitis (UC), or IBD-unclassified, results in chronic inflammation of the gastrointestinal tract in genetically susceptible hosts. Pediatric onset IBD represents ≥ 25% of all IBD diagnoses and often presents with intestinal stricturing, perianal disease, and failed response to conventional treatments. NOD2 was the first and is the most replicated locus associated with adult IBD, to date. However, its role in pediatric onset IBD is not well understood. We performed whole-exome sequencing on a cohort of 1,183 patients with pediatric onset IBD (ages 0–18.5 years). We identified 92 probands with biallelic rare and low frequency NOD2 variants accounting for approximately 8% of our cohort, suggesting a Mendelian inheritance pattern of disease. Additionally, we investigated the contribution of recessive inheritance of NOD2 alleles in adult IBD patients from a large clinical population cohort. We found that recessive inheritance of NOD2 variants explains ~ 7% of cases in this adult IBD cohort, including ~ 10% of CD cases, confirming the observations from our pediatric IBD cohort. Exploration of EHR data showed that several of these adult IBD patients obtained their initial IBD diagnosis before 18 years of age, consistent with early onset disease. While it has been previously reported that carriers of more than one NOD2 risk alleles have increased susceptibility to Crohn’s Disease (CD), our data formally demonstrate that recessive inheritance of NOD2 alleles is a mechanistic driver of early onset IBD, specifically CD, likely due to loss of NOD2 protein function. Collectively, our findings show that recessive inheritance of rare and low frequency deleterious NOD2 variants account for 7–10% of CD cases and implicate NOD2 as a Mendelian disease gene for early onset Crohn’s Disease.
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5
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Somineni HK, Nagpal S, Venkateswaran S, Cutler DJ, Okou DT, Haritunians T, Simpson CL, Begum F, Datta LW, Quiros AJ, Seminerio J, Mengesha E, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Iskandar H, Dryden GW, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kuemmerle JF, Lazarev M, Li E, Mannon P, Moulton DE, Newberry RD, Patel AS, Pekow J, Saeed SA, Valentine JF, Wang MH, McCauley JL, Abreu MT, Jester T, Molle-Rios Z, Palle S, Scherl EJ, Kwon J, Rioux JD, Duerr RH, Silverberg MS, Zwick ME, Stevens C, Daly MJ, Cho JH, Gibson G, McGovern DPB, Brant SR, Kugathasan S. Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease. Am J Hum Genet 2021; 108:431-445. [PMID: 33600772 PMCID: PMC8008495 DOI: 10.1016/j.ajhg.2021.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/01/2021] [Indexed: 12/20/2022] Open
Abstract
Whether or not populations diverge with respect to the genetic contribution to risk of specific complex diseases is relevant to understanding the evolution of susceptibility and origins of health disparities. Here, we describe a large-scale whole-genome sequencing study of inflammatory bowel disease encompassing 1,774 affected individuals and 1,644 healthy control Americans with African ancestry (African Americans). Although no new loci for inflammatory bowel disease are discovered at genome-wide significance levels, we identify numerous instances of differential effect sizes in combination with divergent allele frequencies. For example, the major effect at PTGER4 fine maps to a single credible interval of 22 SNPs corresponding to one of four independent associations at the locus in European ancestry individuals but with an elevated odds ratio for Crohn disease in African Americans. A rare variant aggregate analysis implicates Ca2+-binding neuro-immunomodulator CALB2 in ulcerative colitis. Highly significant overall overlap of common variant risk for inflammatory bowel disease susceptibility between individuals with African and European ancestries was observed, with 41 of 241 previously known lead variants replicated and overall correlations in effect sizes of 0.68 for combined inflammatory bowel disease. Nevertheless, subtle differences influence the performance of polygenic risk scores, and we show that ancestry-appropriate weights significantly improve polygenic prediction in the highest percentiles of risk. The median amount of variance explained per locus remains the same in African and European cohorts, providing evidence for compensation of effect sizes as allele frequencies diverge, as expected under a highly polygenic model of disease.
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Affiliation(s)
- Hari K Somineni
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA 30322, USA; Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Sini Nagpal
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Suresh Venkateswaran
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - David T Okou
- Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Claire L Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ferdouse Begum
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lisa W Datta
- Meyerhoff Inflammatory Bowel Disease Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Antonio J Quiros
- Department of Pediatrics, Medical University of South Carolina, Pediatric Center for Inflammatory Bowel Disorders, Summerville, SC 29485, USA
| | - Jenifer Seminerio
- Department of Gastroenterology, Medical University of South Carolina Digestive Disease Center, Charleston, SC 29425, USA
| | - Emebet Mengesha
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jonathan S Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, LA 71103, USA
| | - Robert N Baldassano
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine & Nursing, Baltimore, MD 21205, USA
| | - Raymond K Cross
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Themistocles Dassopoulos
- Baylor Scott and White Center for Inflammatory Bowel Diseases, Texas A&M University, Dallas, TX 75202, USA
| | - Lee A Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Tanvi A Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Heba Iskandar
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Gerald W Dryden
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Jason K Hou
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sunny Z Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, LA 71101, USA
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, CT 06106, USA
| | - Kim L Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Michael D Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, OH 44106, USA
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX 77030, USA
| | - John F Kuemmerle
- Division of Gastroenterology, Hepatology and Nutrition, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, VA 23284, USA
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, NY 11794, USA
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | | | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ashish S Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joel Pekow
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, IL 60637, USA
| | | | - John F Valentine
- University of Utah, Health Sciences, Salt Lake City, UT 84132, USA
| | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jacob L McCauley
- John P. Hussman Institute for Human Genomics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136 USA; The Dr. John T. Macdonald Foundation Department of Human Genetics, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Maria T Abreu
- Division of Gastroenterology, Department of Medicine, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Department of Microbiology and Immunology, Leonard M. Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Traci Jester
- Department of Pediatrics, UAB Medicine, Birmingham, AL 35233, USA
| | - Zarela Molle-Rios
- Pediatric Gastroenterology and Nutrition, Nemours duPont Hospital for Children, DE 19803, USA
| | - Sirish Palle
- Department of Pediatrics, Oklahoma University School of Medicine, Oklahoma City, OK 73104, USA
| | - Ellen J Scherl
- Gastroenterology and Hepatology, Jill Roberts Center for IBD, Weill Cornell Medicine, New York, NY 10065, USA
| | - John Kwon
- UT Southwestern Department of Internal Medicine, Dallas, TX 75390, USA
| | - John D Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, QC H1Y3N1, Canada
| | - Richard H Duerr
- Human Genetics, and Clinical and Translational Science, Pittsburgh, PA 15213, USA
| | - Mark S Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, ON M5T3L9, Canada
| | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, GA 30322, USA
| | - Christine Stevens
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Judy H Cho
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Steven R Brant
- The Human Genetics Institute of New Jersey, Rutgers University, New Brunswick and Piscataway, NJ 08854, USA
| | - Subra Kugathasan
- Genetics and Molecular Biology Program, Emory University, Atlanta, GA 30322, USA; Division of Pediatric Gastroenterology, Department of Pediatrics, Emory University School of Medicine & Children's Healthcare of Atlanta, Atlanta, GA 30322, USA.
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6
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Hübenthal M, Löscher BS, Erdmann J, Franke A, Gola D, König IR, Emmert H. Current Developments of Clinical Sequencing and the Clinical Utility of Polygenic Risk Scores in Inflammatory Diseases. Front Immunol 2021; 11:577677. [PMID: 33633722 PMCID: PMC7901950 DOI: 10.3389/fimmu.2020.577677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 12/10/2020] [Indexed: 12/03/2022] Open
Abstract
In this mini-review, we highlight selected research by the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence “Precision Medicine in Chronic Inflammation” focusing on clinical sequencing and the clinical utility of polygenic risk scores as well as its implication on precision medicine in the field of the inflammatory diseases inflammatory bowel disease, atopic dermatitis and coronary artery disease. Additionally, we highlight current developments and discuss challenges to be faced in the future. Exemplary, we point to residual challenges in detecting disease-relevant variants resulting from difficulties in the interpretation of candidate variants and their potential interactions. While polygenic risk scores represent promising tools for the stratification of patient groups, currently, polygenic risk scores are not accurate enough for clinical setting. Precision medicine, incorporating additional data from genomics, transcriptomics and proteomics experiments, may enable the identification of distinct disease pathogeneses. In the future, data-intensive biomedical innovation will hopefully lead to improved patient stratification for personalized medicine.
