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Alula KM, Theiss AL. Autophagy in Crohn's Disease: Converging on Dysfunctional Innate Immunity. Cells 2023; 12:1779. [PMID: 37443813 PMCID: PMC10341259 DOI: 10.3390/cells12131779] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Crohn's disease (CD) is a chronic inflammatory bowel disease marked by relapsing, transmural intestinal inflammation driven by innate and adaptive immune responses. Autophagy is a multi-step process that plays a critical role in maintaining cellular homeostasis by degrading intracellular components, such as damaged organelles and invading bacteria. Dysregulation of autophagy in CD is revealed by the identification of several susceptibility genes, including ATG16L1, IRGM, NOD2, LRRK2, ULK1, ATG4, and TCF4, that are involved in autophagy. In this review, the role of altered autophagy in the mucosal innate immune response in the context of CD is discussed, with a specific focus on dendritic cells, macrophages, Paneth cells, and goblet cells. Selective autophagy, such as xenophagy, ERphagy, and mitophagy, that play crucial roles in maintaining intestinal homeostasis in these innate immune cells, are discussed. As our understanding of autophagy in CD pathogenesis evolves, the development of autophagy-targeted therapeutics may benefit subsets of patients harboring impaired autophagy.
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Affiliation(s)
| | - Arianne L. Theiss
- Division of Gastroenterology & Hepatology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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2
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Goren I, Sharar Fischler T, Yanai H, Pal P, Adigopula B, Pendyala S, Ganesh G, Vishnubhotla R, Rabinowitz KM, Shaham Barda E, Yadamreddy D, Godny L, Peleg N, Banerjee R, Dotan I. Newly Diagnosed Crohn's Disease Patients in India and Israel Display Distinct Presentations and Serological Markers: Insights from Prospective Cohorts. J Clin Med 2022; 11:jcm11236899. [PMID: 36498474 PMCID: PMC9737641 DOI: 10.3390/jcm11236899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/12/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Crohn’s disease (CD) incidence is rising in India. However, features of newly diagnosed patients with CD in this population are largely unknown. The Indo-Israeli IBD GastroEnterology paRtnership (TiiiGER) aimed to investigate differences in presentation among patients with newly diagnosed CD in India and Israel, and to explore phenotype−serotype correlations. Methods: A prospective observational cohort study of consecutive adults (>18 years) conducted in two large referral centers in India and Israel (2014−2018). Clinical data, an antiglycan serological panel, and 20 CD-associated genetic variants were analyzed. Outcomes: complicated phenotype at diagnosis and early complicated course (hospitalizations/surgeries) within 2 years of diagnosis. Results: We included 260 patients (104, Indian (65.4%, male; age, 37.8); 156 Israeli (49.4%, male; 31.8, age)). Median lag time from symptoms onset to diagnosis was 10.5 (IQR 3−38) vs. 3 (IQR 1−8) months in Indian vs. Israeli patients (p < 0.001). Complicated phenotype at diagnosis was observed in 48% of Indian and 30% of Israeli patients (p = 0.003). Complicated phenotype was associated with higher anti-Saccharomyces cerevisiae antibody (ASCA) seropositivity rate among Israeli patients (p < 0.001), but not among Indian patients. Antiglycan serology did not correlate with the tested genetic variants. Early complicated course occurred in 28 (18%) Israeli and 13 (12.5%) Indian patients. The time from diagnosis to complication was comparable (log rank p = 0.152). Antiglycan serology did not correlate with a complicated early course in either cohort. Conclusions: There are significant differences in patients presenting with newly diagnosed CD in India and Israel, including phenotype and distinct biomarkers at diagnosis. These differences suggest different genetic and environmental disease modifiers.
