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Senapati S, Singh H, Bk T, Verma N, Kumar U. HLA sequencing identifies novel associations and suggests clinical relevance of DPB1*04:01 in ANCA-associated Granulomatosis with polyangiitis. Gene 2024; 896:148024. [PMID: 38040271 DOI: 10.1016/j.gene.2023.148024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
Granulomatosis with polyangiitis (GPA) is a rare systemic autoimmune disease. Major contributions of HLA genes have been reported; however, HLA typing-based diagnosis or risk prediction in GPA has not been established. We have performed a sequencing-based HLA genotyping in a north Indian GPA cohort and controls to identify clinically relevant novel associations. PR3-ANCA-positive 40 GPA patients and 40 healthy controls from north India were recruited for the study. Targeted sequencing of HLA-A,-B,-C,-DRB1,-DQB1, and -DPB1 was performed. Allelic and haplotypic associations were tested. Molecular docking of susceptibility HLA alleles with reported super-antigen epitopes was performed. The association of substituted amino acids located at the antigen-binding domain of HLA was evaluated. Genetic association of five HLA-alleles was identified in GPA. The novel association was identified for C*15:02 (p = 0.04; OR = 0.27(0.09-0.88)). The strongest association was observed for DPB1*04:01 (p < 0.0001; OR = 6.2(3.08-11.71)), previously reported in European studies. 35 of 40 GPA subjects had at least one DPB1*04:01 allele, and its significant risk was previously not reported from the Indian population. Significantly associated haplotypes DRB1*03:01-DQB1*02:01-DPB1*04:01 (p = 0.02; OR = 3.46(1.11-12.75)) and DRB1*07:01-DQB1*02:02-DPB1*04:01 (p = 0.04; OR = 3.35(0.95-14.84)) were the most frequent in GPA patients. Ranging from 89 % to 100 % of GPA patients with organ involvement can be explained by at least one DPB1*04:01 allele. A strong interaction between the HLA and three epitopes of the reported super antigen TSST-1 of Staphylococcus aureus was confirmed. Our study highlighted the potential applicability of HLA typing for screening and diagnosis of GPA. A large multi-centric study and genotype-phenotype correlation analysis among GPA patients will enable the establishment of HLA-typing based GPA diagnosis.
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Affiliation(s)
- Sabyasachi Senapati
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Punjab, India.
| | - Harinder Singh
- Immunogenomics Laboratory, Department of Human Genetics and Molecular Medicine, Central University of Punjab, Punjab, India
| | - Thelma Bk
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - Narendra Verma
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India
| | - Uma Kumar
- Department of Rheumatology, All India Institute of Medical Sciences, New Delhi, India.
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Akhlaghpour M, Haritunians T, More SK, Thomas LS, Stamps DT, Dube S, Li D, Yang S, Landers CJ, Mengesha E, Hamade H, Murali R, Potdar AA, Wolf AJ, Botwin GJ, Khrom M, Ananthakrishnan AN, Faubion WA, Jabri B, Lira SA, Newberry RD, Sandler RS, Sartor RB, Xavier RJ, Brant SR, Cho JH, Duerr RH, Lazarev MG, Rioux JD, Schumm LP, Silverberg MS, Zaghiyan K, Fleshner P, Melmed GY, Vasiliauskas EA, Ha C, Rabizadeh S, Syal G, Bonthala NN, Ziring DA, Targan SR, Long MD, McGovern DPB, Michelsen KS. Genetic coding variant in complement factor B (CFB) is associated with increased risk for perianal Crohn's disease and leads to impaired CFB cleavage and phagocytosis. Gut 2023; 72:2068-2080. [PMID: 37080587 PMCID: PMC11036449 DOI: 10.1136/gutjnl-2023-329689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/09/2023] [Indexed: 04/22/2023]
Abstract
OBJECTIVE Perianal Crohn's disease (pCD) occurs in up to 40% of patients with CD and is associated with poor quality of life, limited treatment responses and poorly understood aetiology. We performed a genetic association study comparing CD subjects with and without perianal disease and subsequently performed functional follow-up studies for a pCD associated SNP in Complement Factor B (CFB). DESIGN Immunochip-based meta-analysis on 4056 pCD and 11 088 patients with CD from three independent cohorts was performed. Serological and clinical variables were analysed by regression analyses. Risk allele of rs4151651 was introduced into human CFB plasmid by site-directed mutagenesis. Binding of recombinant G252 or S252 CFB to C3b and its cleavage was determined in cell-free assays. Macrophage phagocytosis in presence of recombinant CFB or serum from CFB risk, or protective CD or healthy subjects was assessed by flow cytometry. RESULTS Perianal complications were associated with colonic involvement, OmpC and ASCA serology, and serology quartile sum score. We identified a genetic association for pCD (rs4151651), a non-synonymous SNP (G252S) in CFB, in all three cohorts. Recombinant S252 CFB had reduced binding to C3b, its cleavage was impaired, and complement-driven phagocytosis and cytokine secretion were reduced compared with G252 CFB. Serine 252 generates a de novo glycosylation site in CFB. Serum from homozygous risk patients displayed significantly decreased macrophage phagocytosis compared with non-risk serum. CONCLUSION pCD-associated rs4151651 in CFB is a loss-of-function mutation that impairs its cleavage, activation of alternative complement pathway, and pathogen phagocytosis thus implicating the alternative complement pathway and CFB in pCD aetiology.
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Affiliation(s)
- Marzieh Akhlaghpour
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Talin Haritunians
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shyam K More
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Lisa S Thomas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalton T Stamps
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shishir Dube
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dalin Li
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shaohong Yang
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Carol J Landers
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Emebet Mengesha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Hussein Hamade
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Ramachandran Murali
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Alka A Potdar
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Andrea J Wolf
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gregory J Botwin
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Michelle Khrom
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | | | | | - Bana Jabri
- Biological Sciences Division, University of Chicago, Pritzker School of Medicine, Chicago, Illinois, USA
| | - Sergio A Lira
- Immunology Institute, Mount Sinai Medical Center, New York, New York, USA
| | - Rodney D Newberry
- Division of Gastroenterology, Washington Univ. Sch. of Medicine, Saint Louis, Missouri, USA
| | - Robert S Sandler
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Steven R Brant
- Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Judy H Cho
- Genetics and Genomics Sciences, Mt Sinai School of Medicine, New York, New York, USA
| | - Richard H Duerr
- Departments of Medicine and Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mark G Lazarev
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John D Rioux
- Faculty of Medicine, Universite de Montreal, Montreal, Québec, Canada
| | - L Philip Schumm
- Dept of Health Studies, University of Chicago, Chicago, Illinois, USA
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Karen Zaghiyan
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Phillip Fleshner
- Division of Colorectal Surgery, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gil Y Melmed
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Eric A Vasiliauskas
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christina Ha
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Shervin Rabizadeh
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Gaurav Syal
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Nirupama N Bonthala
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - David A Ziring
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Stephan R Targan
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Millie D Long
- Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Dermot P B McGovern
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Kathrin S Michelsen
- F. Widjaja Inflammatory Bowel Disease Institute, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California, USA
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Pérez-Jeldres T, Magne F, Ascui G, Alvares D, Orellana M, Alvarez-Lobos M, Hernandez-Rocha C, Azocar L, Aguilar N, Espino A, Estela R, Escobar S, Zazueta A, Baez P, Silva V, De La Vega A, Arriagada E, Pavez-Ovalle C, Díaz-Asencio A, Travisany D, Miquel JF, Villablanca EJ, Kronenberg M, Bustamante ML. Amerindian ancestry proportion as a risk factor for inflammatory bowel diseases: results from a Latin American Andean cohort. Front Med (Lausanne) 2023; 10:1258395. [PMID: 37964883 PMCID: PMC10642057 DOI: 10.3389/fmed.2023.1258395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
Background and aims Latin American populations remain underrepresented in genetic studies of inflammatory bowel diseases (IBDs). Most genetic association studies of IBD rely on Caucasian, African, and Asian individuals. These associations have yet to be evaluated in detail in the Andean region of South America. We explored the contribution of IBD-reported genetic risk variants to a Chilean cohort and the ancestry contribution to IBD in this cohort. Methods A total of 192 Chilean IBD patients were genotyped using Illumina's Global Screening Array. Genotype data were combined with similar information from 3,147 Chilean controls. The proportions of Aymara, African, European, and Mapuche ancestries were estimated using the software ADMIXTURE. We calculated the odds ratios (ORs) and 95% confidence intervals (CIs) for gender, age, and ancestry proportions. We also explored associations with previously reported IBD-risk variants independently and in conjunction with genetic ancestry. Results The first and third quartiles of the proportion of Mapuche ancestry in IBD patients were 24.7 and 34.2%, respectively, and the corresponding OR was 2.30 (95%CI 1.52-3.48) for the lowest vs. the highest group. Only one variant (rs7210086) of the 180 reported IBD-risk SNPs was associated with IBD risk in the Chilean cohort (adjusted P = 0.01). This variant is related to myeloid cells. Conclusion The type and proportion of Native American ancestry in Chileans seem to be associated with IBD risk. Variants associated with IBD risk in this Andean region were related to myeloid cells and the innate immune response.
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Affiliation(s)
- Tamara Pérez-Jeldres
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Fabien Magne
- Department of Microbiology, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Gabriel Ascui
- La Jolla Institute for Immunology, San Diego, CA, United States
| | - Danilo Alvares
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom
| | - Matias Orellana
- Department of Computer Science, Faculty of Physical Sciences and Mathematics, Universidad de Chile, Santiago, Chile
| | - Manuel Alvarez-Lobos
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Cristian Hernandez-Rocha
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Lorena Azocar
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nataly Aguilar
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alberto Espino
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ricardo Estela
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Sergio Escobar
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Alejandra Zazueta
- Department of Microbiology, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
| | - Pablo Baez
- Center of Medical Informatics and Telemedicine, University of Chile, Santiago, Chile
| | - Verónica Silva
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Andres De La Vega
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Elizabeth Arriagada
- Department of Gastroenterology, Hospital San Borja Arriarán, Santiago, Chile
| | - Carolina Pavez-Ovalle
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Dante Travisany
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago, Chile
| | - Juan Francisco Miquel
- Department of Gastroenterology, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Eduardo J. Villablanca
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Mitchell Kronenberg
- La Jolla Institute for Immunology, San Diego, CA, United States
- Department of Molecular Biology, University of California San Diego, La Jolla, CA, United States
| | - María Leonor Bustamante
- Department of Human Genetic, Faculty of Medicine, Institute of Biomedical Sciences (ICBM), Universidad de Chile, Santiago, Chile
- Fundación Diagnosis, Santiago, Chile
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Naschberger E, Flierl C, Huang J, Erkert L, Gamez-Belmonte R, Gonzalez-Acera M, Bober M, Mehnert M, Becker C, Schellerer VS, Britzen-Laurent N, Stürzl M. Analysis of the interferon-γ-induced secretome of intestinal endothelial cells: putative impact on epithelial barrier dysfunction in IBD. Front Cell Dev Biol 2023; 11:1213383. [PMID: 37645250 PMCID: PMC10460912 DOI: 10.3389/fcell.2023.1213383] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
The development of inflammatory bowel diseases (IBD) involves the breakdown of two barriers: the epithelial barrier and the gut-vascular barrier (GVB). The destabilization of each barrier can promote initiation and progression of the disease. Interestingly, first evidence is available that both barriers are communicating through secreted factors that may accordingly serve as targets for therapeutic modulation of barrier functions. Interferon (IFN)-γ is among the major pathogenesis factors in IBD and can severely impair both barriers. In order to identify factors transmitting signals from the GVB to the epithelial cell barrier, we analyzed the secretome of IFN-γ-treated human intestinal endothelial cells (HIEC). To this goal, HIEC were isolated in high purity from normal colon tissues. HIEC were either untreated or stimulated with IFN-γ (10 U/mL). After 48 h, conditioned media (CM) were harvested and subjected to comparative hyper reaction monitoring mass spectrometry (HRM™ MS). In total, 1,084 human proteins were detected in the HIEC-CM. Among these, 43 proteins were present in significantly different concentrations between the CM of IFN-γ- and control-stimulated HIEC. Several of these proteins were also differentially expressed in various murine colitis models as compared to healthy animals supporting the relevance of these proteins secreted by inflammatory activated HIEC in the inter-barrier communication in IBD. The angiocrine pathogenic impact of these differentially secreted HIEC proteins on the epithelial cell barrier and their perspectives as targets to treat IBD by modulation of trans-barrier communication is discussed in detail.