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Affiliation(s)
- Matthias Hübenthal
- Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Britt-Sabina Löscher
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | - Damian Gola
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Inke R König
- Institute of Medical Biometry and Statistics, University of Lübeck, Lübeck, Germany
| | - Hila Emmert
- Department of Dermatology, Quincke Research Center, University Hospital Schleswig-Holstein, Kiel, Germany
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7
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Konidari A, Dickens D, Pirmohamed M. Inflammatory Bowel Disease: A Personalized Approach. Front Pediatr 2020; 8:620545. [PMID: 33643966 PMCID: PMC7904676 DOI: 10.3389/fped.2020.620545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 12/30/2020] [Indexed: 11/30/2022] Open
Affiliation(s)
- Anastasia Konidari
- B Pediatric Clinic, Paidon Aglaia Kyriakou Children's Hospital, Athens, Greece.,The Wolfson Centre for Personalized Medicine, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, United Kingdom
| | - David Dickens
- The Wolfson Centre for Personalized Medicine, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, United Kingdom
| | - Munir Pirmohamed
- The Wolfson Centre for Personalized Medicine, Institute of Systems, Molecular and Integrative Biology (ISMIB), University of Liverpool, Liverpool, United Kingdom
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8
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Abstract
Interleukin (IL)-10 is an essential anti-inflammatory cytokine and functions as a negative regulator of immune responses to microbial antigens. IL-10 is particularly important in maintaining the intestinal microbe-immune homeostasis. Loss of IL-10 promotes the development of inflammatory bowel disease (IBD) as a consequence of an excessive immune response to the gut microbiota. IL-10 also functions more generally to prevent excessive inflammation during the course of infection. Although IL-10 can be produced by virtually all cells of the innate and adaptive immune system, T cells constitute a non-redundant source for IL-10 in many cases. The various roles of T cell-derived IL-10 will be discussed in this review. Given that IL-10 is at the center of maintaining the delicate balance between effective immunity and tissue protection, it is not surprising that IL-10 expression is highly dynamic and tightly regulated. We summarize the environmental signals and molecular pathways that regulate IL-10 expression. While numerous studies have provided us with a deep understanding of IL-10 biology, the majority of findings have been made in murine models, prompting us to highlight gaps in our knowledge about T cell-derived IL-10 in the human system.
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9
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Serologic, but Not Genetic, Markers Are Associated With Impaired Anthropometrics at Diagnosis of Pediatric Crohn's Disease. J Pediatr Gastroenterol Nutr 2019; 69:e129-e134. [PMID: 31393333 DOI: 10.1097/mpg.0000000000002462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES Children with Crohn's disease may present with malnutrition and linear growth impairment, which can be secondary to insufficient caloric intake, chronic inflammation, malabsorption, and suppression of growth-promoting hormones. We evaluated clinical, serologic, and genetic data to determine risk factors for impaired anthropometrics in Crohn's disease at diagnosis. METHODS Our study evaluated 772 children newly diagnosed with Crohn's disease, inflammatory phenotype, enrolled in the RISK Stratification Project to determine the factors associated with anthropometric impairment. Data were collected on demographics, growth parameters, disease location, serologic and immunologic markers, and disease severity. We performed a genome-wide association study of genetic polymorphisms associated with inflammatory bowel disease. Regression analysis determined associations between anthropometrics and clinical, serologic, and genetic variables. RESULTS There were 59 (7%) children with height z score <-2, 126 (14%) with a weight z score <-2, and 156 (17%) with a body mass index z score <-2. Linear growth impairment was associated with hypoalbuminemia (P = 0.0052), elevated granulocyte-macrophage colony stimulating factor autoantibodies (P = 0.0110), and elevated CBir antibodies against flagellin (P = 0.0117). Poor weight gain was associated with female sex (P = 0.0401), hypoalbuminemia (P = 0.0162), and thrombocytosis (P = 0.0081). Malnutrition was associated with hypoalbuminemia (P = 0.0061) and thrombocytosis (P = 0.0011). Children with moderate or severe disease had lower weight (P = 0.02 and P = 1.16×10, respectively) and body mass index z scores (P = 2.7 × 10 and P = 1.01 × 10, respectively) than children with quiescent and mild disease. There was no association between age of diagnosis, Tanner stage, or disease location and having impaired anthropometrics. There was no genome-wide association between the genetic polymorphisms and the serologic variables and anthropometric measurements. CONCLUSIONS This is the largest study evaluating growth in treatment-naïve children with Crohn's disease, inflammatory phenotype. It is the first study to use genome-wide sequencing to assess for genetic determinants of growth impairment. Granulocyte-macrophage colony stimulating factor autoantibodies and CBir antibodies are more likely to be elevated in children with growth impairment. Future investigations should evaluate the relationship between genetic polymorphisms, pathologic immune responses, and the biological pathways regulating growth.
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10
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Sun S, Ye Z, Zheng S, Chen G, Qian X, Dong K, Huang Y. Surgical treatment of monogenic inflammatory bowel disease: A single clinical center experience. J Pediatr Surg 2019; 54:2155-2161. [PMID: 31027905 DOI: 10.1016/j.jpedsurg.2019.02.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 02/07/2023]
Abstract
PURPOSE With the wide application of immunologic reconstitution treatment, such as hematopoietic stem-cell transplantation (HSCT), most patients of inflammatory bowel disease (IBD) with immunodeficiency owing to monogenic abnormalities need surgical intervention during the course of treatment, which is quite different from traditional IBD surgery. The aim of this study was to generalize the surgical strategies as a part of comprehensive therapy for these rare diseases. METHODS A retrospective study was conducted based on the clinical data of children with immunodeficiency-derived IBD who underwent surgical treatment in Children's Hospital of Fudan University between January 2015 and December 2017. RESULTS A total of 18 patients with monogenic abnormalities were enrolled. The major surgical indications included 11 cases of acute or chronic intestinal obstructions, 4 refractory intestinal infections, and 3 pneumoperitoneum, while 12 cases had perforations noted during intraoperative exploration. All of the patients underwent varieties of enterostomies to divert the affected or obstructed intestine during the primary surgery. Wound infections or dehiscence occurred in 7 patients, and 2 patients underwent reoperations for adhesive intestinal obstruction and prolapse. Postoperatively, 15 patients survived, 13 of which achieved immune reconstitution through subsequent HSCT or immunoglobulin supplementation. In the second-stage surgery, a posterior sagittal approach rectal resection was performed in 5 patients with complex anorectal complications. Twelve patients had undergone stoma closure procedures. CONCLUSION Surgical intervention should be performed earlier because the perforations are usually insidious in monogenic IBD. Preventative enterostomies are suggested in preparation for HSCT among patients with severe anorectal complications. Wound infections are the most common complication after the primary operation. Posterior sagittal rectal resection is a good option for patients with complex anorectal complications. TYPE OF STUDY Clinical research paper. LEVEL OF EVIDENCE Level IV.
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Affiliation(s)
- Song Sun
- Surgical department, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Ziqing Ye
- Gastroenterology department, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Shan Zheng
- Surgical department, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Gong Chen
- Surgical department, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Xiaowen Qian
- Hematology department, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Kuiran Dong
- Surgical department, Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Ying Huang
- Gastroenterology department, Children's Hospital of Fudan University, Shanghai, 201102, China.
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11
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Gettler K, Giri M, Kenigsberg E, Martin J, Chuang LS, Hsu NY, Denson LA, Hyams JS, Griffiths A, Noe JD, Crandall WV, Mack DR, Kellermayer R, Abraham C, Hoffman G, Kugathasan S, Cho JH. Prioritizing Crohn's disease genes by integrating association signals with gene expression implicates monocyte subsets. Genes Immun 2019; 20:577-588. [PMID: 30692607 DOI: 10.1038/s41435-019-0059-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/27/2018] [Accepted: 01/07/2019] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies have identified ~170 loci associated with Crohn's disease (CD) and defining which genes drive these association signals is a major challenge. The primary aim of this study was to define which CD locus genes are most likely to be disease related. We developed a gene prioritization regression model (GPRM) by integrating complementary mRNA expression datasets, including bulk RNA-Seq from the terminal ileum of 302 newly diagnosed, untreated CD patients and controls, and in stimulated monocytes. Transcriptome-wide association and co-expression network analyses were performed on the ileal RNA-Seq datasets, identifying 40 genome-wide significant genes. Co-expression network analysis identified a single gene module, which was substantially enriched for CD locus genes and most highly expressed in monocytes. By including expression-based and epigenetic information, we refined likely CD genes to 2.5 prioritized genes per locus from an average of 7.8 total genes. We validated our model structure using cross-validation and our prioritization results by protein-association network analyses, which demonstrated significantly higher CD gene interactions for prioritized compared with non-prioritized genes. Although individual datasets cannot convey all of the information relevant to a disease, combining data from multiple relevant expression-based datasets improves prediction of disease genes and helps to further understanding of disease pathogenesis.