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Affiliation(s)
- Idan Goren
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Correspondence:
| | - Tali Sharar Fischler
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
| | - Henit Yanai
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
| | - Partha Pal
- Department of Gastroenterology, Asian Institute of Gastroenterology, Hyderabad 501301, India
| | - Bhargavi Adigopula
- Department of Gastroenterology, Asian Institute of Gastroenterology, Hyderabad 501301, India
| | - Sushmitha Pendyala
- Department of Gastroenterology, Asian Institute of Gastroenterology, Hyderabad 501301, India
| | - Girish Ganesh
- Department of Gastroenterology, Asian Institute of Gastroenterology, Hyderabad 501301, India
| | - Ravikanth Vishnubhotla
- Department of Genomics and Molecular Biology, Institute of Translational Research, Asian Institute of Gastroenterology and AIG Hospitals, Hyderabad 500032, India
| | - Keren Masha Rabinowitz
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
- Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Hospital Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49414, Israel
| | - Efrat Shaham Barda
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
- Felsenstein Medical Research Center, Rabin Medical Center, Beilinson Hospital Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49414, Israel
| | - Durga Yadamreddy
- Department of Genomics and Molecular Biology, Institute of Translational Research, Asian Institute of Gastroenterology and AIG Hospitals, Hyderabad 500032, India
| | - Lihi Godny
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
| | - Noam Peleg
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
| | - Rupa Banerjee
- Department of Gastroenterology, Asian Institute of Gastroenterology, Hyderabad 501301, India
| | - Iris Dotan
- IBD Center, Division of Gastroenterology, Rabin Medical Center Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Petah Tikva 49100, Israel
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3
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Cao C, Kossinna P, Kwok D, Li Q, He J, Su L, Guo X, Zhang Q, Long Q. Disentangling genetic feature selection and aggregation in transcriptome-wide association studies. Genetics 2021; 220:6444993. [PMID: 34849857 DOI: 10.1093/genetics/iyab216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 11/04/2021] [Indexed: 12/14/2022] Open
Abstract
The success of transcriptome-wide association studies (TWAS) has led to substantial research towards improving the predictive accuracy of its core component of Genetically Regulated eXpression (GReX). GReX links expression information with genotype and phenotype by playing two roles simultaneously: it acts as both the outcome of the genotype-based predictive models (for predicting expressions) and the linear combination of genotypes (as the predicted expressions) for association tests. From the perspective of machine learning (considering SNPs as features), these are actually two separable steps-feature selection and feature aggregation-which can be independently conducted. In this work, we show that the single approach of GReX limits the adaptability of TWAS methodology and practice. By conducting simulations and real data analysis, we demonstrate that disentangled protocols adapting straightforward approaches for feature selection (e.g., simple marker test) and aggregation (e.g., kernel machines) outperform the standard TWAS protocols that rely on GReX. Our development provides more powerful novel tools for conducting TWAS. More importantly, our characterization of the exact nature of TWAS suggests that, instead of questionably binding two distinct steps into the same statistical form (GReX), methodological research focusing on optimal combinations of feature selection and aggregation approaches will bring higher power to TWAS protocols.
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Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Pathum Kossinna
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Qing Li
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jingni He
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Liya Su
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Qingrun Zhang
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.,Department of Mathematics & Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Quan Long
- Department of Biochemistry & Molecular Biology, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.,Department of Mathematics & Statistics, University of Calgary, Calgary, AB T2N 1N4, Canada.,Department of Medical Genetics, University of Calgary, Calgary, AB T2N 4N1, Canada.,Hotchkiss Brain Institute, O'Brien Institute for Public Health, University of Calgary, Calgary, AB T2N 4N1, Canada
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4
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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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5
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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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6
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Kee BP, Ng JG, Ng CC, Hilmi I, Goh KL, Chua KH. Genetic polymorphisms of ATG16L1 and IRGM genes in Malaysian patients with Crohn's disease. J Dig Dis 2020; 21:29-37. [PMID: 31654602 DOI: 10.1111/1751-2980.12829] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 10/15/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To investigate the association between genetic polymorphisms in ATG16L1 and IRGM genes and the development of Crohn's disease (CD) in Malaysian patients. METHODS Altogether 335 participants were recruited, including 85 patients with CD and 250 unrelated healthy controls, and their informed consent was obtained. Genomic DNA was extracted via a conventional phenol-chloroform extraction method. Six single nucleotide polymorphisms (SNPs) in ATG16L1 and IRGM genes were genotyped using TaqMan SNP genotyping assays. Associations between SNP and CD were determined using Fisher's exact test, odds ratio, and 95% confidence interval. Statistical power and the Hardy-Weinberg equilibrium were also calculated. RESULTS Two SNPs (rs2241880 and rs6754677) in the ATG16L1 gene were significantly associated with the onset of CD in the Malaysian population. The A allele and homozygous A/A genotype of the rs2241880 A/G polymorphism were protective against CD in the overall Malaysian and Malay population. The G allele and homozygous G/G genotype of the rs6754677 G/A polymorphism were protective in the Indian population, whereas the homozygous A/A genotype showed a risk of developing CD. The homozygous G/G genotype of IRGM rs11747270 was significantly present in the controls. However, this significance was not observed in a race-stratified analysis. All three ATG16L1 SNPs were associated with inflamed terminal ileum. IRGM rs4958847 and rs11747270 increased the risk of developing arthritis in patients with CD. CONCLUSION We found a significant association between SNP, which are located in autophagy-related genes, and CD in a Malaysian population.