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Affiliation(s)
- Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Christian Flierl
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jinghao Huang
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Lena Erkert
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Reyes Gamez-Belmonte
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Miguel Gonzalez-Acera
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | | | - Christoph Becker
- Department of Medicine I, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Vera S. Schellerer
- Department of Pediatric Surgery, University Medicine Greifswald, Greifswald, Germany
| | - Nathalie Britzen-Laurent
- Division of Surgical Research, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
- Comprehensive Cancer Center Erlangen-EMN, Universitätsklinikum Erlangen, Erlangen, Germany
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5
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Zhang H, Ni Y, Ji H, Liu H, Liu S. Research trends of omics in ulcerative colitis: A bibliometric analysis. Front Med (Lausanne) 2023; 10:1115240. [PMID: 37051213 PMCID: PMC10083299 DOI: 10.3389/fmed.2023.1115240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/20/2023] [Indexed: 03/28/2023] Open
Abstract
BackgroundOmics has emerged as a promising biological science to shed light on the etiology, pathogenesis, and treatment of ulcerative colitis (UC). At present, although research on the omics of UC has drawn global attention, there is still a lack of bibliometric analysis in this field. This study aimed to access the trends and hotspots of omics in UC research.MethodPublications related to omics in UC from 1 January 2000 to 15 October 2022 were retrieved from the Web of Science Core Collection database. VOSviewer, CiteSpace, and the online bibliometric analysis platform “Bibliometrix” were adopted to extract and visualize information.ResultsA total of 385 publications were finally included and the annual number of publications fluctuated. The trend in publications increased rapidly after 2019. The United States showed its dominant position in several publications, total citations, and international collaborations. The top five research organizations for publications on the research of omics in UC were Harvard Medical School, the Icahn School of Medicine at Mount Sinai, Karolinska Institutet, the Brigham and Women's Hospital, and the Massachusetts General Hospital. Ashwin Ananthakrishnan from the Massachusetts General Hospital was the most productive author, and Séverine Vermeire from the Catholic University of Leuven was co-cited most often. Inflammatory bowel disease was the most popular and co-cited journal in this field. The reference with citation bursts and trend topics showed that “ulcerative colitis,” “inflammatory bowel disease,” “microbiome,” “transcriptomics,” “genomics,” “metabolomics,” “proteomics,” “dysbiosis,” “biomarkers,” “loci,” and “therapy” are currently research hotspots.ConclusionOur study presents several important insights into the research trends and developments in the field of omics in UC, which will provide key information for further research.
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Affiliation(s)
- He Zhang
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Yuanyuan Ni
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Hangyu Ji
- Office of Good Clinical Practice, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Hongliang Liu
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Shaoneng Liu
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
- *Correspondence: Shaoneng Liu
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Mortlock S, Lord A, Montgomery G, Zakrzewski M, Simms LA, Krishnaprasad K, Hanigan K, Doecke JD, Walsh A, Lawrance IC, Bampton PA, Andrews JM, Mahy G, Connor SJ, Sparrow MP, Bell S, Florin TH, Begun J, Gearry RB, Radford-Smith GL. An Extremes of Phenotype Approach Confirms Significant Genetic Heterogeneity in Patients with Ulcerative Colitis. J Crohns Colitis 2023; 17:277-288. [PMID: 36111848 PMCID: PMC10024548 DOI: 10.1093/ecco-jcc/jjac121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Ulcerative colitis [UC] is a major form of inflammatory bowel disease globally. Phenotypic heterogeneity is defined by several variables including age of onset and disease extent. The genetics of disease severity remains poorly understood. To further investigate this, we performed a genome wide association [GWA] study using an extremes of phenotype strategy. METHODS We conducted GWA analyses in 311 patients with medically refractory UC [MRUC], 287 with non-medically refractory UC [non-MRUC] and 583 controls. Odds ratios [ORs] were calculated for known risk variants comparing MRUC and non-MRUC, and controls. RESULTS MRUC-control analysis had the greatest yield of genome-wide significant single nucleotide polymorphisms [SNPs] [2018], including lead SNP = rs111838972 [OR = 1.82, p = 6.28 × 10-9] near MMEL1 and a locus in the human leukocyte antigen [HLA] region [lead SNP = rs144717024, OR = 12.23, p = 1.7 × 10-19]. ORs for the lead SNPs were significantly higher in MRUC compared to non-MRUC [p < 9.0 × 10-6]. No SNPs reached significance in the non-MRUC-control analysis (top SNP, rs7680780 [OR 2.70, p = 5.56 × 10-8). We replicate findings for rs4151651 in the Complement Factor B [CFB] gene and demonstrate significant changes in CFB gene expression in active UC. Detailed HLA analyses support the strong associations with MHC II genes, particularly HLA-DQA1, HLA-DQB1 and HLA-DRB1 in MRUC. CONCLUSIONS Our MRUC subgroup replicates multiple known UC risk variants in contrast to non-MRUC and demonstrates significant differences in effect sizes compared to those published. Non-MRUC cases demonstrate lower ORs similar to those published. Additional risk and prognostic loci may be identified by targeted recruitment of individuals with severe disease.
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Affiliation(s)
- Sally Mortlock
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Anton Lord
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Centre for Health Services Research, University of Queensland, Brisbane, QLD, Australia
| | - Grant Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Lisa A Simms
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | - James D Doecke
- Australian eHealth Research Centre, CSIRO, Brisbane, QLD, Australia
| | - Alissa Walsh
- Department of Gastroenterology, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ian C Lawrance
- Centre of Inflammatory Bowel Diseases, Saint John of God Hospital Subiaco, University of Western Australia, WA, Australia
| | | | - Jane M Andrews
- Department of Gastroenterology and Hepatology, Royal Adelaide Hospital & University of Adelaide, Adelaide, SA, Australia
| | - Gillian Mahy
- Department of Gastroenterology and Hepatology, Townsville University Hospital, Townsville, QLD, Australia
| | - Susan J Connor
- Department of Gastroenterology and Hepatology, Liverpool Hospital, Sydney, NSW, Australia
- South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Miles P Sparrow
- Department of Gastroenterology, Alfred Health, Melbourne, VIC, Australia
| | - Sally Bell
- Department of Gastroenterology and Hepatology, Monash Health, Melbourne, VIC, Australia
| | - Timothy H Florin
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Jakob Begun
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Inflammatory Disease Biology and Therapeutics Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Graham L Radford-Smith
- Corresponding author: Graham Radford-Smith, Gut Health Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. Tel: +617 3362 0499; Fax: +617 3009 0053;
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Innate and adaptive immune abnormalities underlying autoimmune diseases: the genetic connections. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-021-2187-3. [PMID: 36738430 PMCID: PMC9898710 DOI: 10.1007/s11427-021-2187-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/10/2022] [Indexed: 02/05/2023]
Abstract
With the exception of an extremely small number of cases caused by single gene mutations, most autoimmune diseases result from the complex interplay between environmental and genetic factors. In a nutshell, etiology of the common autoimmune disorders is unknown in spite of progress elucidating certain effector cells and molecules responsible for pathologies associated with inflammatory and tissue damage. In recent years, population genetics approaches have greatly enriched our knowledge regarding genetic susceptibility of autoimmunity, providing us with a window of opportunities to comprehensively re-examine autoimmunity-associated genes and possible pathways. In this review, we aim to discuss etiology and pathogenesis of common autoimmune disorders from the perspective of human genetics. An overview of the genetic basis of autoimmunity is followed by 3 chapters detailing susceptibility genes involved in innate immunity, adaptive immunity and inflammatory cell death processes respectively. With such attempts, we hope to expand the scope of thinking and bring attention to lesser appreciated molecules and pathways as important contributors of autoimmunity beyond the 'usual suspects' of a limited subset of validated therapeutic targets.
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8
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Stem Cell-Based Therapies for Inflammatory Bowel Disease. Int J Mol Sci 2022; 23:ijms23158494. [PMID: 35955628 PMCID: PMC9368934 DOI: 10.3390/ijms23158494] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing disease that severely affects patients’ quality of life. The exact cause of IBD is uncertain, but current studies suggest that abnormal activation of the immune system, genetic susceptibility, and altered intestinal flora due to mucosal barrier defects may play an essential role in the pathogenesis of IBD. Unfortunately, IBD is currently difficult to be wholly cured. Thus, more treatment options are needed for different patients. Stem cell therapy, mainly including hematopoietic stem cell therapy and mesenchymal stem cell therapy, has shown the potential to improve the clinical disease activity of patients when conventional treatments are not effective. Stem cell therapy, an emerging therapy for IBD, can alleviate mucosal inflammation through mechanisms such as immunomodulation and colonization repair. Clinical studies have confirmed the effectiveness of stem cell transplantation in refractory IBD and the ability to maintain long-term remission in some patients. However, stem cell therapy is still in the research stage, and its safety and long-term efficacy remain to be further evaluated. This article reviews the upcoming stem cell transplantation methods for clinical application and the results of ongoing clinical trials to provide ideas for the clinical use of stem cell transplantation as a potential treatment for IBD.