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Affiliation(s)
- Kyle Gettler
- Department of Genetics, Yale University, New Haven, Connecticut, 06510, USA
| | - Mamta Giri
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Ephraim Kenigsberg
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Jerome Martin
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Ling-Shiang Chuang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Nai-Yun Hsu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Oio, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, Connecticut, USA
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | - David R Mack
- Department of Pediatrics, Children's Hospital of Eastern Ontario IBD Centre and University of Ottawa, Ottawa, Ontario, Canada
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Clara Abraham
- Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut, 06510, USA
| | - Gabriel Hoffman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA
| | - Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, Georgia, USA.,Children's Healthcare of Atlanta, Atlanta, Georgia, USA
| | - Judy H Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA. .,Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, 10029, USA.
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12
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Ouahed J, Gordon W, Canavan JB, Zhou H, Du S, von Schack D, Phillips K, Wang L, Dunn WA, Field M, Friel S, Griffith A, Evans S, Tollefson S, Carrellas M, Cao B, Merker A, Bousvaros A, Shouval DS, Hung K, Lepsy C, Afzelius L, Korzenik JR, Snapper SB. Mucosal Gene Expression in Pediatric and Adult Patients With Ulcerative Colitis Permits Modeling of Ideal Biopsy Collection Strategy for Transcriptomic Analysis. Inflamm Bowel Dis 2018; 24:2565-2578. [PMID: 30085215 PMCID: PMC6265054 DOI: 10.1093/ibd/izy242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Transcriptional profiling has been performed on biopsies from ulcerative colitis patients. Limitations in prior studies include the variability introduced by inflammation, anatomic site of biopsy, extent of disease, and medications. We sought to more globally understand the variability of gene expression from patients with ulcerative colitis to advance our understanding of its pathogenesis and to guide clinical study design. METHODS We performed transcriptional profiling on 13 subjects, including pediatric and adult patients from 2 hospital sites. For each patient, we collected 6 biopsies from macroscopically inflamed tissue and 4 biopsies from macroscopically healthy-appearing tissue. Isolated RNA was used for microarray gene expression analysis utilizing Affymetrix Human Primeview microarrays. Ingenuity pathway analysis was used to assess over-representation of gene ontology and biological pathways. RNAseq was also performed, and differential analysis was assessed to compare affected vs unaffected samples. Finally, we modeled the minimum number of biopsies required to reliably detect gene expression across different subject numbers. RESULTS Transcriptional profiles co-clustered independently of the hospital collection site, patient age, sex, and colonic location, which parallels prior gene expression findings. A small set of genes not previously described was identified. Our modeling analysis reveals the number of biopsies and patients per cohort to yield reliable results in clinical studies. CONCLUSIONS Key findings include concordance, including some expansion, of previously published gene expression studies and similarity among different age groups. We also established a reliable statistical model for biopsy collection for future clinical studies.
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Affiliation(s)
- Jodie Ouahed
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - William Gordon
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - James B Canavan
- Department of Medicine, Harvard Medical School, Boston, Massachusetts,Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Huanyu Zhou
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - Sarah Du
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - David von Schack
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | | | - Lu Wang
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - W Augustine Dunn
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Shelby Friel
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Alexandra Griffith
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Spencer Evans
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Sophia Tollefson
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | - Madeline Carrellas
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Bonnie Cao
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Ami Merker
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Athos Bousvaros
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Dror S Shouval
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - BCH IBD Center
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts
| | | | - Kenneth Hung
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | | | - Lovisa Afzelius
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts
| | - Joshua R Korzenik
- Department of Medicine, Harvard Medical School, Boston, Massachusetts,Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women’s Hospital, Boston, Massachusetts
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts,Department of Medicine, Harvard Medical School, Boston, Massachusetts,Division of Gastroenterology, Hepatology and Endoscopy, Brigham & Women’s Hospital, Boston, Massachusetts,Address correspondence to: Scott B. Snapper, MD, PhD, 300 Longwood Ave, Enders 601, Boston, MA 02115 ()
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13
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Molecular Comparison of Adult and Pediatric Ulcerative Colitis Indicates Broad Similarity of Molecular Pathways in Disease Tissue. J Pediatr Gastroenterol Nutr 2018; 67:45-52. [PMID: 29401083 DOI: 10.1097/mpg.0000000000001898] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Efficacy data from adult ulcerative colitis (UC) clinical trials are often extrapolated for pediatric prescribing. Consequently, it is important to understand similarities/differences in pediatric and adult UC. Pediatric UC tends to have more extensive disease at presentation, yet genetic studies have not detected pathways that distinguish the populations, and differences in mucosal gene expression between adult and pediatric UC are not well characterized. METHODS Using colonic microarray data from a phase 3 trial of golimumab in adult UC (87 UC; 21 healthy), the GSE10616 pediatric dataset (10 UC; 11 healthy), and a phase 1B trial of golimumab in pediatric UC (n = 19), UC expression profiles were compared and unique genes were defined as those with significant changes (|FC|>2×, adjusted P < 0.05) in one population, but not the other (|FC| < 1.2×, adjusted P > 0.05). Pathway and upstream regulator analyses were performed. Profiles by disease extent (extensive [pancolitis] vs limited [left-sided] involvement) were compared within each population. RESULTS Pediatric and adult disease profiles overlapped substantially, with ∼50% to 75% overlap, depending on the fold-change cutoff used. Conversely, <10% of the disease profiles were unique to each population. Similar canonical pathways were enriched in both datasets. Predicted upstream regulators were also concordant, including lipopolysaccharide, interleukin-1β, and tumor necrosis factor-α. Expression profiles of extensive UC were indistinguishable from those of patients with limited involvement in each population. CONCLUSIONS The UC gene expression landscape is shared by adults and children, independent of disease extent. This supports extrapolation of efficacy from adults to children in developing new therapies for UC.
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14
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Denson LA, Jurickova I, Karns R, Shaw KA, Cutler DJ, Okou D, Dodd A, Quinn K, Mondal K, Aronow BJ, Haberman Y, Linn A, Price A, Bezold R, Lake K, Jackson K, Walters TD, Griffiths A, Baldassano RN, Noe JD, Hyams JS, Crandall WV, Kirschner BS, Heyman MB, Snapper S, Guthery SL, Dubinsky MC, Leleiko NS, Otley AR, Xavier RJ, Stevens C, Daly MJ, Zwick ME, Kugathasan S. Clinical and Genomic Correlates of Neutrophil Reactive Oxygen Species Production in Pediatric Patients With Crohn's Disease. Gastroenterology 2018; 154:2097-2110. [PMID: 29454792 PMCID: PMC5985211 DOI: 10.1053/j.gastro.2018.02.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Individuals with monogenic disorders of phagocyte function develop chronic colitis that resembles Crohn's disease (CD). We tested for associations between mutations in genes encoding reduced nicotinamide adenine dinucleotide phosphate (NADPH) oxidases, neutrophil function, and phenotypes of CD in pediatric patients. METHODS We performed whole-exome sequence analysis to identify mutations in genes encoding NADPH oxidases (such as CYBA, CYBB, NCF1, NCF2, NCF4, RAC1, and RAC2) using DNA from 543 pediatric patients with inflammatory bowel diseases. Blood samples were collected from an additional 129 pediatric patients with CD and 26 children without IBD (controls); we performed assays for neutrophil activation, reactive oxygen species (ROS) production, and bacteria uptake and killing. Whole-exome sequence analysis was performed using DNA from 46 of the children with CD to examine associations with NADPH gene mutations; RNA sequence analyses were performed using blood cells from 46 children with CD to test for variations in neutrophil gene expression associated with ROS production. RESULTS We identified 26 missense mutations in CYBA, CYBB, NCF1, NCF2, and NCF4. Patients with CD who carried mutations in these genes were 3-fold more likely to have perianal disease (P = .0008) and stricturing complications (P = .002) than children with CD without these mutations. Among patients with CD with none of these mutations, 9% had undergone abdominal surgery; among patients with mutations in these NADPH oxidase genes, 31% had undergone abdominal surgery (P = .0004). A higher proportion of neutrophils from children with CD had low ROS production (47%) than from controls (15%) among the 129 patients tested for ROS (P = .002). Minor alleles of the NADPH genes were detected in 7% of children with CD whose neutrophils produced normal levels of ROS vs 38% of children whose neutrophils produced low levels of ROS (P = .009). Neutrophils that produced low levels of ROS had specific alterations in genes that regulate glucose metabolism and antimicrobial responses. CONCLUSIONS We identified missense mutations in genes that encode NADPH oxidases in children with CD; these were associated with a more aggressive disease course and reduced ROS production by neutrophils from the patients.