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Affiliation(s)
- Boon Pin Kee
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jin Guan Ng
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Ching Ching Ng
- Division of Genetics and Molecular Biology, Institute of Biological Science, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Ida Hilmi
- Division of Gastroenterology and Hepatology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Khean Lee Goh
- Division of Gastroenterology and Hepatology, Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
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7
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Mehto S, Jena KK, Nath P, Chauhan S, Kolapalli SP, Das SK, Sahoo PK, Jain A, Taylor GA, Chauhan S. The Crohn's Disease Risk Factor IRGM Limits NLRP3 Inflammasome Activation by Impeding Its Assembly and by Mediating Its Selective Autophagy. Mol Cell 2019; 73:429-445.e7. [PMID: 30612879 PMCID: PMC6372082 DOI: 10.1016/j.molcel.2018.11.018] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/19/2018] [Accepted: 11/15/2018] [Indexed: 12/12/2022]
Abstract
Several large-scale genome-wide association studies genetically linked IRGM to Crohn’s disease and other inflammatory disorders in which the IRGM appears to have a protective function. However, the mechanism by which IRGM accomplishes this anti-inflammatory role remains unclear. Here, we reveal that IRGM/Irgm1 is a negative regulator of the NLRP3 inflammasome activation. We show that IRGM expression, which is increased by PAMPs, DAMPs, and microbes, can suppress the pro-inflammatory responses provoked by the same stimuli. IRGM/Irgm1 negatively regulates IL-1β maturation by suppressing the activation of the NLRP3 inflammasome. Mechanistically, we show that IRGM interacts with NLRP3 and ASC and hinders inflammasome assembly by blocking their oligomerization. Further, IRGM mediates selective autophagic degradation of NLRP3 and ASC. By suppressing inflammasome activation, IRGM/Irgm1 protects from pyroptosis and gut inflammation in a Crohn’s disease experimental mouse model. This study for the first time identifies the mechanism by which IRGM is protective against inflammatory disorders. IRGM negatively regulates NLRP3/ASC inflammasome activation IRGM obstructs NLRP3/ASC inflammasome assembly IRGM mediates selective autophagic degradation of NLRP3/ASC inflammasome Irgm1 by suppressing Nlrp3 inflammasome prevents gut inflammation in an IBD mouse model
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Affiliation(s)
- Subhash Mehto
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Kautilya Kumar Jena
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Parej Nath
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar 751024, India
| | - Swati Chauhan
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | | | - Saroj Kumar Das
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Pradyumna Kumar Sahoo
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Ashish Jain
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway; Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gregory A Taylor
- Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, NC 27705, USA
| | - Santosh Chauhan
- Cell Biology and Infectious Diseases Unit, Institute of Life Sciences, Bhubaneswar 751023, India.