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9
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Luu LDW, Popple G, Tsang SPW, Vinasco K, Hilmi I, Ng RT, Chew KS, Wong SY, Riordan S, Lee WS, Mitchell HM, Kaakoush NO, Castaño-Rodríguez N. Genetic variants involved in innate immunity modulate the risk of inflammatory bowel diseases in an understudied Malaysian population. J Gastroenterol Hepatol 2022; 37:342-351. [PMID: 34888949 DOI: 10.1111/jgh.15752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIM Inflammatory bowel diseases (IBD) are chronic gastrointestinal inflammatory conditions comprising two major subtypes: Crohn's disease (CD) and ulcerative colitis (UC). The incidence of IBD is increasing in Asian countries including Malaysia. The aim of this study was to determine whether 32 single nucleotide polymorphisms (SNPs) strongly associated with IBD from genome-wide association studies, performed mainly in Caucasian populations, are associated with IBD in a Malaysian population, correlating these findings with local and systemic inflammation. METHODS Selected SNPs were investigated in a Malaysian cohort comprising 36 IBD patients and 75 controls using customized matrix-assisted laser desorption ionization time-of-flight genotyping. Local mRNA and/or systemic protein levels of IL-10, IL-12, IL-22, IL-23, and TNF-α were measured in these same subjects. RESULTS ATG16L2 rs11235667 and LINC00824 rs6651252 was significantly associated with increased CD risk while IL12B rs56167332 was a significant protective factor. Three SNPs (SBNO2 rs2024092, CARD9 rs10781499, and rs17085007 between GPR12-USP12) were significantly associated with increased UC risk while NKX2-3 rs4409764 was a significant protective factor. After adjusting for age, gender, and ethnicity, SBNO2 rs2024092, ATG16L2 rs11235667, CARD9 rs10781499, and LINC00824 rs6651252 remained associated with IBD. Interestingly, the risk alleles of IL10 rs3024505, CARD9 rs1078149, and IL12 rs6556412 were associated with higher levels of IL-10, IL-22, and IL-23 in these same subjects, respectively. CONCLUSIONS This study identified eight SNPs associated with IBD and/or its subtypes in the Malaysia population, significantly advancing our understanding of the genetic contribution to IBD in this understudied population. Three of these SNPs modulated relevant cytokine levels and thus, may directly contribute to IBD pathogenesis.
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Affiliation(s)
- Laurence Don Wai Luu
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Georgia Popple
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Samuel Pok Wei Tsang
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Karla Vinasco
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Ida Hilmi
- Department of Medicine, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Ruey Terng Ng
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Kee Seang Chew
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Shin Yee Wong
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Stephen Riordan
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, University of New South Wales, Sydney, New South Wales, Australia
| | - Way Seah Lee
- Department of Paediatrics, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Hazel M Mitchell
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
| | - Nadeem O Kaakoush
- School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Natalia Castaño-Rodríguez
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, Sydney, New South Wales, Australia
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10
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Zou M, Zeng QS, Nie J, Yang JH, Luo ZY, Gan HT. The Role of E3 Ubiquitin Ligases and Deubiquitinases in Inflammatory Bowel Disease: Friend or Foe? Front Immunol 2021; 12:769167. [PMID: 34956195 PMCID: PMC8692584 DOI: 10.3389/fimmu.2021.769167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/17/2021] [Indexed: 02/05/2023] Open
Abstract
Inflammatory bowel disease (IBD), which include Crohn’s disease (CD) and ulcerative colitis (UC), exhibits a complex multifactorial pathogenesis involving genetic susceptibility, imbalance of gut microbiota, mucosal immune disorder and environmental factors. Recent studies reported associations between ubiquitination and deubiquitination and the occurrence and development of inflammatory bowel disease. Ubiquitination modification, one of the most important types of post-translational modifications, is a multi-step enzymatic process involved in the regulation of various physiological processes of cells, including cell cycle progression, cell differentiation, apoptosis, and innate and adaptive immune responses. Alterations in ubiquitination and deubiquitination can lead to various diseases, including IBD. Here, we review the role of E3 ubiquitin ligases and deubiquitinases (DUBs) and their mediated ubiquitination and deubiquitination modifications in the pathogenesis of IBD. We highlight the importance of this type of posttranslational modification in the development of inflammation, and provide guidance for the future development of targeted therapeutics in IBD.
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Affiliation(s)
- Min Zou
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Qi-Shan Zeng
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jiao Nie
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Jia-Hui Yang
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Zhen-Yi Luo
- Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
| | - Hua-Tian Gan
- Department of Gastroenterology and the Center of Inflammatory Bowel Disease, West China Hospital, Sichuan University, Chengdu, China.,Lab of Inflammatory Bowel Disease, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China.,Department of Geriatrics and National Clinical Research Center for Geriatric, West China Hospital, Sichuan University, Chengdu, China
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11
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Abstract
Inflammatory bowel disease (IBD) in recent times is causing a significant healthcare burden as both ulcerative colitis and Crohn's disease (CD) require lifelong therapy and constant monitoring. The current review highlights the concerns in a country like India with special reference to the changing trends of IBD, risk attribution and the financial issues. Indian immigrants behave like residential Indians, whereas their children show IBD prevalence similar to the West, highlighting the role of environmental triggers. However, the environmental and genetic factors in Indians with IBD are not well understood. Men appear to be more frequently affected than women in India. The disease severity is milder in the patients, both males and females, but the risk for colorectal cancer (CRC) is similar to the West. The incidence of paediatric IBD is on the rise. The major burden of IBD in the Indian subcontinent at present is in children, adolescents and teens. Cost towards the management of complications, non-adherence to treatment, differentiating tuberculosis from CD and finally screening for CRC in patients with IBD are the points to ponder in the Indian scenario.
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Affiliation(s)
- Mayank Jain
- Department of Medical Gastroenterology, Gleneagles Global Health City, Chennai, India
| | - Jayanthi Venkataraman
- Department of Medical Gastroenterology, Gleneagles Global Health City, Chennai, India
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12
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Treatments of inflammatory bowel disease toward personalized medicine. Arch Pharm Res 2021; 44:293-309. [PMID: 33763844 DOI: 10.1007/s12272-021-01318-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory disease characterized by intestinal inflammation and epithelial injury. For the treatment of IBD, 5-aminosalicylic acids, corticosteroids, immunomodulators, and biologic agents targeting tumor necrosis factor (TNF)-α, α4β7-integrin, and interleukin (IL)-12/23 have been widely used. Especially, anti-TNF-α antibodies are the first biologic agents that presently remain at the forefront. However, 10-30% of patients resist biologic agents, including anti-TNF-α agents (primary non-responder; PNR), and 20-50% of primary responders develop treatment resistance within one year (secondary loss of response; SLR). Nonetheless, the etiologies of PNR and SLR are not clearly understood, and predictors of response to biologic agents are also not defined yet. Numerous studies are being performed to discover prediction markers of the response to biologic agents, and this review will introduce currently available therapeutic options for IBD, biologics under investigation, and recent studies exploring various predictive factors related to PNR and SLR.
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13
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Park J, Cheon JH. Incidence and Prevalence of Inflammatory Bowel Disease across Asia. Yonsei Med J 2021; 62:99-108. [PMID: 33527789 PMCID: PMC7859683 DOI: 10.3349/ymj.2021.62.2.99] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/17/2022] Open
Abstract
Inflammatory bowel diseases (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), are chronic inflammatory disorders of the gastrointestinal tract caused by interactions between genetic, environmental, immunological, and microbial factors. While the incidence and prevalence of IBD in Asian populations were relatively lower than those in Western countries, they appear to be gradually increasing. A Westernized diet, high socioeconomic status, improvement of hygiene, and development of vaccination could affect the increases in IBD incidence and prevalence in Asian countries. This review describes the latest trends in the incidence and prevalence of IBD in Asia. Studying the epidemiology of IBD in Asia may unravel the etiopathogenesis of and risk factors for IBD.
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Affiliation(s)
- Jihye Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
| | - Jae Hee Cheon
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
- Institute of Gastroenterology, Yonsei University College of Medicine, Seoul, Korea
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
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14
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Karmiris K. Racial Differences in Inflammatory Bowel Disease: A Race With Alternating Winners? Inflamm Bowel Dis 2020; 26:1878-1879. [PMID: 32144931 DOI: 10.1093/ibd/izaa022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Indexed: 12/16/2022]
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15
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Two Variants in the NOTCH4 and HLA-C Genes Contribute to Familial Clustering of Psoriasis. Int J Genomics 2020; 2020:6907378. [PMID: 33134369 PMCID: PMC7593743 DOI: 10.1155/2020/6907378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/05/2022] Open
Abstract
Psoriasis is a multifactorial immune-mediated skin disease with a strong genetic background. Previous studies reported that psoriasis with a family history (PFH) and sporadic psoriasis (SP) have a distinct manifestation and genetic predisposition. However, the genetic heterogeneity of PFH and SP in the major histocompatibility complex (MHC) region has not been fully elucidated. To explore genetic variants in the MHC region that drive family aggregation of psoriasis, we included a total of 8,127 psoriasis cases and 9,906 healthy controls from Han Chinese and divided psoriasis into two subtypes, PFH (n = 1,538) and SP (n = 5,262). Then, we calculated the heritability of PFH and SP and performed a large-scale stratified association analysis. We confirmed that variants in the MHC region collectively explained a higher heritability of PFH (16.8%) than SP (13.3%). Further stratified association analysis illustrated that HLA-C∗06:02 and NOTCH4:G511S contribute to the family aggregation of psoriasis, and BTNL2:R281K specifically confers risk for SP. HLA-C∗06:02 and NOTCH4:G511S could partially explain why patients with PFH have a stronger genetic predisposition, more complex phenotypes, and more frequent other autoimmune diseases. The identification of the SP-specific variant BTNL2:R281K revealed that the genetic architecture of SP is not just a subset of PFH.
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16
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Snell A, Segal J, Limdi J, Banerjee R. Inflammatory bowel disease in India: challenges and opportunities. Frontline Gastroenterol 2020; 12:390-396. [PMID: 35401961 PMCID: PMC8988999 DOI: 10.1136/flgastro-2020-101500] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/06/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023] Open
Abstract
Evidence is emerging that inflammatory bowel diseases (IBDs) are becoming increasingly prevalent in developing countries, altering the previously held view that these were diseases of the West. Within this is a substantial increase in the burden of this disease in India, a matter of great importance to the country itself as well as in furthering our understanding of the disease. There is comparatively less data on this, both from the epidemiological standpoint as well as on disease pathogenesis in this particular cohort and is very much a subject matter of evolving understanding and research. This article aims to look at the changing global distribution of the disease and its implications. The Indian disease phenotype, and the aetiology of disease development will also be addressed with particular focus on differing pathogenetic processes in the Indian subpopulation, with consideration of what clues may be offered by the increasing incidence of the disease in this developing nation. Available evidence will be evaluated with the objective of providing a comprehensive overview of the development of IBD in India.
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Affiliation(s)
- Alice Snell
- Department of Gastroenterology, Northwick Park Hospital, London, UK
| | - Jonathan Segal
- Department of Gastroenterology, Saint Mary's Hospital Medical School, London, UK
| | - Jimmy Limdi
- Department of Gastroenterology, Pennine Acute Hospitals NHS Trust, Manchester, UK,Manchester Academic Health Science Centre, Manchester, UK
| | - Rupa Banerjee
- Asian Institute of Gastroenterology, Hyderabad, Telangana, India
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17
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Sood A, Kaur K, Mahajan R, Midha V, Singh A, Sharma S, Puri AS, Goswami B, Desai D, Pai CG, Peddi K, Philip M, Kochhar R, Nijhawan S, Bhatia S, Rao NS. Colitis and Crohn's Foundation (India): a first nationwide inflammatory bowel disease registry. Intest Res 2020; 19:206-216. [PMID: 32646197 PMCID: PMC8100380 DOI: 10.5217/ir.2019.09169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/29/2020] [Indexed: 12/30/2022] Open
Abstract
Background/Aims The national registry for inflammatory bowel disease (IBD) was designed to study epidemiology and prescribing pattern of treatment of IBD in India. Methods A multicenter, cross-sectional, prospective registry was established across four geographical zones of India. Adult patients with ulcerative colitis (UC) or Crohn’s disease (CD) were enrolled between January 2014 and December 2015. Information related to demographics; disease features; complications; and treatment history were collected and analyzed. Results A total of 3,863 patients (mean age, 36.7 ± 13.6 years; 3,232 UC [83.7%] and 631 CD [16.3%]) were enrolled. The majority of patients with UC (n = 1,870, 57.9%) were from north, CD was more common in south (n = 348, 55.5%). The UC:CD ratio was 5.1:1. There was a male predominance (male:female = 1.6:1). The commonest presentation of UC was moderately severe (n = 1,939, 60%) and E2 disease (n = 1,895, 58.6%). Patients with CD most commonly presented with ileocolonic (n = 229, 36.3%) inflammatory (n = 504, 79.9%) disease. Extraintestinal manifestations were recorded among 13% and 20% of patients in UC and CD respectively. Less than 1% patients from both cohorts developed colon cancer (n = 26, 0.7%). The commonly used drugs were 5-aminosalicylates (99%) in both UC and CD followed by azathioprine (34.4%). Biologics were used in only 1.5% of patients; more commonly for UC in north and CD in south. Conclusions The national IBD registry brings out diversities in the 4 geographical zones of India. This will help in aiding research on IBD and improving quality of patient care.