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Affiliation(s)
- Lee A. Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA,to whom correspondence should be addressed: MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229, Tel: 513-636-7575, Fax: 513-636-5581,
| | - Ingrid Jurickova
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Rebekah Karns
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kelly A. Shaw
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Okou
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Anne Dodd
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Kathryn Quinn
- Cancer and Blood Disease Institute, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kajari Mondal
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Bruce J. Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aaron Linn
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Adam Price
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Ramona Bezold
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathleen Lake
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kimberly Jackson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Cincinnati College of Medicine and the Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thomas D. 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
| | - Robert N. Baldassano
- Department of Pediatrics, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua D. Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeffrey S. Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children’s Medical Center, Hartford, CT, USA
| | - Wallace V. Crandall
- Department of Pediatric Gastroenterology, Nationwide Children’s Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | | | - Melvin B. Heyman
- Department of Pediatrics, University of California at San Francisco, San Francisco, CA, USA
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | | | | | - Neal S. Leleiko
- Department of Pediatrics, Hasbro Children’s Hospital, Providence, RI, USA
| | - Anthony R. Otley
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | | | - Mark J. Daly
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University, Atlanta, GA, USA
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15
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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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16
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Shaw KA, Cutler DJ, Okou D, Dodd A, Aronow BJ, Haberman Y, Stevens C, Walters TD, Griffiths A, Baldassano RN, Noe JD, Hyams JS, Crandall WV, Kirschner BS, Heyman MB, Snapper S, Guthery S, Dubinsky MC, Shapiro JM, Otley AR, Daly M, Denson LA, Kugathasan S, Zwick ME. Genetic variants and pathways implicated in a pediatric inflammatory bowel disease cohort. Genes Immun 2018; 20:131-142. [PMID: 29593342 PMCID: PMC6162182 DOI: 10.1038/s41435-018-0015-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/28/2017] [Accepted: 09/11/2017] [Indexed: 12/13/2022]
Abstract
In the United States, approximately 5% of individuals with inflammatory bowel disease (IBD) are younger than 20 years old. Studies of pediatric cohorts can provide unique insights into genetic architecture of IBD, which includes Crohn's disease (CD) and ulcerative colitis (UC). Large genome-wide association studies have found more than 200 IBD-associated loci but explain a minority of disease variance for CD and UC. We sought to characterize the contribution of rare variants to disease development, comparing exome sequencing of 368 pediatric IBD patients to publicly available exome sequencing (dbGaP) and aggregate frequency data (ExAC). Using dbGaP data, we performed logistic regression for common variants and optimal unified association tests (SKAT-O) for rare, likely-deleterious variants. We further compared rare variants to ExAC counts with Fisher's exact tests. We did pathway enrichment analysis on the most significant genes from each comparison. Many variants overlapped with known IBD-associated genes (e.g. NOD2). Rare variants were enriched in CD-associated loci (p = 0.009) and showed suggestive enrichment in neutrophil function genes (p = 0.05). Pathway enrichment implicated immune-related pathways, especially cell killing and apoptosis. Variants in extracellular matrix genes also emerged as an important theme in our analysis.
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Affiliation(s)
- Kelly A Shaw
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David J Cutler
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - David Okou
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Anne Dodd
- Department of Pediatrics, Emory University, Atlanta, GA, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Yael Haberman
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Robert N Baldassano
- Department of Pediatrics, University of Pennsylvania, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Barbara S Kirschner
- Department of Pediatrics, The University of Chicago Comer Children's Hospital, Chicago, IL, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California at San Francisco, San Francisco, CA, USA
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Stephen Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
| | - Jason M Shapiro
- Department of Pediatrics, Hasbro Children's Hospital, Providence, RI, USA
| | - Anthony R Otley
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Mark Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Michael E Zwick
- Department of Human Genetics, Emory University, Atlanta, GA, USA.
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17
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NOX1 loss-of-function genetic variants in patients with inflammatory bowel disease. Mucosal Immunol 2018; 11:562-574. [PMID: 29091079 PMCID: PMC5924597 DOI: 10.1038/mi.2017.74] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/20/2017] [Indexed: 02/07/2023]
Abstract
Genetic defects that affect intestinal epithelial barrier function can present with very early-onset inflammatory bowel disease (VEOIBD). Using whole-genome sequencing, a novel hemizygous defect in NOX1 encoding NAPDH oxidase 1 was identified in a patient with ulcerative colitis-like VEOIBD. Exome screening of 1,878 pediatric patients identified further seven male inflammatory bowel disease (IBD) patients with rare NOX1 mutations. Loss-of-function was validated in p.N122H and p.T497A, and to a lesser degree in p.Y470H, p.R287Q, p.I67M, p.Q293R as well as the previously described p.P330S, and the common NOX1 SNP p.D360N (rs34688635) variant. The missense mutation p.N122H abrogated reactive oxygen species (ROS) production in cell lines, ex vivo colonic explants, and patient-derived colonic organoid cultures. Within colonic crypts, NOX1 constitutively generates a high level of ROS in the crypt lumen. Analysis of 9,513 controls and 11,140 IBD patients of non-Jewish European ancestry did not reveal an association between p.D360N and IBD. Our data suggest that loss-of-function variants in NOX1 do not cause a Mendelian disorder of high penetrance but are a context-specific modifier. Our results implicate that variants in NOX1 change brush border ROS within colonic crypts at the interface between the epithelium and luminal microbes.
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18
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Haberman Y, BenShoshan M, Di Segni A, Dexheimer PJ, Braun T, Weiss B, Walters TD, Baldassano RN, Noe JD, Markowitz J, Rosh J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Kellermayer R, Patel A, Otley A, Steiner SJ, Gulati AS, Guthery SL, LeLeiko N, Moulton D, Kirschner BS, Snapper S, Avivi C, Barshack I, Oliva-Hemker M, Cohen SA, Keljo DJ, Ziring D, Anikster Y, Aronow B, Hyams JS, Kugathasan S, Denson LA. Long ncRNA Landscape in the Ileum of Treatment-Naive Early-Onset Crohn Disease. Inflamm Bowel Dis 2018; 24:346-360. [PMID: 29361088 PMCID: PMC6231367 DOI: 10.1093/ibd/izx013] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNA) are key regulators of gene transcription and many show tissue-specific expression. We previously defined a novel inflammatory and metabolic ileal gene signature in treatment-naive pediatric Crohn disease (CD). We now extend our analyses to include potential regulatory lncRNA. METHODS Using RNAseq, we systematically profiled lncRNAs and protein-coding gene expression in 177 ileal biopsies. Co-expression analysis was used to identify functions and tissue-specific expression. RNA in situ hybridization was used to validate expression. Real-time polymerase chain reaction was used to test lncRNA regulation by IL-1β in Caco-2 enterocytes. RESULTS We characterize widespread dysregulation of 459 lncRNAs in the ileum of CD patients. Using only the lncRNA in discovery and independent validation cohorts showed patient classification as accurate as the protein-coding genes, linking lncRNA to CD pathogenesis. Co-expression and functional annotation enrichment analyses across several tissues and cell types 1showed that the upregulated LINC01272 is associated with a myeloid pro-inflammatory signature, whereas the downregulated HNF4A-AS1 exhibits association with an epithelial metabolic signature. We confirmed tissue-specific expression in biopsies using in situ hybridization, and validated regulation of prioritized lncRNA upon IL-1β exposure in differentiated Caco-2 cells. Finally, we identified significant correlations between LINC01272 and HNF4A-AS1 expression and more severe mucosal injury. CONCLUSIONS We systematically define differentially expressed lncRNA in the ileum of newly diagnosed pediatric CD. We show lncRNA utility to correctly classify disease or healthy states and demonstrate their regulation in response to an inflammatory signal. These lncRNAs, after mechanistic exploration, may serve as potential new tissue-specific targets for RNA-based interventions.