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8
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Ajayi TA, Innes CL, Grimm SA, Rai P, Finethy R, Coers J, Wang X, Bell DA, McGrath JA, Schurman SH, Fessler MB. Crohn's disease IRGM risk alleles are associated with altered gene expression in human tissues. Am J Physiol Gastrointest Liver Physiol 2019; 316:G95-G105. [PMID: 30335469 PMCID: PMC6383377 DOI: 10.1152/ajpgi.00196.2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Crohn's disease (CD) is a chronic inflammatory gastrointestinal disorder. Genetic association studies have implicated dysregulated autophagy in CD. Among risk loci identified are a promoter single nucleotide polymorphism (SNP)( rs13361189 ) and two intragenic SNPs ( rs9637876 , rs10065172 ) in immunity-related GTPase family M ( IRGM) a gene that encodes a protein of the autophagy initiation complex. All three SNPs have been proposed to modify IRGM expression, but reports have been divergent and largely derived from cell lines. Here, analyzing RNA-Sequencing data of human tissues from the Genotype-Tissue Expression Project, we found that rs13361189 minor allele carriers had reduced IRGM expression in whole blood and terminal ileum, and upregulation in ileum of ZNF300P1, a locus adjacent to IRGM on chromosome 5q33.1 that encodes a long noncoding RNA. Whole blood and ileum from minor allele carriers had altered expression of multiple additional genes that have previously been linked to colitis and/or autophagy. Notable among these was an increase in ileum of LTF (lactoferrin), an established fecal inflammatory biomarker of CD, and in whole blood of TNF, a key cytokine in CD pathogenesis. Last, we confirmed that risk alleles at all three loci associated with increased risk for CD but not ulcerative colitis in a case-control study. Taken together, our findings suggest that genetically encoded IRGM deficiency may predispose to CD through dysregulation of inflammatory gene networks. Gene expression profiling of disease target tissues in genetically susceptible populations is a promising strategy for revealing new leads for the study of molecular pathogenesis and, potentially, for precision medicine. NEW & NOTEWORTHY Single nucleotide polymorphisms in immunity-related GTPase family M ( IRGM), a gene that encodes an autophagy initiation protein, have been linked epidemiologically to increased risk for Crohn's disease (CD). Here, we show for the first time that subjects with risk alleles at two such loci, rs13361189 and rs10065172 , have reduced IRGM expression in whole blood and terminal ileum, as well as dysregulated expression of a wide array of additional genes that regulate inflammation and autophagy.
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Affiliation(s)
- Teminioluwa A. Ajayi
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina,2Duke University School of Medicine, Durham, North Carolina
| | - Cynthia L. Innes
- 3Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Sara A. Grimm
- 4Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Prashant Rai
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Ryan Finethy
- 5Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina
| | - Jörn Coers
- 5Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, North Carolina
| | - Xuting Wang
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Douglas A. Bell
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | | | - Shepherd H. Schurman
- 3Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Michael B. Fessler
- 1Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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9
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Juyal G, Sood A, Midha V, Thelma BK. Genetics of ulcerative colitis: putting into perspective the incremental gains from Indian studies. J Genet 2018; 97:1493-1507. [PMID: 30555100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Ulcerative colitis (UC), one of the two clinical subtypes of inflammatory bowel disease is perceived as a potential 'sleeping giant' in the Indian subcontinent. Clinical manifestation is overall believed to be the same across ethnic groups but overwhelming genetics from large European and fewer non-European studies have revealed shared as well as unique disease susceptibly signaturesbetween them, pointing to population specific differences at genomic and environmental levels. A systematic recount of the four major eras in UC genetics spanning earliest linkage analysis, cherry picked candidate gene association studies, unbiased genomewide association studies, their logical extension in trans-ethnic setting (Immunochip study), lastly whole exome sequencing efforts forrare variant burden; and lessons learnt thereof in context of genetically distinct Indian population was attempted in this review. Genetic heterogeneity manifesting at allelic/locus level across these approaches has been the consistent finding through the range of pan India studies. On the other hand, these salient findings also highlight the limitations of even the best of these genetic leadsfor prognostic/clinical application. The imminent need, therefore, for the UC research community to adopt newer approaches/tools with improved study design to (i) gain better insight into genetic/mechanistic basis of disease; (ii) identify biomarkers of immediate translational value; and (iii) develop new/alternate therapeutic options is emphasized at the end.
