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Su WM, Gu XJ, Hou YB, Zhang LY, Cao B, Ou RW, Wu Y, Chen XP, Song W, Zhao B, Shang HF, Chen YP. Association Analysis of WNT3, HLA-DRB5 and IL1R2 Polymorphisms in Chinese Patients With Parkinson's Disease and Multiple System Atrophy. Front Genet 2021; 12:765833. [PMID: 34868249 PMCID: PMC8636743 DOI: 10.3389/fgene.2021.765833] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/29/2021] [Indexed: 02/05/2023] Open
Abstract
Background: The association between inflammation and neurodegeneration has long been observed in parkinson's disease (PD) and multiple system atrophy (MSA). Previous genome-wide association studies (GWAS) and meta-analyses have identified several risk loci in inflammation-associated genes associated with PD. Objective: To investigate whether polymorphisms in some inflammation-associated genes could modulate the risk of developing PD and MSA in a Southwest Chinese population. Methods: A total of 2,706 Chinese subjects comprising 1340 PD, 483 MSA and 883 healthy controls were recruited in the study. Three polymorphisms (rs2074404 GG/GT/TT, rs17425622 CC/CT/TT, rs34043159 CC/CT/TT) in genes linked to inflammation in all the subjects were genotyped by using the Sequenom iPLEX Assay. Results: The allele G of WNT3 rs2074404 can increase risk on PD (OR: 1.048, 95% CI: 1.182-1.333, p = 0.006), exclusively in the LOPD subgroup (OR: 1.166, 95% CI:1.025-1.327, p = 0.019), but not in EOPD or MSA. And the recessive model analysis also demonstrated an increased PD risk in GG genotype of this locus (OR = 1.331, p = 0.007). However, no significant differences were observed in the genotype distributions and alleles of HLA-DRB5 rs17425622 and IL1R2 rs34043159 between the PD patients and controls, between the MSA patients and controls, or between subgroups of PD or MSA and controls. Conclusion: Our results suggested the allele G of WNT3 rs2074404 have an adverse effect on PD and particularly, on the LOPD subgroup among a Chinese population.
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Affiliation(s)
- Wei-Ming Su
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiao-Jing Gu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yan-Bing Hou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ling-Yu Zhang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bei Cao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ru-Wei Ou
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Wu
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xue-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wei Song
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Bi Zhao
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Hui-Fang Shang
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yong-Ping Chen
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, China
- Laboratory of Neurodegenerative Disorders, West China Hospital, Sichuan University, Chengdu, China
- Rare Disease Center, West China Hospital, Sichuan University, Chengdu, China
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2
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García-Santisteban I, Romero-Garmendia I, Cilleros-Portet A, Bilbao JR, Fernandez-Jimenez N. Celiac disease susceptibility: The genome and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 358:1-45. [PMID: 33707051 DOI: 10.1016/bs.ircmb.2020.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Celiac Disease (CeD) is an immune-mediated complex disease that is triggered by the ingestion of gluten and develops in genetically susceptible individuals. It has been known for a long time that the Human Leucocyte Antigen (HLA) molecules DQ2 and DQ8 are necessary, although not sufficient, for the disease development, and therefore other susceptibility genes and (epi)genetic events must participate in CeD pathogenesis. The advances in Genomics during the last 15 years have made CeD one of the immune-related disorders with the best-characterized genetic component. In the present work, we will first review the main Genome-Wide Association Studies (GWAS) carried out in the disorder, and emphasize post-GWAS discoveries, including diverse integrative strategies, SNP prioritization approaches, and insights into the Microbiome through the host Genomics. Second, we will explore CeD-related Epigenetics and Epigenomics, mostly focusing on the emerging knowledge of the celiac methylome, and the vast but yet under-explored non-coding RNA (ncRNA) landscape. We conclude that much has been done in the field although there are still completely unvisited areas in the post-Genomics of CeD. Chromatin conformation and accessibility, and Epitranscriptomics are promising domains that need to be unveiled to complete the big picture of the celiac Genome.
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Affiliation(s)
- Iraia García-Santisteban
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Irati Romero-Garmendia
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Ariadna Cilleros-Portet
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain
| | - Jose Ramon Bilbao
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain; Spanish Biomedical Research Center in Diabetes and associated Metabolic Disorders, CIBERDEM, Madrid, Spain
| | - Nora Fernandez-Jimenez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU) and Biocruces-Bizkaia Health Research Institute, Leioa, Spain.