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Affiliation(s)
- Yael Haberman
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio,Sheba Medical Center, Israel,Address correspondence to: Yael Haberman, Division of Pediatric Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, MLC 2010, 3333 Burnet Avenue, Cincinnati, OH 45229 ()
| | | | | | | | | | - Batia Weiss
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | - Thomas D Walters
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - Joshua D Noe
- Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Joel Rosh
- Goryeb Children’s Hospital/Atlantic Health, Morristown, New Jersey
| | - Melvin B Heyman
- University of California, San Francisco, San Francisco, California
| | - Anne M Griffiths
- Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | | | - David R Mack
- Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada
| | | | | | - Ashish Patel
- UT Southwestern Medical Center at Dallas, Dallas, Texas
| | | | | | - Ajay S Gulati
- University of North Carolina, Chapel Hill, North Carolina
| | | | | | | | | | | | | | - Iris Barshack
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | | | - Stanley A Cohen
- Children’s Center for Digestive Healthcare, Atlanta, Georgia
| | - David J Keljo
- Children’s Hospital of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Yair Anikster
- Sheba Medical Center, Israel,Tel Aviv University, Israel
| | - Bruce Aronow
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Jeffrey S Hyams
- Connecticut Children’s Medical Center, Hartford, Connecticut
| | | | - Lee A Denson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
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19
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Abstract
Very early onset inflammatory bowel disease (VEO-IBD) represents a unique and growing subset of patients with inflammatory bowel disease (IBD). Some VEO-IBD patients present with immunodeficiency and possess loss of function genetic mutations involving immune pathways that cause their IBD. A search for Mendelian causes of IBD is likely most beneficial when the presentation involves extra-intestinal autoimmunity or involves intestinal histopathology that is atypical for IBD. While a subset of these young patients will have highly aggressive courses (and likely present with immunodeficiency), the majority of patients with VEO-IBD appear to have disease courses similar to that of their older counterparts. Most notably, many of these young children will require long courses of immunosuppression simply as a result of the profoundly early presentation-thus increasing their long-term risks of cancer and opportunistic infections.
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Affiliation(s)
- Christopher J Moran
- Harvard Medical School, Department of Pediatrics, 175 Cambridge St, Suite 567, Boston, MA 02114.
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20
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Petersen BS, August D, Abt R, Alddafari M, Atarod L, Baris S, Bhavsar H, Brinkert F, Buchta M, Bulashevska A, Chee R, Cordeiro AI, Dara N, Dückers G, Elmarsafy A, Frede N, Galal N, Gerner P, Glocker EO, Goldacker S, Hammermann J, Hasselblatt P, Havlicekova Z, Hübscher K, Jesenak M, Karaca NE, Karakoc-Aydiner E, Kharaghani MM, Kilic SS, Kiykim A, Klein C, Klemann C, Kobbe R, Kotlarz D, Laass MW, Leahy TR, Mesdaghi M, Mitton S, Neves JF, Öztürk B, Pereira LF, Rohr J, Restrepo JLR, Ruzaike G, Saleh N, Seneviratne S, Senol E, Speckmann C, Tegtmeyer D, Thankam P, van der Werff Ten Bosch J, von Bernuth H, Zeissig S, Zeissig Y, Franke A, Grimbacher B. Targeted Gene Panel Sequencing for Early-onset Inflammatory Bowel Disease and Chronic Diarrhea. Inflamm Bowel Dis 2017; 23:2109-2120. [PMID: 28930861 DOI: 10.1097/mib.0000000000001235] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND In contrast to adult-onset inflammatory bowel disease (IBD), where many genetic loci have been shown to be involved in complex disease etiology, early-onset IBD (eoIBD) and associated syndromes can sometimes present as monogenic conditions. As a result, the clinical phenotype and ideal disease management in these patients often differ from those in adult-onset IBD. However, due to high costs and the complexity of data analysis, high-throughput screening for genetic causes has not yet become a standard part of the diagnostic work-up of eoIBD patients. METHODS We selected 28 genes of interest associated with monogenic IBD and performed targeted panel sequencing in 71 patients diagnosed with eoIBD or early-onset chronic diarrhea to detect causative variants. We compared these results to whole-exome sequencing (WES) data available for 25 of these patients. RESULTS Target coverage was significantly higher in the targeted gene panel approach compared with WES, whereas the cost of the panel was considerably lower (approximately 25% of WES). Disease-causing variants affecting protein function were identified in 5 patients (7%), located in genes of the IL10 signaling pathway (3), WAS (1), and DKC1 (1). The functional effects of 8 candidate variants in 5 additional patients (7%) are under further investigation. WES did not identify additional causative mutations in 25 patients. CONCLUSIONS Targeted gene panel sequencing is a fast and effective screening method for monogenic causes of eoIBD that should be routinely established in national referral centers.
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Affiliation(s)
- Britt-Sabina Petersen
- 1Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany; 2Center for Chronic Immunodeficiency (CCI), DZIF Satellite Center, Medical Center, Faculty of Medicine, Germany; 3Paediatric Gastroenterology, Klinikum Nürnberg, Nuremberg, Germany; 4Laboratory of Applied Molecular Biology and Immunology, University of Abou-Bekr Belkaïd, Tlemcen, Algeria; 5Department of Pediatrics, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; 6Clinic of Pediatric Allergy and Immunology, Marmara University Pendik Training and Research Hospital, Istanbul, Turkey; 7Department of Gastroenterology and Clinical Nutrition, Birmingham Children's Hospital, Birmingham, United Kingdom; 8Department of Paediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; 9Department of Immunology, Royal Free Hospital, London, United Kingdom; 10Primary Immunodeficiencies Unit, Hospital Dona Estefania, Pediatric University Hospital, and CEDOC, Chronic Diseases Research Center, NOVA Medical School, Lisbon, Portugal; 11Department of Pediatric Gasteroentrology and Hepatology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 12Helios Kliniken, Childrens Hospital, Krefeld, Germany; 13Pediatrics Department, Faculty of Medicine, Cairo University, Cairo, Egypt; 14Paediatric Gastroenterology/Hepatology, University of Freiburg, Freiburg, Germany; 15Institute of Medical Microbiology and Hygiene, University of Freiburg, Freiburg, Germany; 16Department of Pediatrics, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany; 17Department of Medicine II, University Hospital and Medical Faculty, University Freiburg, Freiburg, Germany; 18Department of Paediatrics, Centre for Diagnosis and Treatment of Primary Immunodeficiencies, Jessenius Faculty of Medicine, Commenius University in Bratislava, Martin, Slovakia; 19Department of Pediatrics, Faculty of Medicine, Ege University, Izmir, Turkey; 20Department of Allergy and Clinical Immunology, Mofid Children's Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 21Pediatric Immunology Division, Uludag University Medical Faculty, Department of Pediatrics, Bursa, Turkey; 22Dr. von Hauner Children's Hospital, Department of Pediatrics, Ludwig-Maximilians-Universität Munich, Munich, Germany; 23Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; 24Center for Pediatrics, Department of Pediatric Hematology and Oncology, University Medical Center, University of Freiburg, Faculty of Medicine, University of Freiburg, Germany; 25Department of Paediatric Immunology and Infectious Diseases, Our Lady's Children's Hospital, Dublin, Ireland; 26Department of Immunology, Mofid Children Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran; 27Department of Paediatric Gastroenterology, St. George's Healthcare NHS Trust and University of London, London, United Kingdom; 28Department of Gastroenterology and Clinical Nutrition, Marmara University Medical Faculty, Istanbul, Turkey; 29Service of Clinical Laboratory, Division of Immunology, San Pedro De Alcántara Hospital, Cáceres, Spain; 30Bone Marrow Failure Group, Division of Pediatric Hematology and Oncology, University of Freiburg, Germany; 31Children's Hospital, University of Bonn, Germany; 32University College London Institute of Immunity and Transplantation, Royal Free Campus, London, United Kingdom; 33Department of Paediatrics, St. George's Hospital, University of London, London, United Kingdom; 34Department of Pediatrics, Universitair Ziekenhuis Brussel, Brussels, Belgium; 35Pediatric Pneumology and Immunology, Department of Immunology, Charité University Medicine Labor Berlin Charité Vivantes GmbH, Berlin, Germany; 36Department of Medicine I, University Medical Center Dresden, Technische Universität Dresden, Dresden, Germany; 37Center for Regenerative Therapies, Technische Universität Dresden, Dresden, Germany; and 38Institute of Laboratory Medicine, Brandenburg Hospital, Brandenburg Medical School, Brandenburg/Havel, Germany
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21
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Pal LR, Kundu K, Yin Y, Moult J. CAGI4 Crohn's exome challenge: Marker SNP versus exome variant models for assigning risk of Crohn disease. Hum Mutat 2017; 38:1225-1234. [PMID: 28512778 PMCID: PMC5576730 DOI: 10.1002/humu.23256] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/18/2022]
Abstract
Understanding the basis of complex trait disease is a fundamental problem in human genetics. The CAGI Crohn's Exome challenges are providing insight into the adequacy of current disease models by requiring participants to identify which of a set of individuals has been diagnosed with the disease, given exome data. For the CAGI4 round, we developed a method that used the genotypes from exome sequencing data only to impute the status of genome wide association studies marker SNPs. We then used the imputed genotypes as input to several machine learning methods that had been trained to predict disease status from marker SNP information. We achieved the best performance using Naïve Bayes and with a consensus machine learning method, obtaining an area under the curve of 0.72, larger than other methods used in CAGI4. We also developed a model that incorporated the contribution from rare missense variants in the exome data, but this performed less well. Future progress is expected to come from the use of whole genome data rather than exomes.