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Affiliation(s)
- Garima Juyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India. ,
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10
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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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Khan S, Imran A, Malik A, Chaudhary AA, Rub A, Jan AT, Syed JB, Rolfo C. Bacterial imbalance and gut pathologies: Association and contribution of E. coli in inflammatory bowel disease. Crit Rev Clin Lab Sci 2018; 56:1-17. [DOI: 10.1080/10408363.2018.1517144] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Shahanavaj Khan
- Nanomedicine Research Unit, Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
- Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, India
| | - Ahamad Imran
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
| | - Abdul Malik
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Pharmacology, College of Medicine, Al-Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
| | - Abdur Rub
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Al Majmaah, Saudi Arabia
| | - Arif Tasleem Jan
- School of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Jakeera Begum Syed
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh, Saudi Arabia
- College of Medicine and Dentistry, Dar Al Uloom University, Riyadh, Saudi Arabia
| | - Christian Rolfo
- Phase I-Early Clinical Trials Unit, Oncology Department and Multidisciplinary Oncology Center Antwerp (MOCA), Antwerp University Hospital, Edegem, Belgium
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Polymorphisms in Autophagy-Related Gene IRGM Are Associated with Susceptibility to Autoimmune Thyroid Diseases. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7959707. [PMID: 29992164 PMCID: PMC6016217 DOI: 10.1155/2018/7959707] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Accepted: 03/26/2018] [Indexed: 01/19/2023]
Abstract
Background To date, studies have shown that polymorphisms in an autophagy-related gene, IRGM, are linked with different diseases, especially autoimmune diseases. The present study aimed to examine the roles of IRGM polymorphisms in autoimmune thyroid diseases (AITD). Methods Three polymorphisms in IRGM gene (rs10065172, rs4958847, and rs13361189) were genotyped in 1569 participants (488 with Graves' disease, 292 with Hashimoto's thyroiditis, and 789 healthy controls) using PCR-based ligase detection reaction method. Gene-disease associations were evaluated for the three SNPs. Results T allele of rs10065172, A allele of rs4958847, and C allele of rs13361189 were all higher in Graves' disease patients than controls, and the ORs were OR = 1.207 (P = 0.022), OR = 1.207 (P = 0.027), and OR = 1.200 (P = 0.027), respectively. After adjusting for sex and age, rs10065172 and rs13361189 were still associated with GD under both the allele model and dominant model, and the adjusted ORs for rs10065172 were 1.20 (P = 0.033) and 1.33 (P = 0.024), while the adjusted ORs for rs13361189 were 1.19 (P = 0.042) and 1.33 (P = 0.026), respectively. No significant difference was found between Hashimoto's thyroiditis patients and controls. Haplotype analysis found that CTA frequency was distinguishingly higher in Graves' disease patients (OR = 1.195, P = 0.030). The frequency of TCG haplotype was distinguishingly lower in AITD and Graves' disease patients (OR = 0.861, P = 0.044; OR = 0.816, P = 0.017). Conclusions Our study reveals IRGM as a susceptibility gene of AITD and Graves' disease for the first time.