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Affiliation(s)
- Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Kirandeep Kaur
- Department of Pharmacology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Ramit Mahajan
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Vandana Midha
- Department of Internal Medicine, Dayanand Medical College and Hospital, Ludhiana, India
| | - Arshdeep Singh
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, India
| | - Sarit Sharma
- Department of Community Medicine, Dayanand Medical College and Hospital, Ludhiana, India
| | | | - Bhabhadev Goswami
- Department of Gastroenterology, Gauhati Medical College, Guwahati, India
| | - Devendra Desai
- P. D. Hinduja Hospital and Medical Research Centre, Mumbai, India
| | - C Ganesh Pai
- Department of Gastroenterology, Kasturba Medical College, Manipal, India
| | - Kiran Peddi
- Citizens Centre for Digestive Disorders, Hyderabad, India
| | | | - Rakesh Kochhar
- Department of Gastroenterology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sandeep Nijhawan
- Department of Gastroenterology, Sawai Man Singh Medical College, Jaipur, India
| | - Shobna Bhatia
- Department of Gastroenterology, King Edward Memorial Hospital, Mumbai, India
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18
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Identification of susceptibility locus shared by IgA nephropathy and inflammatory bowel disease in a Chinese Han population. J Hum Genet 2019; 65:241-249. [PMID: 31857673 DOI: 10.1038/s10038-019-0699-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 02/07/2023]
Abstract
Genome-wide association studies (GWAS) had discovered several genetic risk loci for IgA nephropathy (IgAN), where the susceptibility genes of CARD9 and HORMAD2 for IgAN were also implicated in inflammatory bowel disease (IBD), suggesting a shared genetic etiology of these two diseases. The aim of this study is to explore the common susceptibility loci between IgAN and IBD and provide evidences to elucidate the shared pathogenesis between these two autoimmune diseases. Nineteen single-nucleotide polymorphisms (SNPs) associated with IBD in Asian populations were selected through the National Human Genome Research Institute (NHGRI) GWAS Catalog, and 2078 IgAN patients and 2085 healthy individuals of Chinese Han ancestry were included in the two-stage case-control association study. Serum levels of complement factor B (CFB) and complement split product C3a were detected by enzyme-linked immunosorbent assay (ELISA). One significant shared association at rs4151657 (OR = 1.28, 95%CI = 1.13-1.45, P = 1.42 × 10-4) was discovered between these two diseases, which implicated CFB as a susceptibility gene for IgAN. Genotype-phenotype correlation analysis found significant association of the rs4151657-C allele with decreased serum C3 levels. In addition, the rs4151657-C allele was also associated with higher CFB levels and C3a levels, which suggested a certain degree of systemic complement activation in IgAN patients with the rs4151657-CT or CC genotypes. Our study identified one risk locus (CFB) shared by IgAN and IBD, and genetic variants of CFB may affect complement activation and associate with the predisposition to IgAN.
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Misra R, Limdi J, Cooney R, Sakuma S, Brookes M, Fogden E, Pattni S, Sharma N, Iqbal T, Munkholm P, Burisch J, Arebi N. Ethnic differences in inflammatory bowel disease: Results from the United Kingdom inception cohort epidemiology study. World J Gastroenterol 2019; 25:6145-6157. [PMID: 31686769 PMCID: PMC6824277 DOI: 10.3748/wjg.v25.i40.6145] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/01/2019] [Accepted: 09/09/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The current epidemiology of inflammatory bowel disease (IBD) in the multi-ethnic United Kingdom is unknown. The last incidence study in the United Kingdom was carried out over 20 years ago.
AIM To describe the incidence and phenotype of IBD and distribution within ethnic groups.
METHODS Adult patients (> 16 years) with newly diagnosed IBD (fulfilling Copenhagen diagnostic criteria) were prospectively recruited over one year in 5 urban catchment areas with high South Asian population. Patient demographics, ethnic codes, disease phenotype (Montreal classification), disease activity and treatment within 3 months of diagnosis were recorded onto the Epicom database.
RESULTS Across a population of 2271406 adults, 339 adult patients were diagnosed with IBD over one year: 218 with ulcerative colitis (UC, 64.3%), 115 with Crohn's disease (CD, 33.9%) and 6 with IBD unclassified (1.8%). The crude incidence of IBD, UC and CD was 17.0/100000, 11.3/100000 and 5.3/100000 respectively. The age adjusted incidence of IBD and UC were significantly higher in the Indian group (25.2/100000 and 20.5/100000) compared to White European (14.9/100000, P = 0.009 and 8.2/100000, P < 0.001) and Pakistani groups (14.9/100000, P = 0.001 and 11.2/100000, P = 0.007). The Indian group were significantly more likely to have extensive disease than White Europeans (52.7% vs 41.7%, P = 0.031). There was no significant difference in time to diagnosis, disease activity and treatment.
CONCLUSION This is the only prospective study to report the incidence of IBD in an ethnically diverse United Kingdom population. The Indian ethnic group showed the highest age-adjusted incidence of UC (20.5/100000). Further studies on dietary, microbial and metabolic factors that might explain these findings in UC are underway.
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Affiliation(s)
- Ravi Misra
- Gastroenterology, St. Mark’s Hospital and Academic Institute, London HA1 3UJ, United Kingdom
| | - Jimmy Limdi
- The Pennine Acute Hospitals NHS Trust, Institute of Inflammation and Repair, University of Manchester, Manchester BL9 7TD, United Kingdom
| | - Rachel Cooney
- Gastroenterology, University Hospitals Birmingham, Birmingham B12 2TH, United Kingdom
| | - Samia Sakuma
- Gastroenterology, St. Mark’s Hospital and Academic Institute, London HA1 3UJ, United Kingdom
| | - Matthew Brookes
- Gastroenterology, Royal Wolverhampton NHS Trust, London WV10 0QP, United Kingdom
| | - Edward Fogden
- Gastroenterology, Sandwell and West Birmingham Hospitals, Birmingham B71 4HJ, United Kingdom
| | - Sanjeev Pattni
- Gastroenterology, University Leicester Hospitals, Leicester LE1 5WW, United Kingdom
| | - Naveen Sharma
- Gastroenterology, Heartlands Hospital, Birmingham B9 5SS, United Kingdom
| | - Tariq Iqbal
- Gastroenterology, University Hospitals Birmingham, Birmingham B12 2TH, United Kingdom
| | - Pia Munkholm
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund 3600, Denmark
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund 3600, Denmark
| | - Naila Arebi
- Gastroenterology, St. Mark’s Hospital and Academic Institute, London HA1 3UJ, United Kingdom
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20
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Willis-Owen SAG, Cookson WOC, Moffatt MF. The Genetics and Genomics of Asthma. Annu Rev Genomics Hum Genet 2019; 19:223-246. [PMID: 30169121 DOI: 10.1146/annurev-genom-083117-021651] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Asthma is a common, clinically heterogeneous disease with strong evidence of heritability. Progress in defining the genetic underpinnings of asthma, however, has been slow and hampered by issues of inconsistency. Recent advances in the tools available for analysis-assaying transcription, sequence variation, and epigenetic marks on a genome-wide scale-have substantially altered this landscape. Applications of such approaches are consistent with heterogeneity at the level of causation and specify patterns of commonality with a wide range of alternative disease traits. Looking beyond the individual as the unit of study, advances in technology have also fostered comprehensive analysis of the human microbiome and its varied roles in health and disease. In this article, we consider the implications of these technological advances for our current understanding of the genetics and genomics of asthma.
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Affiliation(s)
- Saffron A G Willis-Owen
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
| | - William O C Cookson
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom; , ,
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Genetic Studies of Inflammatory Bowel Disease-Focusing on Asian Patients. Cells 2019; 8:cells8050404. [PMID: 31052430 PMCID: PMC6563043 DOI: 10.3390/cells8050404] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/19/2019] [Accepted: 04/26/2019] [Indexed: 12/25/2022] Open
Abstract
The pathogenesis of inflammatory bowel disease (IBD) is not well-understood; however, increased and persistent intestinal inflammation, due to inappropriate immune responses that are caused by interactions between genetic factors, gut microbiota, and environmental factors, are thought to lead to IBD. Various studies have identified more than 240 genetic variants related to IBD. These genetic variants are involved in innate and adaptive immunity, autophagy, defective bacterial handing, interleukin-23 and 10 signaling, and so on. According to several epidemiological and clinical studies, the phenotypes and clinical course of IBD differ between Asians and Europeans. Although the risk loci for IBD typically overlap between Asians and Westerners, genetic heterogeneity has been detected in many loci/genes, such as NOD2/CARD15, TNFSF15 and human leukocyte antigen, contributing to the risk of IBD. Thus, although common pathways exist between Westerners and Asians in the development of IBD, their significance may differ for individual pathways. Although genetic studies are not universally applicable in the clinical field, they may be useful for diagnosing and categorizing IBD, predicting therapeutic responses and toxicity to drugs, and assessing prognosis by risk modeling, thereby enabling precision medicine for individual patients.
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Abstract
Covering: up to the end of 2017 The human body is composed of an equal number of human and microbial cells. While the microbial community inhabiting the human gastrointestinal tract plays an essential role in host health, these organisms have also been connected to various diseases. Yet, the gut microbial functions that modulate host biology are not well established. In this review, we describe metabolic functions of the human gut microbiota that involve metalloenzymes. These activities enable gut microbial colonization, mediate interactions with the host, and impact human health and disease. We highlight cases in which enzyme characterization has advanced our understanding of the gut microbiota and examples that illustrate the diverse ways in which metalloenzymes facilitate both essential and unique functions of this community. Finally, we analyze Human Microbiome Project sequencing datasets to assess the distribution of a prominent family of metalloenzymes in human-associated microbial communities, guiding future enzyme characterization efforts.