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Affiliation(s)
- Lipika R. Pal
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
| | - Kunal Kundu
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Yizhou Yin
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - John Moult
- Institute for Bioscience and Biotechnology Research, University of Maryland, 9600 Gudelsky Drive, Rockville, MD 20850
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
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22
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DPB, Kugathasan S. Re: Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:2082-2083. [PMID: 28478146 PMCID: PMC6033331 DOI: 10.1053/j.gastro.2017.02.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 02/17/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn’s disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10−8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10−6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide signifi-cance on conditioning), IL12B, PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R. Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee,Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, Medical University of South Carolina, Pediatric Center for Inflammatory Bowel Disorders, Summerville, South Carolina
| | - Jenifer Seminerio
- Department of Gastroenterology, Medical University of South Carolina Digestive Disease Center, Charleston, South Carolina
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan S. Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | - Robert N. Baldassano
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine & Nursing, Baltimore, Maryland
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Lee A. Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Tanvi A. Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, Kentucky
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, North Carolina
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; Veterans Affairs Health Services Research and Development Service, Center for Innovations in Quality Effectiveness and Safety; Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, Louisiana
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Michael D. Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, Ohio
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children’s Hospital, Houston, Texas
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children’s Hospital, Chicago, Illinois
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, Virginia
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, New York
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | | | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida, Jacksonville, Florida
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, Quebec, Canada
| | - Richard H. Duerr
- Department of Medicine and Clinical and Translational Science Institute, School of Medicine and Department of Human Genetics, Graduate School of Public Health; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Personalized Medicine, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Dermot P. B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia,Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
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23
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Blutt SE, Broughman JR, Zou W, Zeng XL, Karandikar UC, In J, Zachos NC, Kovbasnjuk O, Donowitz M, Estes MK. Gastrointestinal microphysiological systems. Exp Biol Med (Maywood) 2017; 242:1633-1642. [PMID: 28534432 DOI: 10.1177/1535370217710638] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Gastrointestinal diseases are a significant health care and economic burden. Prevention and treatment of these diseases have been limited by the available human biologic models. Microphysiological systems comprise organ-specific human cultures that recapitulate many structural, biological, and functional properties of the organ in smaller scale including aspects of flow, shear stress and chemical gradients. The development of intestinal microphysiological system platforms represents a critical component in improving our understanding, prevention, and treatment of gastrointestinal diseases. This minireview discusses: shortcomings of classical cell culture models of the gastrointestinal tract; human intestinal enteroids as a new model and their advantages compared to cell lines; why intestinal microphysiological systems are needed; potential functional uses of intestinal microphysiological systems in areas of drug development and modeling acute and chronic diseases; and current challenges in the development of intestinal microphysiological systems. Impact statement The development of a gastrointestinal MPS has the potential to facilitate the understanding of GI physiology. An ultimate goal is the integration of the intestinal MPS with other organ MPS. The development and characterization of nontransformed human intestinal cultures for use in MPS have progressed significantly since the inception of the MPS program in 2012, and these cultures are a key component of advancing MPS. Continued efforts are needed to optimize MPS to comprehensively and accurately recapitulate the complexity of the intestinal epithelium within intestinal tissue. These systems will need to include peristalsis, flow, and oxygen gradients, with incorporation of vascular, immune, and nerve cells. Regional cellular organization of crypt and villus areas will also be necessary to better model complete intestinal structure.
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Affiliation(s)
- Sarah E Blutt
- 1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Broughman
- 1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Winnie Zou
- 1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xi-Lei Zeng
- 1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Umesh C Karandikar
- 1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julie In
- 2 Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Nicholas C Zachos
- 2 Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Olga Kovbasnjuk
- 2 Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mark Donowitz
- 2 Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Mary K Estes
- 1 Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA.,3 Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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24
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Stephens MC, Boardman LA, Lazaridis KN. Individualized Medicine in Gastroenterology and Hepatology. Mayo Clin Proc 2017; 92:810-825. [PMID: 28473040 DOI: 10.1016/j.mayocp.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 02/23/2017] [Accepted: 03/02/2017] [Indexed: 02/08/2023]
Abstract
After the completion of the Human Genome Project, there has been an acceleration in methodologies on sequencing nucleic acids (DNA and RNA) at a high precision and with ever-decreasing turnaround time and cost. Collectively, these approaches are termed next-generation sequencing and are already affecting the transformation of medical practice. In this symposium article, we highlight the current knowledge of the genetics of selected gastrointestinal tract and liver diseases, namely, inflammatory bowel disease, hereditary cholestatic liver disease, and familial colon cancer syndromes. In addition, we provide a stepwise approach to use next-generation sequencing methodologies for clinical practice with the goal to improve the diagnosis as well as management of and/or therapy of the chosen digestive diseases. This early experience of applying next-generation sequencing in the practice of gastroenterology and hepatology will delineate future best practices in the field, ultimately for the benefit of our patients.
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Affiliation(s)
- Michael C Stephens
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN
| | - Lisa A Boardman
- Division of Gastroenterology and Hepatology, College of Medicine, Mayo Clinic, Rochester, MN
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25
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Kugathasan S, Denson LA, Walters TD, Kim MO, Marigorta UM, Schirmer M, Mondal K, Liu C, Griffiths A, Noe JD, Crandall WV, Snapper S, Rabizadeh S, Rosh JR, Shapiro JM, Guthery S, Mack DR, Kellermayer R, Kappelman MD, Steiner S, Moulton DE, Keljo D, Cohen S, Oliva-Hemker M, Heyman MB, Otley AR, Baker SS, Evans JS, Kirschner BS, Patel AS, Ziring D, Trapnell BC, Sylvester FA, Stephens MC, Baldassano RN, Markowitz JF, Cho J, Xavier RJ, Huttenhower C, Aronow BJ, Gibson G, Hyams JS, Dubinsky MC. Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study. Lancet 2017; 389:1710-1718. [PMID: 28259484 PMCID: PMC5719489 DOI: 10.1016/s0140-6736(17)30317-3] [Citation(s) in RCA: 437] [Impact Index Per Article: 62.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 11/18/2016] [Accepted: 11/26/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Stricturing and penetrating complications account for substantial morbidity and health-care costs in paediatric and adult onset Crohn's disease. Validated models to predict risk for complications are not available, and the effect of treatment on risk is unknown. METHODS We did a prospective inception cohort study of paediatric patients with newly diagnosed Crohn's disease at 28 sites in the USA and Canada. Genotypes, antimicrobial serologies, ileal gene expression, and ileal, rectal, and faecal microbiota were assessed. A competing-risk model for disease complications was derived and validated in independent groups. Propensity-score matching tested the effect of anti-tumour necrosis factor α (TNFα) therapy exposure within 90 days of diagnosis on complication risk. FINDINGS Between Nov 1, 2008, and June 30, 2012, we enrolled 913 patients, 78 (9%) of whom experienced Crohn's disease complications. The validated competing-risk model included age, race, disease location, and antimicrobial serologies and provided a sensitivity of 66% (95% CI 51-82) and specificity of 63% (55-71), with a negative predictive value of 95% (94-97). Patients who received early anti-TNFα therapy were less likely to have penetrating complications (hazard ratio [HR] 0·30, 95% CI 0·10-0·89; p=0·0296) but not stricturing complication (1·13, 0·51-2·51; 0·76) than were those who did not receive early anti-TNFα therapy. Ruminococcus was implicated in stricturing complications and Veillonella in penetrating complications. Ileal genes controlling extracellular matrix production were upregulated at diagnosis, and this gene signature was associated with stricturing in the risk model (HR 1·70, 95% CI 1·12-2·57; p=0·0120). When this gene signature was included, the model's specificity improved to 71%. INTERPRETATION Our findings support the usefulness of risk stratification of paediatric patients with Crohn's disease at diagnosis, and selection of anti-TNFα therapy. FUNDING Crohn's and Colitis Foundation of America, Cincinnati Children's Hospital Research Foundation Digestive Health Center.