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Rogala AR, Schoenborn AA, Fee BE, Cantillana VA, Joyce MJ, Gharaibeh RZ, Roy S, Fodor AA, Sartor RB, Taylor GA, Gulati AS. Environmental factors regulate Paneth cell phenotype and host susceptibility to intestinal inflammation in Irgm1-deficient mice. Dis Model Mech 2018; 11:dmm.031070. [PMID: 29361512 PMCID: PMC5894938 DOI: 10.1242/dmm.031070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/14/2017] [Indexed: 12/29/2022] Open
Abstract
Crohn's disease (CD) represents a chronic inflammatory disorder of the intestinal tract. Several susceptibility genes have been linked to CD, though their precise role in the pathogenesis of this disorder remains unclear. Immunity-related GTPase M (IRGM) is an established risk allele in CD. We have shown previously that conventionally raised (CV) mice lacking the IRGM ortholog, Irgm1 exhibit abnormal Paneth cells (PCs) and increased susceptibility to intestinal injury. In the present study, we sought to utilize this model system to determine if environmental conditions impact these phenotypes, as is thought to be the case in human CD. To accomplish this, wild-type and Irgm1−/− mice were rederived into specific pathogen-free (SPF) and germ-free (GF) conditions. We next assessed how these differential housing environments influenced intestinal injury patterns, and epithelial cell morphology and function in wild-type and Irgm1−/− mice. Remarkably, in contrast to CV mice, SPF Irgm1−/− mice showed only a slight increase in susceptibility to dextran sodium sulfate-induced inflammation. SPF Irgm1−/− mice also displayed minimal abnormalities in PC number and morphology, and in antimicrobial peptide expression. Goblet cell numbers and epithelial proliferation were also unaffected by Irgm1 in SPF conditions. No microbial differences were observed between wild-type and Irgm1−/− mice, but gut bacterial communities differed profoundly between CV and SPF mice. Specifically, Helicobacter sequences were significantly increased in CV mice; however, inoculating SPF Irgm1−/− mice with Helicobacter hepaticus was not sufficient to transmit a pro-inflammatory phenotype. In summary, our findings suggest the impact of Irgm1-deficiency on susceptibility to intestinal inflammation and epithelial function is critically dependent on environmental influences. This work establishes the importance of Irgm1−/− mice as a model to elucidate host-environment interactions that regulate mucosal homeostasis and intestinal inflammatory responses. Defining such interactions will be essential for developing novel preventative and therapeutic strategies for human CD. Summary: In this study, we rederived conventionally raised Irgm1-deficient mice into specific pathogen-free and germ-free conditions. We show that these environments determine how Irgm1 regulates Paneth cell function and gut inflammation susceptibility.
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Affiliation(s)
- Allison R Rogala
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alexi A Schoenborn
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian E Fee
- Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, NC 27705, USA
| | - Viviana A Cantillana
- Departments of Medicine; Molecular Genetics and Microbiology; and Immunology; Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC 27710, USA
| | - Maria J Joyce
- Department of Medicine, Division of Infectious Disease, Duke University Medical Center, Durham, NC 27710, USA
| | - Raad Z Gharaibeh
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Sayanty Roy
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anthony A Fodor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - R Balfour Sartor
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Medicine, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gregory A Taylor
- Geriatric Research, Education, and Clinical Center, VA Medical Center, Durham, NC 27705, USA.,Departments of Medicine; Molecular Genetics and Microbiology; and Immunology; Division of Geriatrics, and Center for the Study of Aging and Human Development, Duke University Medical Center, Durham, NC 27710, USA
| | - Ajay S Gulati
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA .,Department of Pediatrics, Division of Gastroenterology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Sharma A, Changotra H. Mutagenic primer-based PCR-RFLP assay for genotyping IRGM gene promoter variant rs4958843 (C/T). J Clin Lab Anal 2017; 32:e22346. [PMID: 29178192 DOI: 10.1002/jcla.22346] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/12/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Single-nucleotide polymorphisms play an important role in the susceptibility of many diseases, evolutionary studies, and genetic mapping. The rs4958843 in IRGM promoter is associated with tuberculosis and Crohn's disease. As this SNP is not present in any of the restriction sites, PCR-RFLP is not possible. Therefore, we have developed artificial-RFLP method to genotype this SNP. METHODS We designed forward primer with mismatches that resulted in the creation of a restriction site for enzyme NheI in the amplicon. Control samples of known genotypes were obtained by sequencing. The amplified product for SNP rs4958843 was digested with NheI restriction enzyme and resolved on an agarose gel to know the genotypes of the samples. RESULTS Results of sequencing and A-RFLP were concordant. The developed method was applied to genotype this polymorphism in 100 samples from healthy individuals. The allelic frequencies of SNP rs4958843 were C (0.16) and T (0.84), while corresponding genotypic distribution was CC (2), CT (29), and TT (69). CONCLUSION The newly developed method is simple, easy, and cost-effective which could be used to genotype IRGM polymorphism -1161 C/T (rs4958843) in various populations in the replication studies and has its applicability in the clinical settings. The developed method was applied for genotyping samples from healthy individuals from North India. For the first time, we report the frequency of this polymorphism from this region.