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Compound heterozygous mutations in IL10RA combined with a complement factor properdin mutation in infantile-onset inflammatory bowel disease. Eur J Gastroenterol Hepatol 2018; 30:1491-1496. [PMID: 30199474 DOI: 10.1097/meg.0000000000001247] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Inflammatory bowel diseases (IBDs) are chronic and multifactorial diseases resulting from a complex interaction of host genetic factors and environmental stimuli. Although many genome-wide association studies have identified host genetic factors associated with IBD, rare Mendelian forms of IBD have been reported in patients with very early onset forms. Therefore, this study aimed to identify genetic variants associated with infantile-onset IBD. PARTICIPANTS AND METHODS We obtained genomic DNA from whole blood samples of a male patient with infantile-onset IBD and nonconsanguineous Korean parents. Whole-exome sequencing was performed using trio samples. Then, we analyzed the data using susceptibility genes for monogenic forms of IBD and various immunodeficiencies and protein structural analysis. RESULTS The patient who presented with oral aphthous ulcers at the age of 14 days suffered from severe colitis and was refractory to medical treatment. Compound heterozygous mutations in IL10RA (p.R101W; p.T179T) were found in the patient. In addition, a hemizygous mutation in complement factor properdin (CFP) (p.L456V) located on the X-chromosome was detected, inherited from the patient's mother. Protein structural modeling suggested impaired properdin subunit interactions by p.L456V that may hamper protein oligomerization required for complement activation. CONCLUSION This study identified compound heterozygous mutations in IL10RA combined with a hemizygous CFP mutation in infantile-onset IBD by using whole-exome sequencing. CFP p.L456V may exacerbate symptoms of infantile-onset IBD by disturbing oligomerization of properdin.
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Zhou X, Li H, Guo S, Wang J, Shi C, Espitia M, Guo X, Wang Q, Liu M, Assassi S, Reveille JD, Mayes MD. Associations of Multiple NOTCH4 Exonic Variants with Systemic Sclerosis. J Rheumatol 2018; 46:184-189. [PMID: 30442821 DOI: 10.3899/jrheum.180094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2018] [Indexed: 01/02/2023]
Abstract
OBJECTIVE Findings from previous genome-wide association studies indicated an association of the NOTCH4 gene with systemic sclerosis (SSc). This is a followup study to fine-map exonic variants of NOTCH4 in SSc. METHODS All exons of NOTCH4 were sequenced and analyzed in a total of 1006 patients with SSc and 1004 controls of US white ancestry with the Ion Torrent system. Identified SSc-associated variants were confirmed with Sanger sequencing, and then examined in a Chinese Han cohort consisting of 576 patients with SSc and 574 controls. The NOTCH4 variants were analyzed for association with SSc as a whole and with SSc clinical and autoantibody subtypes with and without the influence of specific HLA-class II alleles that had been previously identified as major genetic factors in SSc. RESULTS A total of 12 SSc-associated and SSc subtype-associated exonic variants of NOTCH4 were identified in the US cohort. Three of them are nonsynonymous single-nucleotide polymorphisms and 1 is a CTG tandem repeat that encodes for a poly-leucine, all of which are located in the NOTCH4 extracellular domain (NECD). Conditional logistic regression analysis on SSc-associated HLA-class II alleles indicated an independent association of the NOTCH4 variants with SSc autoantibody subtypes. Analysis of the Chinese cohort supported a genetic contribution of NOTCH4 to SSc and its subtypes. CONCLUSION Multiple NOTCH4 exonic variants were associated with SSc and/or SSc subtypes. Several of these variants encode nonsynonymous sequence changes occurring in the NECD, which implicates a potentially functional effect of NOTCH4.
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Affiliation(s)
- Xiaodong Zhou
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China. .,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School.
| | - Hongye Li
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Shicheng Guo
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Jiucun Wang
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Chunhua Shi
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Maribel Espitia
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Xinjian Guo
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Qingwen Wang
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Mengyuan Liu
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Shervin Assassi
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - John D Reveille
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
| | - Maureen D Mayes
- From the Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health, Houston, Texas, USA; State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai; Department of Rheumatology, Jiangxi People's Hospital, Nanchang; Department of Rheumatology, Peking University-Shenzhen Hospital, Shenzhen; Life Sciences College, Hubei University, Wuhan, China.,X. Zhou, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; H. Li, MD, PhD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; S. Guo, PhD, Human Genetics Center, Division of Biostatistics, The University of Texas School of Public Health; J. Wang, PhD, State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University; C. Shi, MD, Department of Rheumatology, Jiangxi People's Hospital; M. Espitia, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; X. Guo, BS, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; Q. Wang, MD, PhD, Department of Rheumatology, Peking University-Shenzhen Hospital; M. Liu, PhD, Life Sciences College, Hubei University; S. Assassi, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; J.D. Reveille, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School; M.D. Mayes, MD, Division of Rheumatology, Department of Internal Medicine, University of Texas McGovern Medical School
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Genetics of ulcerative colitis: putting into perspective the incremental gains from Indian studies. J Genet 2018. [DOI: 10.1007/s12041-018-1015-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shadrina A, Tsepilov Y, Sokolova E, Smetanina M, Voronina E, Pakhomov E, Sevost'ianova K, Shevela A, Ilyukhin E, Seliverstov E, Zolotukhin I, Filipenko M. Genome-wide association study in ethnic Russians suggests an association of the MHC class III genomic region with the risk of primary varicose veins. Gene 2018; 659:93-99. [DOI: 10.1016/j.gene.2018.03.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/16/2018] [Accepted: 03/14/2018] [Indexed: 10/17/2022]
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Misra R, Faiz O, Munkholm P, Burisch J, Arebi N. Epidemiology of inflammatory bowel disease in racial and ethnic migrant groups. World J Gastroenterol 2018; 24:424-437. [PMID: 29391765 PMCID: PMC5776404 DOI: 10.3748/wjg.v24.i3.424] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2017] [Revised: 11/15/2017] [Accepted: 11/21/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To summarise the current literature and define patterns of disease in migrant and racial groups.
METHODS A structured key word search in Ovid Medline and EMBASE was undertaken in accordance with PRISMA guidelines. Studies on incidence, prevalence and disease phenotype of migrants and races compared with indigenous groups were eligible for inclusion.
RESULTS Thirty-three studies met the inclusion criteria. Individual studies showed significant differences in incidence, prevalence and disease phenotype between migrants or race and indigenous groups. Pooled analysis could only be undertaken for incidence studies on South Asians where there was significant heterogeneity between the studies [95% for ulcerative colitis (UC), 83% for Crohn’s disease (CD)]. The difference between incidence rates was not significant with a rate ratio South Asian: Caucasian of 0.78 (95%CI: 0.22-2.78) for CD and 1.39 (95%CI: 0.84-2.32) for UC. South Asians showed consistently higher incidence and more extensive UC than the indigenous population in five countries. A similar pattern was observed for Hispanics in the United States. Bangladeshis and African Americans showed an increased risk of CD with perianal disease.
CONCLUSION This review suggests that migration and race influence the risk of developing inflammatory bowel disease. This may be due to different inherent responses upon exposure to an environmental trigger in the adopted country. Further prospective studies on homogenous migrant populations are needed to validate these observations, with a parallel arm for in-depth investigation of putative drivers.
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Affiliation(s)
- Ravi Misra
- Department of Gastroenterology, St. Marks Academic Institute, London HA1 3UJ, United Kingdom
| | - Omar Faiz
- Surgical Epidemiology, Trials and Outcome Centre, St. Marks Academic Institute, London HA1 3UJ, United Kingdom
| | - Pia Munkholm
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund Frederikssundsvej 30, Denmark
| | - Johan Burisch
- Department of Gastroenterology, North Zealand University Hospital, Frederikssund Frederikssundsvej 30, Denmark
| | - Naila Arebi
- Department of Gastroenterology, St. Marks Academic Institute, London HA1 3UJ, United Kingdom
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28
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Abstract
BACKGROUND Inflammatory bowel disease (IBD), once considered to be a Western disease, is increasingly being reported from India and other Asian countries. The present review summarizes epidemiology and disease characteristics of IBD in India with reference to other Asian countries and the West. SUMMARY India is projected to have one of the highest disease burden of IBD across the globe. The overall genetic risk and microbial signature in Indian IBD patients are similar to those of patients in the West as demonstrated by the similar incidence of IBD in second-generation Indian immigrants and matching perturbations in the structural and functional component of gut microbiota in Indian studies. The concept of the hygiene hypothesis continues to remain controversial with Indian studies demonstrating contradictory findings. The disease characteristics, long-term outcomes including the risk of colorectal cancer, and the effect of pregnancy on IBD and vice versa in Indian patients with IBD are in general similar with few differences. Unlike patients in the West, very few Indian patients have a positive family history. KEY MESSAGE The Indian disease pattern is going through a phase of epidemiological transition with a surge in the incidence of IBD. The epidemiology and disease characteristics of IBD mirror the patterns observed in the West.
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Affiliation(s)
| | - Vineet Ahuja
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, New Delhi, India
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29
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Gupta A, Bopanna S, Kedia S, Yadav DP, Goyal S, Jain S, Makharia G, Ahuja V. Familial aggregation of inflammatory bowel disease in patients with ulcerative colitis. Intest Res 2017; 15:388-394. [PMID: 28670236 PMCID: PMC5478764 DOI: 10.5217/ir.2017.15.3.388] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/07/2016] [Accepted: 10/12/2016] [Indexed: 12/18/2022] Open
Abstract
Background/Aims Familial occurrence of inflammatory bowel disease (IBD) is well documented. Reports from Western countries have shown a higher familial occurrence of ulcerative colitis (UC) in first- and second-degree relatives than that in the Asian UC population. No data are currently available from the Indian subcontinent in this regard. We present our data on the familial aggregation of UC. Methods Records of patients with UC followed at the Inflammatory Bowel Disease Clinic at the All India Institute of Medical Sciences, New Delhi from August 2004 to January 2016 were reviewed. Details regarding the prevalence of family history and characteristics of these patients were recorded. Affected family members were contacted and disease characteristics were noted for assessment of familial aggregation. Results Of the 2,058 UC patients included in the analysis, a positive family history of IBD was confirmed in 31 patients (1.5%), 24 (77.4%) of whom had only first-degree relatives affected. All the affected relatives had UC and none had Crohn's disease. Among first-degree relatives, siblings were found to have the highest prevalence of IBD (53.3%), followed by parents (26.7%). Conclusions The probability of occurrence of IBD in family members of affected North Indian UC patients is lower than that reported in Western populations.
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Affiliation(s)
- Akshita Gupta
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Sawan Bopanna
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Kedia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Dawesh Prakash Yadav
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Sandeep Goyal
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Saransh Jain
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Govind Makharia
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, India
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30
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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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31
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Takahashi S, Andreoletti G, Chen R, Munehira Y, Batra A, Afzal NA, Beattie RM, Bernstein JA, Ennis S, Snyder M. De novo and rare mutations in the HSPA1L heat shock gene associated with inflammatory bowel disease. Genome Med 2017; 9:8. [PMID: 28126021 PMCID: PMC5270254 DOI: 10.1186/s13073-016-0394-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/23/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disease of the gastrointestinal tract which includes ulcerative colitis and Crohn's disease. Genetic risk factors for IBD are not well understood. METHODS We performed a family-based whole exome sequencing (WES) analysis on a core family (Family A) to identify potential causal mutations and then analyzed exome data from a Caucasian pediatric cohort (136 patients and 106 controls) to validate the presence of mutations in the candidate gene, heat shock 70 kDa protein 1-like (HSPA1L). Biochemical assays of the de novo and rare (minor allele frequency, MAF < 0.01) mutation variant proteins further validated the predicted deleterious effects of the identified alleles. RESULTS In the proband of Family A, we found a heterozygous de novo mutation (c.830C > T; p.Ser277Leu) in HSPA1L. Through analysis of WES data of 136 patients, we identified five additional rare HSPA1L mutations (p.Gly77Ser, p.Leu172del, p.Thr267Ile, p.Ala268Thr, p.Glu558Asp) in six patients. In contrast, rare HSPA1L mutations were not observed in controls, and were significantly enriched in patients (P = 0.02). Interestingly, we did not find non-synonymous rare mutations in the HSP70 isoforms HSPA1A and HSPA1B. Biochemical assays revealed that all six rare HSPA1L variant proteins showed decreased chaperone activity in vitro. Moreover, three variants demonstrated dominant negative effects on HSPA1L and HSPA1A protein activity. CONCLUSIONS Our results indicate that de novo and rare mutations in HSPA1L are associated with IBD and provide insights into the pathogenesis of IBD, and also expand our understanding of the roles of HSP70s in human disease.