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Affiliation(s)
- Subra Kugathasan
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA; Children's Healthcare of Atlanta, Atlanta, GA, USA.
| | - Lee A Denson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Thomas D Walters
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Mi-Ok Kim
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Urko M Marigorta
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Melanie Schirmer
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Kajari Mondal
- Division of Pediatric Gastroenterology, Emory University School of Medicine, Atlanta, GA, USA
| | - Chunyan Liu
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anne Griffiths
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Joshua D Noe
- Department of Pediatric Gastroenterology, Hepatology, and Nutrition, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Wallace V Crandall
- Department of Pediatric Gastroenterology, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Scott Snapper
- Department of Gastroenterology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Joel R Rosh
- Department of Pediatrics, Goryeb Children's Hospital, Morristown, NJ, USA
| | - Jason M Shapiro
- Department of Pediatrics, Hasbro Children's Hospital, Providence, RI, USA
| | - Stephen Guthery
- Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - David R Mack
- Department of Pediatrics, Children's Hospital of Eastern Ontario IBD Centre and University of Ottawa, ON, Canada
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael D Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Steven Steiner
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dedrick E Moulton
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Keljo
- Department of Gastroenterology, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
| | - Stanley Cohen
- Children's Healthcare of Atlanta, Atlanta, GA, USA; Children's Center for Digestive Health Care, Atlanta, GA, USA
| | - Maria Oliva-Hemker
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Melvin B Heyman
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Anthony R Otley
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Susan S Baker
- Department of Digestive Diseases and Nutrition Center, University at Buffalo, Buffalo, NY, USA
| | - Jonathan S Evans
- Department of Pediatrics, Nemours Children's Specialty Care, Jacksonville, FL, USA
| | | | - Ashish S Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David Ziring
- Department of Pediatrics, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - Bruce C Trapnell
- Division of Pulmonary Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Francisco A Sylvester
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael C Stephens
- Department of Pediatric Gastroenterology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Judy Cho
- Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
| | - Ramnik J Xavier
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Center for Computational and Integrative Biology, Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Curtis Huttenhower
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Biostatistics, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Bruce J Aronow
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Greg Gibson
- Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Jeffrey S Hyams
- Division of Digestive Diseases, Hepatology, and Nutrition, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Marla C Dubinsky
- Department of Pediatrics, Mount Sinai Hospital, New York, NY, USA
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26
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Abstract
The human epigenome may link environmental exposures and commensal microbiota changes to host pathology in respect to the developmental origins of inflammatory bowel diseases (ulcerative colitis [UC] and Crohn's disease [more appropriately Crohn disease, CD]). Genetic predisposition - prenatal, perinatal and pediatric environmental influences - microbiome aberration (dysbiosis) and immune dysregulation appear to be important elements in disease development, progression and maintenance. The prevalence of combined genetic and epigenetic susceptibility toward UC and CD is calculated herein to be as high as 2%, and approximately 1% for UC and CD in highly developed countries, respectively. This review emphasizes the significant challenges for epigenetic research in inflammatory bowel diseases. Overcoming these challenges, however, could reveal unique opportunities for disease prevention, treatment and possible cure.
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Affiliation(s)
- Richard Kellermayer
- Section of Pediatric Gastroenterology, Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, USDA/ARS Children's Nutrition Research Center, Houston, TX 77030, USA
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27
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Brant SR, Okou DT, Simpson CL, Cutler DJ, Haritunians T, Bradfield JP, Chopra P, Prince J, Begum F, Kumar A, Huang C, Venkateswaran S, Datta LW, Wei Z, Thomas K, Herrinton LJ, Klapproth JMA, Quiros AJ, Seminerio J, Liu Z, Alexander JS, Baldassano RN, Dudley-Brown S, Cross RK, Dassopoulos T, Denson LA, Dhere TA, Dryden GW, Hanson JS, Hou JK, Hussain SZ, Hyams JS, Isaacs KL, Kader H, Kappelman MD, Katz J, Kellermayer R, Kirschner BS, Kuemmerle JF, Kwon JH, Lazarev M, Li E, Mack D, Mannon P, Moulton DE, Newberry RD, Osuntokun BO, Patel AS, Saeed SA, Targan SR, Valentine JF, Wang MH, Zonca M, Rioux JD, Duerr RH, Silverberg MS, Cho JH, Hakonarson H, Zwick ME, McGovern DPB, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:206-217.e2. [PMID: 27693347 PMCID: PMC5164948 DOI: 10.1053/j.gastro.2016.09.032] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 09/14/2016] [Accepted: 09/17/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. METHODS We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10-8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. RESULTS We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10-6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B,PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. CONCLUSIONS We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the importance of studying the genetics of IBD and other complex diseases in populations beyond those of European ancestry.
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Affiliation(s)
- Steven R Brant
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David T Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Claire L Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, Tennessee; Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan P Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | | | - Lisa W Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | | | - Antonio J Quiros
- Department of Pediatrics, Medical University of South Carolina, Pediatric Center for Inflammatory Bowel Disorders, Summerville, South Carolina
| | - Jenifer Seminerio
- Department of Gastroenterology, Medical University of South Carolina Digestive Disease Center, Charleston, South Carolina
| | - Zhenqiu Liu
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jonathan S Alexander
- Department of Molecular and Cellular Physiology, Louisiana State University Health Sciences Center, Shreveport, Louisiana
| | - Robert N Baldassano
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Sharon Dudley-Brown
- Department of Medicine, Johns Hopkins University Schools of Medicine & Nursing, Baltimore, Maryland
| | - Raymond K Cross
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | | | - Lee A Denson
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Tanvi A Dhere
- Department of Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Gerald W Dryden
- Department of Medicine, University of Louisville, Louisville, Kentucky
| | - John S Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, North Carolina
| | - Jason K Hou
- Department of Medicine, Baylor College of Medicine; Veterans Affairs Health Services Research and Development Service, Center for Innovations in Quality Effectiveness and Safety; Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Sunny Z Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport, Louisiana
| | - Jeffrey S Hyams
- Connecticut Children's Medical Center, Hartford, Connecticut
| | - Kim L Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Howard Kader
- Department of Pediatrics, University of Maryland School of Medicine, Baltimore, Maryland
| | - Michael D Kappelman
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jeffry Katz
- Case Western Reserve University, Cleveland, Ohio
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Barbara S Kirschner
- Department of Pediatrics, University of Chicago Comer Children's Hospital, Chicago, Illinois
| | - John F Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, Virginia
| | - John H Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Mark Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ellen Li
- Department of Medicine, Stony Brook University School of Medicine, Stony Brook, New York
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | | | - Rodney D Newberry
- Department of Internal Medicine, Washington University School of Medicine, St Louis, Missouri
| | | | - Ashish S Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Shehzad A Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Stephan R Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida, Jacksonville, Florida
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, Michigan
| | - John D Rioux
- Department of Medicine, Université de Montréal and the Montreal Heart Institute Research Center, Montreal, Quebec, Canada
| | - Richard H Duerr
- Department of Medicine and Clinical and Translational Science Institute, School of Medicine and Department of Human Genetics, Graduate School of Public Health; University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mark S Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, Canada
| | - Judy H Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Personalized Medicine, New York, New York
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael E Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia
| | - Dermot P B McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Subra Kugathasan
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia; Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia.