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Affiliation(s)
- Ambika Sharma
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Harish Changotra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
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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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A haplotypic variant at the IRGM locus and rs11747270 are related to the susceptibility for chronic periodontitis. Inflamm Res 2017; 67:129-138. [PMID: 28983640 DOI: 10.1007/s00011-017-1101-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/25/2017] [Accepted: 09/27/2017] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE AND DESIGN Immunity-regulated GTPase M (IRGM) plays a critical role in the defense against intracellular bacteria by regulating autophagy formation. This direct genetic association study aimed to determine whether variants at the IRGM genetic locus are associated with chronic periodontitis. MATERIALS AND SUBJECTS Using PCR and melting curve analysis 390 periodontitis patients and 770 healthy controls have been genotyped regarding six polymorphisms in the IRGM gene (rs13361189, rs10065172, rs4958847, rs1000113, rs11747270, rs931058). RESULTS Frequency distribution of alleles and genotypes for the six polymorphisms were not significantly different between the periodontitis and the control group. Also following stratification according to gender and smoking no significant linkage was found for any of the IRGM variants with periodontitis. Analysis of a subsample of patients revealed a significant association for rs11747270 with severe periodontitis (p = 0.003). Pairwise linkage analysis revealed one block composed of rs13361189, rs10065172, rs4958847, rs1000113 and 11747270 with strong or even complete linkage disequilibrium (r 2 > 0.9). Four haplotypes showed a frequency of > 1%, among which the haplotype C-T-A-T-G was significantly associated with chronic periodontitis (p = 0.0051; OR 4.66, 95% CI 1.41-15.42). CONCLUSIONS One rare haplotype of the IRGM locus is significantly associated with chronic periodontitis in a German cohort.
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Zhang X, Han R, Wang M, Li X, Yang X, Xia Q, Liu R, Yuan Y, Hu X, Chen M, Jiang G, Ma Y, Yang J, Xu S, Xu J, Shuai Z, Pan F. Association between the autophagy-related gene ULK1 and ankylosing spondylitis susceptibility in the Chinese Han population: a case-control study. Postgrad Med J 2017; 93:752-757. [PMID: 28667165 DOI: 10.1136/postgradmedj-2017-134964] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/24/2017] [Accepted: 05/27/2017] [Indexed: 01/29/2023]
Abstract
PURPOSE Ankylosing spondylitis (AS), inflammatory bowel disease and Crohn's disease (CD) often coexist in the same patient and these diseases have remarkably strong overlaps in genetic association. The association between Unc51like kinase 1 (ULK1) gene polymorphisms and CD has been reported, and the aim of the current study was to investigate whether ULK1 polymorphisms are also associated with susceptibility to AS in the Chinese Han population. METHODS Five tagging single nucleotide polymorphisms in the ULK1 gene (rs9652059, rs11616018, rs12303764, rs4964879 and rs7300908) were genotyped by the improved multiplex ligase detection reaction method in a cohort of patients with AS (n=649) and controls (n=628). Various genetic models were performed and haplotypes were constructed after linkage disequilibrium analysis. RESULTS A statistically significant difference was found in the dominant model of the rs9652059 polymorphism (OR (95% CI) = 0.796 (0.638 to 0.994), χ2 = 4.064, p= 0.044). Haplotypes were conducted between rs9652059 and rs11616018, rs11616018 and rs4964879, rs9652059 and rs4964879 based on D' ≥0.9 and r2 ≥ 0.6. Ht5 (rs9652059C-rs4964879G) haplotype was associated with AS (OR (95% CI) = 0.834 (0.706 to 0.985), χ2=4.555, p= 0.0328) and other two haplotypes were marginally correlated with AS (ht2 (rs9652059C-rs11616018T): OR (95% CI) = 0.846 (0.717 to 1.000), χ2= 3.864, p= 0.0493); ht3 (rs9652059T-rs11616018T): OR (95% CI) = 1.440 (0.999 to 2.076), χ2 = 3.849, p = 0.0498). CONCLUSIONS Our findings suggest that rs9652059 variation (C→T) could increase AS susceptibility and haplotypes of rs9652059C-rs4964879G, rs9652059C-rs11616018T and rs9652059T-rs11616018T may be associatd with AS.