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Affiliation(s)
- Shinichi Takahashi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Rare Disease & LCM Laboratories, R & D Division, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Gaia Andreoletti
- Human Genetics and Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Rui Chen
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Yoichi Munehira
- Department of Biology, Stanford University, Stanford, CA, USA.,Oncology Laboratories, Oncology Function, Daiichi Sankyo Co., Ltd, Tokyo, Japan
| | - Akshay Batra
- Department of Paediatric Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road, Southampton, UK
| | - Nadeem A Afzal
- Department of Paediatric Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Tremona Road, Southampton, UK
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
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32
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Peng LL, Wang Y, Zhu FL, Xu WD, Ji XL, Ni J. IL-23R mutation is associated with ulcerative colitis: A systemic review and meta-analysis. Oncotarget 2017; 8:4849-4863. [PMID: 27902482 PMCID: PMC5354875 DOI: 10.18632/oncotarget.13607] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 11/12/2016] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVES Since a genome-wide association study revealed that Interleukin-23 receptor (IL-23R) gene is a candidate gene for Ulcerative Colitis (UC), many studies have investigated the association between the IL-23R polymorphisms and UC. However, the results were controversial. The aim of the study was to determine whether the IL-23R polymorphisms confer susceptibility to UC. METHODS A systematic literature search was carried out to identify all potentially relevant studies. Pooled odds ratios (ORs) with 95% confidence intervals (CIs) were used to estimate the strength of association. RESULTS A total of 33 studies in 32 articles, including 10,527 UC cases and 15,142 healthy controls, were finally involved in the meta-analysis. Overall, a significant association was found between all UC cases and the rs11209026A allele (OR = 0.665, 95% CI = 0.604~0.733, P < 0.001). Similarly, meta-analyses of the rs7517847, rs1004819, rs10889677, rs2201841, rs11209032, rs1495965, rs1343151 and rs11465804 polymorphisms also indicated significant association with all UC (all P < 0.05). Stratification by ethnicity revealed that the rs11209026, rs7517847, rs10889677, rs2201841 andrs11465804 polymorphisms were associated with UC in the Caucasian group, but not in Asians, while the rs1004819 and rs11209032 polymorphisms were found to be related to UC for both Caucasian and Asian groups. However, subgroup analysis failed to unveil any association between the rs1495965 and rs1343151 polymorphisms and UC in Caucasians or Asians. CONCLUSIONS The meta-analysis suggests significant association between IL-23R polymorphisms and UC, especially in Caucasians.
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Affiliation(s)
- Ling-Long Peng
- Department of Science and Education, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, China
| | - Ying Wang
- Department of Environmental Health, Suzhou Municipal Center for Disease Prevention and Control, Suzhou, Jiangsu 215004, China
| | - Feng-Ling Zhu
- Department of Science and Education, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, China
| | - Wang-Dong Xu
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xue-Lei Ji
- Department of Science and Education, The Second People's Hospital of Wuhu, Wuhu, Anhui 241000, China
| | - Jing Ni
- The Teaching Centre for Preventive Medicine, School of Public Health, Anhui Medical University, Hefei, Anhui 230032, China
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33
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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 DP, Kugathasan S. Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease. Gastroenterology 2017; 152:206-217.e2. [PMID: 27693347 PMCID: PMC5164948 DOI: 10.1053/j.gastro.2016.09.032] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [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, MD, 21231, USA,Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - David T. Okou
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Claire L. Simpson
- Department of Genetics, Genomics and Informatics, University of Tennessee
Health Science Center, Memphis, TN, 38163, USA,Computational and Statistical Genomics Branch, National Human Genome
Research Institute, National Institutes of Health, Baltimore, MD 21224, USA
| | - David J. Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Talin Haritunians
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Jonathan P. Bradfield
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Pankaj Chopra
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Jarod Prince
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Archana Kumar
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Chengrui Huang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health,
Baltimore, MD, 21205, USA
| | - Suresh Venkateswaran
- Department of Pediatrics, Emory University School of Medicine, Atlanta, GA,
30322, USA
| | - Lisa W. Datta
- Department of Medicine, Meyerhoff Inflammatory Bowel Disease Center, Johns
Hopkins University School of Medicine, Baltimore, MD, 21231, USA
| | - Zhi Wei
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kelly Thomas
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | | | - Antonio J. Quiros
- Department of Pediatrics, MUSC Pediatric Center for Inflammatory Bowel
Disorders, Summerville, SC, 29485, USA
| | - Jenifer Seminerio
- Department of Gastroenterology, MUSC Digestive Disease Center, Charleston,
SC, 29486, USA
| | - Zhenqiu Liu
- 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, 71130, 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, 21287, USA
| | - Raymond K. Cross
- Department of Medicine, University of Maryland School of Medicine,
Baltimore, MD, 21201, 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
| | - Gerald W. Dryden
- Department of Medicine, University of Louisville, Louisville, KY, 40202,
USA
| | - John S. Hanson
- Charlotte Gastroenterology and Hepatology, Charlotte, NC, 28207, USA
| | - Jason K. Hou
- Department of Medicine, Baylor College of Medicine; VA HSR&D Center for
Innovations in Quality Effectiveness and Safety; Michael E. DeBakey VA Medical Center,
Houston, TX, 77030, USA
| | - Sunny Z. Hussain
- Department of Pediatrics, Willis-Knighton Physician Network, Shreveport,
LA, 71118, USA
| | | | - Kim L. Isaacs
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel
Hill, NC, 27514, 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
| | - Barbara S. Kirschner
- Department of Pediatrics, University of Chicago Comer Children's
Hospital, Chicago, IL, 60637, USA
| | - John F. Kuemmerle
- Medicine and Physiology and Biophysics, Medical College of Virginia Campus
of Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - John H. Kwon
- Department of Internal Medicine, University of Texas Southwestern Medical
Center, Dallas, TX, 75390, 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
| | - David Mack
- Department of Pediatrics, University of Ottawa and Children’s
Hospital of Eastern Ontario, Ottawa, Ontario, K1H 8L1, Canada
| | - Peter Mannon
- Department of Medicine, University of Alabama at Birmingham, Birmingham,
AL, 35294, USA
| | | | - Rodney D. Newberry
- Department of Internal Medicine, Washington University School of Medicine,
St. Louis, MO, 63110, USA
| | - Bankole O. Osuntokun
- Department of Pediatrics, Cook Children's Medical Center, Fort Worth,
TX, 76104, USA
| | - Ashish S. Patel
- Department of Pediatrics, University of Texas Southwestern Medical Center,
Dallas, TX, 75390, USA
| | - Shehzad A. Saeed
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati
Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Stephan R. Targan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Ming-Hsi Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic Florida,
Jacksonville, FL, 32224, USA
| | - Martin Zonca
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI,
48202, USA
| | - John D. Rioux
- Department of Medicine, Université de Montréal and the
Montreal Heart Institute Research Center, Montreal, Quebec, H1T 1C8, 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, PA, 15261, USA
| | - Mark S. Silverberg
- Department of Medicine, Zane Cohen Centre for Digestive Diseases, Mount
Sinai Hospital, University of Toronto, Toronto, Toronto, Ontario, M5G1X5, Canada
| | - Judy H. Cho
- Medicine and Genetics, Icahn School of Medicine at Mount Sinai, Charles
Bronfman Institute for Personalized Medicine, New York, NY, 10029, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's
Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Michael E. Zwick
- Department of Human Genetics, Emory University School of Medicine, Atlanta,
GA, 30322, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research
Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - 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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Uniken Venema WT, Voskuil MD, Dijkstra G, Weersma RK, Festen EA. The genetic background of inflammatory bowel disease: from correlation to causality. J Pathol 2016; 241:146-158. [PMID: 27785786 DOI: 10.1002/path.4817] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/13/2016] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
Recent studies have greatly improved our insight into the genetic background of inflammatory bowel disease (IBD). New high-throughput technologies and large-scale international collaborations have contributed to the identification of 200 independent genetic risk loci for IBD. However, in most of these loci, it is unclear which gene conveys the risk for IBD. More importantly, it is unclear which variant within or near the gene is causal to the disease. Using targeted GWAS, imputation, resequencing of risk loci, and in silico fine-mapping of densely typed loci, several causal variants have been identified in IBD risk genes, and various pathological pathways have been uncovered. Current research in the field of IBD focuses on the effect of these causal variants on gene expression and protein function. However, more elements than only the genome must be taken into account to disentangle the multifactorial pathology of IBD. The genetic risk loci identified to date only explain a small part of genetic variance in disease risk. Currently, large multi-omics studies are incorporating factors ranging from the gut microbiome to the environment. In this review, we present the progress that has been made in IBD genetic research and stress the importance of studying causality to increase our understanding of the pathogenesis of IBD. We highlight important causal genetic variants in the candidate genes NOD2, ATG16L1, IRGM, IL23R, CARD9, RNF186, and PRDM1. We describe their downstream effects on protein function and their direct effects on the gut immune system. Furthermore, we discuss the future role of genetics in unravelling disease mechanisms in IBD. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Werna Tc Uniken Venema
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Michiel D Voskuil
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Eleonora Am Festen
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
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Cardinale CJ, Li D, Tian L, Connolly JJ, March ME, Hou C, Wang F, Snyder J, Kim CE, Chiavacci RM, Sleiman PM, Burnham JM, Hakonarson H. Association of a rare NOTCH4 coding variant with systemic sclerosis: a family-based whole exome sequencing study. BMC Musculoskelet Disord 2016; 17:462. [PMID: 27829420 PMCID: PMC5103422 DOI: 10.1186/s12891-016-1320-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Accepted: 11/01/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a rheumatologic disease with a multifactorial etiology. Genome-wide association studies imply a polygenic, complex mode of inheritance with contributions from variation at the human leukocyte antigen locus and non-coding variation at a locus on chromosome 6p21, among other modestly impactful loci. Here we describe an 8-year-old female proband presenting with diffuse cutaneous SSc/scleroderma and a family history of SSc in a grandfather and maternal aunt. METHODS We employed whole exome sequencing (WES) of three members of this family. We examined rare missense, nonsense, splice-altering, and coding indels matching an autosomal dominant inheritance model. We selected one missense variant for Sanger sequencing confirmation based on its predicted impact on gene function and location in a known SSc genetic locus. RESULTS Bioinformatic analysis found eight candidate variants meeting our criteria. We identified a very rare missense variant in the regulatory NODP domain of NOTCH4 located at the 6p21 locus, c.4245G > A:p.Met1415Ile, segregating with the phenotype. This allele has a frequency of 1.83 × 10-5 by the data of the Exome Aggregation Consortium. CONCLUSION This family suggests a novel mechanism of SSc pathogenesis in which a rare and penetrant coding variation can substantially elevate disease risk in contrast to the more modest non-coding variation typically found at this locus. These results suggest that modulation of the NOTCH4 gene might be responsible for the association signal at chromosome 6p21 in SSc.