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Genetic architecture differences between pediatric and adult-onset inflammatory bowel diseases in the Polish population. Sci Rep 2016; 6:39831. [PMID: 28008999 PMCID: PMC5180213 DOI: 10.1038/srep39831] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/29/2016] [Indexed: 12/15/2022] Open
Abstract
Most inflammatory bowel diseases (IBDs) are classic complex disorders represented by common alleles. Here we aimed to define the genetic architecture of pediatric and adult-onset IBDs for the Polish population. A total of 1495 patients were recruited, including 761 patients with Crohn’s disease (CD; 424 pediatric), 734 patients with ulcerative colitis (UC; 390 pediatric), and 934 healthy controls. Allelotyping employed a pooled-DNA genome-wide association study (GWAS) and was validated by individual genotyping. Whole exome sequencing (WES) was performed on 44 IBD patients diagnosed before 6 years of age, 45 patients diagnosed after 40 years of age, and 18 healthy controls. Altogether, out of 88 selected SNPs, 31 SNPs were replicated for association with IBD. A novel BRD2 (rs1049526) association reached significance of P = 5.2 × 10−11 and odds ratio (OR) = 2.43. Twenty SNPs were shared between pediatric and adult patients; 1 and 7 were unique to adult-onset and pediatric-onset IBD, respectively. WES identified numerous rare and potentially deleterious variants in IBD-associated or innate immunity-associated genes. Deleterious alleles in both groups were over-represented among rare variants in affected children. Our GWAS revealed differences in the polygenic architecture of pediatric- and adult-onset IBD. A significant accumulation of rare and deleterious variants in affected children suggests a contribution by yet unexplained genetic components.
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Targeted Sequencing and Immunological Analysis Reveal the Involvement of Primary Immunodeficiency Genes in Pediatric IBD: a Japanese Multicenter Study. J Clin Immunol 2016; 37:67-79. [PMID: 27747465 DOI: 10.1007/s10875-016-0339-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/21/2016] [Indexed: 12/13/2022]
Abstract
PURPOSE Pediatric inflammatory bowel disease (IBD) is a heterogeneous disorder caused by multiple factors. Although genetic and immunological analyses are required for a definitive diagnosis, no reports of a comprehensive genetic study of a Japanese population are available. METHODS In total, 35 Japanese patients <16 years of age suffering from IBD, including 27 patients aged <6 years with very early-onset IBD, were enrolled in this multicenter study. Exome and targeted gene panel sequencing was performed for all patients. Mutations in genes responsible for primary immunodeficiency diseases (PID) and clinical and immunological parameters were evaluated according to disease type. RESULTS We identified monogenic mutations in 5 of the 35 patients (14.3 %). We identified compound heterozygous and homozygous splice-site mutations in interleukin-10 receptor A (IL-10RA) in two patients, nonsense mutations in X-linked inhibitor of apoptosis protein (XIAP) in two patients, and a missense mutation in cytochrome b beta chain in one patient. Using assays for protein expression levels, IL-10 signaling, and cytokine production, we confirmed that the mutations resulted in loss of function. For each patient, genotype was significantly associated with clinical findings. We successfully treated a patient with a XIAP mutation by allogeneic cord blood hematopoietic stem cell transplantation, and his symptoms were ameliorated completely. CONCLUSIONS Targeted sequencing and immunological analysis are useful for screening monogenic disorders and selecting curative therapies in pediatric patients with IBD. The genes responsible for PID are frequently involved in pediatric IBD and play critical roles in normal immune homeostasis in the gastrointestinal tract.
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Ananthakrishnan AN, Shi HY, Tang W, Law CCY, Sung JJY, Chan FKL, Ng SC. Systematic Review and Meta-analysis: Phenotype and Clinical Outcomes of Older-onset Inflammatory Bowel Disease. J Crohns Colitis 2016; 10:1224-36. [PMID: 26928965 PMCID: PMC6082591 DOI: 10.1093/ecco-jcc/jjw054] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 02/09/2016] [Accepted: 02/11/2016] [Indexed: 12/18/2022]
Abstract
BACKGROUND Little is known of the clinical outcome of patients with older-onset inflammatory bowel disease [IBD]. We performed a systematic review to determine phenotype and outcomes of older-onset IBD compared with younger-onset subjects. METHODS A systematic search of Embase and Medline up to June 2015 identified studies investigating phenotype and outcomes of older-onset [diagnosed at age ≥ 50 years] Crohn's disease [CD] and ulcerative colitis [UC] subjects. Pooled analyses of disease phenotype, medication use, and disease-related surgery were calculated. RESULTS We analysed findings from 43 studies comprising 8274 older-onset and 34641 younger-onset IBD subjects. Compared with younger-onset patients, older-onset CD patients were more likely to have colonic disease (odds ratio [OR] 2.56, 95% confidence interval [CI] 1.88 - 3.48) and inflammatory behaviour [OR 1.19, 95% CI 1.07 - 1.33], and less likely to have penetrating disease or perianal involvement. More older-onset UC patients had left-sided colitis [OR 1.49, 95% CI 1.18 - 1.88]. Although fewer older-onset IBD patients received immunomodulators [CD: OR 0.44; UC: OR 0.60] or biologicals [CD: OR 0.34; UC: OR 0.41], older-onset CD was similar in the need for surgery [OR 0.70, 95% CI 0.40 - 1.22] whereas more older-onset UC patients underwent surgery [OR 1.36, 95% CI 1.18 - 1.57]. CONCLUSIONS Elderly IBD patients present with less complicated disease, but have similar or higher rates of surgery than non-elderly patients. Whether this reflects a non-benign disease course, physicians' reluctance to employ immunomodulators, or both, merits further study which is essential for improving the care of IBD in the elderly.
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Affiliation(s)
- Ashwin N Ananthakrishnan
- Division of Gastroenterology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hai Yun Shi
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Whitney Tang
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Cindy C Y Law
- University of Ottawa School of Medicine, Ottawa, ON, Canada
| | - Joseph J Y Sung
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Francis K L Chan
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
| | - Siew C Ng
- Department of Medicine and Therapeutics, Institute of Digestive Disease, Chinese University of Hong Kong, Hong Kong
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31
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Li X, Song P, Timofeeva M, Meng X, Rudan I, Little J, Satsangi J, Campbell H, Theodoratou E. Systematic meta-analyses and field synopsis of genetic and epigenetic studies in paediatric inflammatory bowel disease. Sci Rep 2016; 6:34076. [PMID: 27670835 PMCID: PMC5037432 DOI: 10.1038/srep34076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 09/01/2016] [Indexed: 02/08/2023] Open
Abstract
We provide a comprehensive field synopsis of genetic and epigenetic associations for paediatric Inflammatory Bowel Disease (IBD). A systematic review was performed and included 84 genetic association studies reporting data for 183 polymorphisms in 71 genes. Meta-analyses were conducted for 20 SNPs in 10 genes of paediatric Crohn’s disease (CD) and for 8 SNPs in 5 genes of paediatric ulcerative colitis (UC). Five epigenetic studies were also included, but formal meta-analysis was not possible. Venice criteria and Bayesian false discovery probability test were applied to assess the credibility of associations. Nine SNPs in 4 genes were considered to have highly credible associations with paediatric CD, of which four variants (rs2066847, rs12521868, rs26313667, rs1800629) were not previously identified in paediatric GWAS. Differential DNA methylation in NOD2 and TNF-α, dysregulated expression in let-7 and miR-124 were associated with paediatric IBD, but not as yet replicated. Highly credible SNPs associated with paediatric IBD have also been implicated in adult IBD, with similar magnitudes of associations. Early onset and distinct phenotypic features of paediatric IBD might be due to distinct epigenetic changes, but these findings need to be replicated. Further progress identifying genetic and epigenetic susceptibility of paediatric IBD will require international collaboration, population diversity and harmonization of protocols.
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Affiliation(s)
- Xue Li
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peige Song
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Maria Timofeeva
- Colon Cancer Genetics Group and Academic Coloproctology, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Xiangrui Meng
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Julian Little
- School of Epidemiology, Public Health and Preventive Medicine, University of Ottawa, Ottawa, Canada
| | - Jack Satsangi
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh and Western General Hospital Edinburgh, Edinburgh, United Kingdom
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Evropi Theodoratou
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Frey MR. Disease-Associated Microbial Communities in Healthy Relatives: A Bacteria-Filled Crystal Ball? Cell Mol Gastroenterol Hepatol 2016; 2:710-711. [PMID: 28174743 PMCID: PMC5247345 DOI: 10.1016/j.jcmgh.2016.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Affiliation(s)
- Mark R. Frey
- Correspondence Address correspondence to: Mark R. Frey, PhD, The Saban Research Institute, Children’s Hospital Los Angeles, 4650 Sunset Boulevard, MS 137, Los Angeles, California 90027.The Saban Research InstituteChildren’s Hospital Los Angeles4650 Sunset BoulevardMS 137Los AngelesCalifornia 90027
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Capriati T, Cardile S, Papadatou B, Romano C, Knafelz D, Bracci F, Diamanti A. Pediatric inflammatory bowel disease: specificity of very early onset. Expert Rev Clin Immunol 2016; 12:963-72. [DOI: 10.1080/1744666x.2016.1184571] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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