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Affiliation(s)
- Xu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Renfang Han
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Mengmeng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Xiaona Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Xiao Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Qing Xia
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Rui Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Yaping Yuan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Xingxing Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Mengya Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Guangming Jiang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Yubo Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Jiajia Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
| | - Shengqian Xu
- Department of Rheumatism and Immunity, First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Jianhua Xu
- Department of Rheumatism and Immunity, First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Zongwen Shuai
- Department of Rheumatism and Immunity, First Affiliated Hospital of Anhui Medical University, Anhui, China
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China.,The Key Laboratory of Major Autoimmune Diseases, Anhui, China
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Autophagy-related IRGM genes confer susceptibility to ankylosing spondylitis in a Chinese female population: a case-control study. Genes Immun 2016; 18:42-47. [PMID: 28031552 DOI: 10.1038/gene.2016.48] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 10/15/2016] [Accepted: 11/08/2016] [Indexed: 12/16/2022]
Abstract
It is known that ankylosing spondylitis (AS) and inflammatory bowel disease (IBD) shared a common genetic component. The gist of current study is to assess the role of IBD-associated autophagy gene IRGM on AS susceptibility in a Chinese Han population. A total of 1270 unrelated subjects (643 AS and 627 controls) were enrolled. Two tag single-nucleotide polymorphisms (SNPs) (rs10065172 and rs4958846) were selected and were genotyped by iMLDR Assay technology. Genotypes and haplotype analysis were conducted by using SPSS 16.0 and haploview 4.2 software. Among two tag SNPs of IRGM, no correlation was observed between rs10065172 and AS susceptibility. For rs4958846, genotype and allelic frequencies were marginally discrepant between female cases and controls before, not after, Bonferroni correction (P=0.049; P=0.031). Logistic regression analysis revealed that carriers with CT+TT or CT genotype had a significantly decreased risk for developing AS among female subjects when compared with CC genotype (OR=0.514, 95% CI=0.301-0.876, P=0.014; OR=0.518, 95% CI=0.297-0.902, P=0.020, respectively). Additionally, a risk haplotype rs4958846C-rs10065172C (OR=2.093, 95% CI=1.301-3.368) and a protective haplotype rs4958846T-rs10065172C (OR=0.652, 95% CI=0.441-0.964) were also identified to be associated with female AS. IBD-associated IRGM gene is also associated with AS susceptibility in the Chinese female population, indicating that autophagy pathway may involve in AS genetic predisposition.
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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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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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Ramakrishna BS, Makharia GK, Ahuja V, Ghoshal UC, Jayanthi V, Perakath B, Abraham P, Bhasin DK, Bhatia SJ, Choudhuri G, Dadhich S, Desai D, Goswami BD, Issar SK, Jain AK, Kochhar R, Loganathan G, Misra SP, Ganesh Pai C, Pal S, Philip M, Pulimood A, Puri AS, Ray G, Singh SP, Sood A, Subramanian V. Indian Society of Gastroenterology consensus statements on Crohn's disease in India. Indian J Gastroenterol 2015; 34:3-22. [PMID: 25772856 DOI: 10.1007/s12664-015-0539-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023]
Abstract
In 2012, the Indian Society of Gastroenterology's Task Force on Inflammatory Bowel Diseases undertook an exercise to produce consensus statements on Crohn's disease (CD). This consensus, produced through a modified Delphi process, reflects our current recommendations for the diagnosis and management of CD in India. The consensus statements are intended to serve as a reference point for teaching, clinical practice, and research in India.
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