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Affiliation(s)
- Christopher J Cardinale
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Dong Li
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Lifeng Tian
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - John J Connolly
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Michael E March
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Cuiping Hou
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Fengxiang Wang
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - James Snyder
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Cecilia E Kim
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Rosetta M Chiavacci
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA
| | - Patrick M Sleiman
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jon M Burnham
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Rheumatology, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Pediatric Research Center, The Children's Hospital of Philadelphia, 3615 Civic Center Blvd Ste 1216, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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36
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A cross-ethnic survey of CFB and SLC44A4, Indian ulcerative colitis GWAS hits, underscores their potential role in disease susceptibility. Eur J Hum Genet 2016; 25:111-122. [PMID: 27759029 DOI: 10.1038/ejhg.2016.131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Revised: 08/16/2016] [Accepted: 08/23/2016] [Indexed: 12/14/2022] Open
Abstract
The first ever genome-wide association study (GWAS) of ulcerative colitis in genetically distinct north Indian population identified two novel genes namely CFB and SLC44A4. Considering their biological relevance, we investigated allelic/genetic heterogeneity in these genes among ulcerative colitis cohorts of north Indian, Japanese and Dutch origin using high-density ImmunoChip case-control genotype data. Comparative linkage disequilibrium profiling and test of association were performed. Of the 28 CFB SNPs, similar strength of association was observed for rs4151657 (novel ulcerative colitis GWAS SNP) in north Indians (P=1.73 × 10-10) and Japanese (P=2.02 × 10-12) but not in the Dutch. Further, a three-marker haplotype was shared between north Indians and Japanese (P<10-8), but a different five-marker haplotype was associated (P=2.07 × 10-6) in the Dutch. Of the 22 SLC44A4 SNPs, rs2736428 (novel ulcerative colitis GWAS SNP) was found significantly associated in north Indians (P=4.94 × 10-10) and Japanese (P=3.37 × 10-9), but not among the Dutch. These results suggest (i) apparent allelic heterogeneity in CFB and genetic heterogeneity in SLC44A4 across different ethnic groups; (ii) shared ulcerative colitis genetic etiological factors among Asians; and finally (iii) re-exploration of GWAS findings together with high-density genotyping/sequencing and trans-ethnic fine mapping approaches may help identify shared and population-specific risk variants and enable to explain missing disease heritability.
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Jin Y, Andersen G, Yorgov D, Ferrara TM, Ben S, Brownson KM, Holland PJ, Birlea SA, Siebert J, Hartmann A, Lienert A, van Geel N, Lambert J, Luiten RM, Wolkerstorfer A, Wietze van der Veen JP, Bennett DC, Taïeb A, Ezzedine K, Kemp EH, Gawkrodger DJ, Weetman AP, Kõks S, Prans E, Kingo K, Karelson M, Wallace MR, McCormack WT, Overbeck A, Moretti S, Colucci R, Picardo M, Silverberg NB, Olsson M, Valle Y, Korobko I, Böhm M, Lim HW, Hamzavi I, Zhou L, Mi QS, Fain PR, Santorico SA, Spritz RA. Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants. Nat Genet 2016; 48:1418-1424. [PMID: 27723757 PMCID: PMC5120758 DOI: 10.1038/ng.3680] [Citation(s) in RCA: 186] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/29/2016] [Indexed: 12/15/2022]
Abstract
Vitiligo is an autoimmune disease in which depigmented skin results from destruction of melanocytes1, with epidemiologic association with other autoimmune diseases2. In previous linkage and genome-wide association studies (GWAS1, GWAS2), we identified 27 vitiligo susceptibility loci in patients of European (EUR) ancestry. We carried out a third GWAS (GWAS3) in EUR subjects, with augmented GWAS1 and GWAS2 controls, genome-wide imputation, and meta-analysis of all three GWAS, followed by an independent replication. The combined analyses, with 4,680 cases and 39,586 controls, identified 23 new loci and 7 suggestive loci, most encoding immune and apoptotic regulators, some also associated with other autoimmune diseases, as well as several melanocyte regulators. Bioinformatic analyses indicate a predominance of causal regulatory variation, some corresponding to eQTL at these loci. Together, the identified genes provide a framework for vitiligo genetic architecture and pathobiology, highlight relationships to other autoimmune diseases and melanoma, and offer potential targets for treatment.
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Affiliation(s)
- Ying Jin
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Genevieve Andersen
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Daniel Yorgov
- Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA
| | - Tracey M Ferrara
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Songtao Ben
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Kelly M Brownson
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Paulene J Holland
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stanca A Birlea
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Dermatology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Anke Hartmann
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Anne Lienert
- Department of Dermatology, University Hospital Erlangen, Erlangen, Germany
| | - Nanja van Geel
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Jo Lambert
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Rosalie M Luiten
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands
| | - Albert Wolkerstorfer
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands
| | - J P Wietze van der Veen
- Netherlands Institute for Pigment Disorders, Department of Dermatology, Academic Medical Centre University of Amsterdam, Amsterdam, the Netherlands.,Department of Dermatology, Medical Centre Haaglanden, The Hague, the Netherlands
| | - Dorothy C Bennett
- Molecular and Clinical Sciences Research Institute, St. George's, University of London, London, UK
| | - Alain Taïeb
- Centre de Référence des Maladies Rares de la Peau, Department of Dermatology, Hôpital St.-André, Bordeaux, France
| | - Khaled Ezzedine
- Centre de Référence des Maladies Rares de la Peau, Department of Dermatology, Hôpital St.-André, Bordeaux, France
| | - E Helen Kemp
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - David J Gawkrodger
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Anthony P Weetman
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Sulev Kõks
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Ele Prans
- Department of Pathophysiology, University of Tartu, Tartu, Estonia
| | - Külli Kingo
- Department of Dermatology, University of Tartu, Tartu, Estonia
| | - Maire Karelson
- Department of Dermatology, University of Tartu, Tartu, Estonia
| | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Wayne T McCormack
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, Florida, USA
| | | | - Silvia Moretti
- Section of Dermatology, Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Roberta Colucci
- Section of Dermatology, Department of Surgery and Translational Medicine, University of Florence, Florence, Italy
| | - Mauro Picardo
- Laboratorio Fisiopatologia Cutanea, Istituto Dermatologico San Gallicano, Rome, Italy
| | - Nanette B Silverberg
- Department of Dermatology, Columbia University College of Physicians and Surgeons, New York, New York, USA.,Pediatric and Adolescent Dermatology, St. Luke's-Roosevelt Hospital Center, New York, New York, USA
| | - Mats Olsson
- International Vitiligo Center, Uppsala, Sweden
| | - Yan Valle
- Vitiligo Research Foundation, New York, New York, USA
| | - Igor Korobko
- Vitiligo Research Foundation, New York, New York, USA.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Markus Böhm
- Department of Dermatology, University of Münster, Münster, Germany
| | - Henry W Lim
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Iltefat Hamzavi
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Li Zhou
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Qing-Sheng Mi
- Department of Dermatology, Henry Ford Hospital, Detroit, Michigan, USA
| | - Pamela R Fain
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Stephanie A Santorico
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Mathematical and Statistical Sciences, University of Colorado Denver, Denver, Colorado, USA.,Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado, Aurora, Colorado, USA
| | - Richard A Spritz
- Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA
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Ye BD, McGovern DP. Genetic variation in IBD: progress, clues to pathogenesis and possible clinical utility. Expert Rev Clin Immunol 2016; 12:1091-107. [PMID: 27156530 PMCID: PMC5083126 DOI: 10.1080/1744666x.2016.1184972] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epidemiological and clinical studies have suggested that the pathogenesis of inflammatory bowel disease (IBD) is strongly influenced by genetic predisposition. Beyond the limitations of linkage analysis, multiple genome-wide association studies, their meta-analyses, and targeted genotyping array techniques have broadened our understanding of the genetic architecture of IBD. Currently, over 200 single nucleotide polymorphisms are known to be associated with susceptibility to IBD and through functional analysis of genes and loci, a substantial proportion of pathophysiologic mechanisms have been revealed. However, because only a modest fraction of predicted heritability can be explained by known genes/loci, additional strategies are needed including the identification of rare variants with large effect sizes to help explain the missing heritability. Considerable progress is also being made on applying outcomes of genetic research in diagnostics, classification, prognostics, and the development of new therapeutics of IBD.
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Affiliation(s)
- Byong Duk Ye
- Department of Gastroenterology and Inflammatory Bowel Disease Center, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dermot P.B. McGovern
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Medical Genetics Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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39
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Ray G. Inflammatory bowel disease in India - Past, present and future. World J Gastroenterol 2016; 22:8123-8136. [PMID: 27688654 PMCID: PMC5037081 DOI: 10.3748/wjg.v22.i36.8123] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/09/2016] [Accepted: 08/23/2016] [Indexed: 02/06/2023] Open
Abstract
There is rising incidence and prevalence of inflammatory bowel disease (IBD) in India topping the Southeast Asian (SEA) countries. The common genes implicated in disease pathogenesis in the West are not causal in Indian patients and the role of “hygiene hypothesis” is unclear. There appears to be a North-South divide with more ulcerative colitis (UC) in north and Crohn’s disease (CD) in south India. IBD in second generation Indian migrants to the West takes the early onset and more severe form of the West whereas it retains the nature of its country of origin in migrants to SEA countries. The clinical presentation is much like other SEA countries (similar age and sex profile, low positive family history and effect of smoking, roughly similar disease location, use of aminosalicylates for CD, low use of biologics and similar surgical rates) with some differences (higher incidence of inflammatory CD, lower perianal disease, higher use of aminosalicylates and azathioprine and lower current use of corticosteroids). UC presents more with extensive disease not paralleled in severity clinically or histologically, follows benign course with easy medical control and low incidence of fulminant disease, cancer, complications, and surgery. UC related colorectal cancer develop in an unpredictable manner with respect to disease duration and site questioning the validity of strict screening protocol. About a third of CD patients get antituberculosis drugs and a significant number presents with small intestinal bleed which is predominantly afflicted by aggressive inflammation. Biomarkers have inadequate diagnostic sensitivity and specificity for both. Pediatric IBD tends to be more severe than adult. Population based studies are needed to address the lacunae in epidemiology and definition of etiological factors. Newer biomarkers and advanced diagnostic techniques (in the field of gastrointestinal endoscopy, molecular pathology and genetics) needs to be developed for proper disease definition and treatment.
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40
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Guo C, Wu K. Risk Genes of Inflammatory Bowel Disease in Asia: What Are the Most Important Pathways Affected? Dig Dis 2016; 34:5-11. [PMID: 26982027 DOI: 10.1159/000442917] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Genetic factors play an important role in the pathogenesis of inflammatory bowel disease (IBD), and IBD is now recognized as a complex disease that results from interplay between genetic and environment factors. To date, over 160 IBD-susceptible loci have been identified using genome-wide association studies (GWAS). The risk genes identified in these studies are involved in various pathways in innate and adaptive immune response such as innate bacterial sensing, autophagy and interleukin-23 receptor/T-helper cell 17 pathway. It was initially believed that the genetic backgrounds of Asian IBD patients differ from that of other populations. Recent GWAS and meta-analysis found that there is pervasive sharing of risk loci between the East and West. Overlapping risk genes between populations of different ancestries indicate that pathways underlying the etiology of IBD may be common between Asia and other areas. However, the importance of individual pathways may be different in Asia from the Western countries. Identifying the most important pathways affected in Asian IBD patients may provide a better understanding of pathogenesis of IBD in Asia and improve the clinical management of the patients.
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Affiliation(s)
- Changcun Guo
- Department of Gastroenterology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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41
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Gupta A, Thelma BK. Identification of critical variants within SLC44A4, an ulcerative colitis susceptibility gene identified in a GWAS in north Indians. Genes Immun 2016; 17:105-9. [PMID: 26741288 DOI: 10.1038/gene.2015.53] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/14/2022]
Abstract
SLC44A4 is one of the seven novel susceptibility genes that were discovered in the first ever genome-wide association study (GWAS) on ulcerative colitis (UC) in the genetically distinct north Indians. This gene seems to be functionally relevant to disease biology as it may contribute to the associated phenotype of Vitamin B1 deficiency among UC patients, hence playing a role in disease pathogenesis. A large number of single-nucleotide polymorphisms (SNPs) are known to be distributed throughout this gene, but the functional status of most are not known. Thus, an extensive investigation of structural and regulatory variants within this gene was undertaken in this study to identify the critical variants amongst them using a combination of fine mapping, in silico and in vitro approaches. A few intronic SNPs were predicted to have regulatory roles on the basis of in silico analysis, suggesting that they may be the critical variants within SLC44A4. This highlights the importance of this gene in UC biology, thus confirming the finding of the GWAS and also warranting additional studies.
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Affiliation(s)
- A Gupta
- Department of Genetics, University of Delhi South Campus, New Delhi, India
| | - B K Thelma
- Department of Genetics, University of Delhi South Campus, New Delhi, India
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Colectomy Rates for Ulcerative Colitis Differ between Ethnic Groups: Results from a 15-Year Nationwide Cohort Study. Can J Gastroenterol Hepatol 2016; 2016:8723949. [PMID: 28074174 PMCID: PMC5198146 DOI: 10.1155/2016/8723949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 11/28/2016] [Indexed: 12/21/2022] Open
Abstract
Introduction. Previous epidemiological studies suggest a higher rate of pancolonic disease in South Asians (SA) compared with White Europeans (WE). The aim of the study was to compare colectomy rates for ulcerative colitis (UC) in SA to those of WE. Methods. Patients with UC were identified from a national administrative dataset (Hospital Episode Statistics, HES) between 1997 and 2012 according to ICD-10 diagnosis code K51 for UC. The colectomy rate for each ethnic group was calculated as the proportion of patients who underwent colectomy from the total UC cases for that group. Results. Of 212,430 UC cases, 73,318 (35.3%) were coded for ethnicity. There was no significant difference in the colectomy rate between SA and WE (6.93% versus 6.90%). Indians had a significantly higher colectomy rate than WE (9.8% versus 6.9%, p < 0.001). Indian patients were 21% more likely to require colectomy for UC compared with WE group (OR: 1.21, 95% CI: 1.04-1.42, and p = 0.001). Conclusions. Given the limitations in coding, the colectomy rate in this cohort was higher in Indians compared to WE. A prospectively recruited ethnic cohort study will decipher whether this reflects a more aggressive phenotype or is due to other confounding factors.
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Combination Testing Using a Single MSH5 Variant alongside HLA Haplotypes Improves the Sensitivity of Predicting Coeliac Disease Risk in the Polish Population. PLoS One 2015; 10:e0139197. [PMID: 26406233 PMCID: PMC4583383 DOI: 10.1371/journal.pone.0139197] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 09/09/2015] [Indexed: 12/21/2022] Open
Abstract
Assessment of non-HLA variants alongside standard HLA testing was previously shown to improve the identification of potential coeliac disease (CD) patients. We intended to identify new genetic variants associated with CD in the Polish population that would improve CD risk prediction when used alongside HLA haplotype analysis. DNA samples of 336 CD and 264 unrelated healthy controls were used to create DNA pools for a genome wide association study (GWAS). GWAS findings were validated with individual HLA tag single nucleotide polymorphism (SNP) typing of 473 patients and 714 healthy controls. Association analysis using four HLA-tagging SNPs showed that, as was found in other populations, positive predicting genotypes (HLA-DQ2.5/DQ2.5, HLA-DQ2.5/DQ2.2, and HLA-DQ2.5/DQ8) were found at higher frequencies in CD patients than in healthy control individuals in the Polish population. Both CD-associated SNPs discovered by GWAS were found in the CD susceptibility region, confirming the previously-determined association of the major histocompatibility (MHC) region with CD pathogenesis. The two most significant SNPs from the GWAS were rs9272346 (HLA-dependent; localized within 1 Kb of DQA1) and rs3130484 (HLA-independent; mapped to MSH5). Specificity of CD prediction using the four HLA-tagging SNPs achieved 92.9%, but sensitivity was only 45.5%. However, when a testing combination of the HLA-tagging SNPs and the MSH5 SNP was used, specificity decreased to 80%, and sensitivity increased to 74%. This study confirmed that improvement of CD risk prediction sensitivity could be achieved by including non-HLA SNPs alongside HLA SNPs in genetic testing.
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de Lange KM, Barrett JC. Understanding inflammatory bowel disease via immunogenetics. J Autoimmun 2015; 64:91-100. [PMID: 26257098 DOI: 10.1016/j.jaut.2015.07.013] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 07/23/2015] [Indexed: 01/01/2023]
Abstract
The major inflammatory bowel diseases, Crohn's disease and ulcerative colitis, are both debilitating disorders of the gastrointestinal tract, characterized by a dysregulated immune response to unknown environmental triggers. Both disorders have an important and overlapping genetic component, and much progress has been made in the last 20 years at elucidating some of the specific factors contributing to disease pathogenesis. Here we review our growing understanding of the immunogenetics of inflammatory bowel disease, from the twin studies that first implicated a role for the genome in disease susceptibility to the latest genome-wide association studies that have identified hundreds of associated loci. We consider the insight this offers into the biological mechanisms of the inflammatory bowel diseases, such as autophagy, barrier defence and T-cell differentiation signalling. We reflect on these findings in the context of other immune-related disorders, both common and rare. These observations include links both obvious, such as to pediatric colitis, and more surprising, such as to leprosy. As a changing picture of the underlying genetic architecture emerges, we turn to future directions for the study of complex human diseases such as these, including the use of next generation sequencing technologies for the identification of rarer risk alleles, and potential approaches for narrowing down associated loci to casual variants. We consider the implications of this work for translation into clinical practice, for example via early therapeutic hypotheses arising from our improved understanding of the biology of inflammatory bowel disease. Finally, we present potential opportunities to better understand environmental risk factors, such as the human microbiota in the context of immunogenetics.
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Affiliation(s)
- Katrina M de Lange
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom
| | - Jeffrey C Barrett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom; European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom; Centre for Therapeutic Target Validation, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, United Kingdom.
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Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet 2015; 47:979-986. [PMID: 26192919 DOI: 10.1038/ng.3359] [Citation(s) in RCA: 1575] [Impact Index Per Article: 175.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 06/24/2015] [Indexed: 02/07/2023]
Abstract
Ulcerative colitis and Crohn's disease are the two main forms of inflammatory bowel disease (IBD). Here we report the first trans-ancestry association study of IBD, with genome-wide or Immunochip genotype data from an extended cohort of 86,640 European individuals and Immunochip data from 9,846 individuals of East Asian, Indian or Iranian descent. We implicate 38 loci in IBD risk for the first time. For the majority of the IBD risk loci, the direction and magnitude of effect are consistent in European and non-European cohorts. Nevertheless, we observe genetic heterogeneity between divergent populations at several established risk loci driven by differences in allele frequency (NOD2) or effect size (TNFSF15 and ATG16L1) or a combination of these factors (IL23R and IRGM). Our results provide biological insights into the pathogenesis of IBD and demonstrate the usefulness of trans-ancestry association studies for mapping loci associated with complex diseases and understanding genetic architecture across diverse populations.
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Jin G, Zhu M, Yin R, Shen W, Liu J, Sun J, Wang C, Dai J, Ma H, Wu C, Yin Z, Huang J, Higgs BW, Xu L, Yao Y, Christiani DC, Amos CI, Hu Z, Zhou B, Shi Y, Lin D, Shen H. Low-frequency coding variants at 6p21.33 and 20q11.21 are associated with lung cancer risk in Chinese populations. Am J Hum Genet 2015; 96:832-40. [PMID: 25937444 DOI: 10.1016/j.ajhg.2015.03.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/24/2015] [Indexed: 11/29/2022] Open
Abstract
Genome-wide association studies have successfully identified a subset of common variants associated with lung cancer risk. However, these variants explain only a fraction of lung cancer heritability. It has been proposed that low-frequency or rare variants might have strong effects and contribute to the missing heritability. To assess the role of low-frequency or rare variants in lung cancer development, we analyzed exome chips representing 1,348 lung cancer subjects and 1,998 control subjects during the discovery stage and subsequently evaluated promising associations in an additional 4,699 affected subjects and 4,915 control subjects during the replication stages. Single-variant and gene-based analyses were carried out for coding variants with a minor allele frequency less than 0.05. We identified three low-frequency missense variants in BAT2 (rs9469031, c.1544C>T [p.Pro515Leu]; odds ratio [OR] = 0.55, p = 1.28 × 10(-10)), FKBPL (rs200847762, c.410C>T [p.Pro137Leu]; OR = 0.25, p = 9.79 × 10(-12)), and BPIFB1 (rs6141383, c.850G>A [p.Val284Met]; OR = 1.72, p = 1.79 × 10(-7)); these variants were associated with lung cancer risk. rs9469031 in BAT2 and rs6141383 in BPIFB1 were also associated with the age of onset of lung cancer (p = 0.001 and 0.006, respectively). BAT2 and FKBPL at 6p21.33 and BPIFB1 at 20q11.21 were differentially expressed in lung tumors and paired normal tissues. Gene-based analysis revealed that FKBPL, in which two independent variants were identified, might account for the association with lung cancer risk at 6p21.33. Our results highlight the important role low-frequency variants play in lung cancer susceptibility and indicate that candidate genes at 6p21.33 and 20q11.21 are potentially biologically relevant to lung carcinogenesis.
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Affiliation(s)
- Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention, and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Rong Yin
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Jie Sun
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China
| | - Chen Wu
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zhihua Yin
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110001, China
| | | | | | - Lin Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | | | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA
| | - Christopher I Amos
- Center for Genomic Medicine, Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03755, USA
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention, and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Baosen Zhou
- Department of Epidemiology, School of Public Health, China Medical University, Shenyang 110001, China
| | - Yongyong Shi
- Ministry of Education Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing 211166, China; Jiangsu Key Laboratory of Cancer Biomarkers, Prevention, and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing 211166, China.
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