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3
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Fernandez-Jimenez N, Bilbao JR. Mendelian randomization analysis of celiac GWAS reveals a blood expression signature with diagnostic potential in absence of gluten consumption. Hum Mol Genet 2020; 28:3037-3042. [PMID: 31127932 PMCID: PMC6737291 DOI: 10.1093/hmg/ddz113] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/10/2019] [Accepted: 05/20/2019] [Indexed: 12/26/2022] Open
Abstract
Celiac disease (CeD) is an immune-mediated enteropathy with a strong genetic component where the main environmental trigger is dietary gluten, and currently a correct diagnosis of the disease is impossible if gluten-free diet (GFD) has already been started. We hypothesized that merging different levels of genomic information through Mendelian randomization (MR) could help discover genetic biomarkers useful for CeD diagnosis. MR was performed using public databases of expression quantitative trait loci (QTL) and methylation QTL as exposures and the largest CeD genome-wide association study conducted to date as the outcome, in order to identify potential causal genes. As a result, we identified UBE2L3, an ubiquitin ligase located in a CeD-associated region. We interrogated the expression of UBE2L3 in an independent data set of peripheral blood mononuclear cells (PBMCs) and found that its expression is altered in CeD patients on GFD when compared to non-celiac controls. The relative expression of UBE2L3 isoforms predicts CeD with 100% specificity and sensitivity and could be used as a diagnostic marker, especially in the absence of gluten consumption. This approach could be applicable to other diseases where diagnosis of asymptomatic patients can be complicated.
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Affiliation(s)
- Nora Fernandez-Jimenez
- University of the Basque Country (UPV/EHU), BioCruces-Bizkaia Health Research Institute, Leioa, Basque Country, Spain
| | - Jose Ramon Bilbao
- University of the Basque Country (UPV/EHU), BioCruces-Bizkaia Health Research Institute, Leioa, Basque Country, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) Madrid, Spain
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4
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Profiling Celiac Disease-Related Transcriptional Changes. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2018; 336:149-174. [DOI: 10.1016/bs.ircmb.2017.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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5
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Eldridge MJG, Sanchez-Garrido J, Hoben GF, Goddard PJ, Shenoy AR. The Atypical Ubiquitin E2 Conjugase UBE2L3 Is an Indirect Caspase-1 Target and Controls IL-1β Secretion by Inflammasomes. Cell Rep 2017; 18:1285-1297. [PMID: 28147281 PMCID: PMC5300903 DOI: 10.1016/j.celrep.2017.01.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 12/12/2016] [Accepted: 01/09/2017] [Indexed: 11/06/2022] Open
Abstract
Caspase-1 activation by inflammasome signaling scaffolds initiates inflammation and antimicrobial responses. Caspase-1 proteolytically converts newly induced pro-interleukin 1 beta (IL-1β) into its mature form and directs its secretion, triggering pyroptosis and release of non-substrate alarmins such as interleukin 1 alpha (IL-1α) and HMGB1. While some caspase-1 substrates involved in these events are known, the identities and roles of non-proteolytic targets remain unknown. Here, we use unbiased proteomics to show that the UBE2L3 ubiquitin conjugase is an indirect target of caspase-1. Caspase-1, but not caspase-4, controls pyroptosis- and ubiquitin-independent proteasomal degradation of UBE2L3 upon canonical and non-canonical inflammasome activation by sterile danger signals and bacterial infection. Mechanistically, UBE2L3 acts post-translationally to promote K48-ubiquitylation and turnover of pro-IL-1β and dampen mature-IL-1β production. UBE2L3 depletion increases pro-IL-1β levels and mature-IL-1β secretion by inflammasomes. These findings regarding UBE2L3 as a molecular rheostat have implications for IL-1-driven pathology in hereditary fever syndromes and in autoinflammatory conditions associated with UBE2L3 polymorphisms. Caspase-1 inflammasomes induce loss of UBE2L3 in macrophages and dendritic cells UBE2L3 loss is proteasome-dependent, ubiquitin- and pyroptosis-independent UBE2L3 participates in K48 ubiquitylation and proteasomal turnover of pro-IL-1β UBE2L3 modulates levels of pro-IL-1β available for processing by caspase-1
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Affiliation(s)
- Matthew J G Eldridge
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Julia Sanchez-Garrido
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gil Ferreira Hoben
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Philippa J Goddard
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Avinash R Shenoy
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK.
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6
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Jonkers IH, Wijmenga C. Context-specific effects of genetic variants associated with autoimmune disease. Hum Mol Genet 2017; 26:R185-R192. [PMID: 28977443 PMCID: PMC5886469 DOI: 10.1093/hmg/ddx254] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/22/2022] Open
Abstract
Autoimmune diseases such as rheumatoid arthritis and coeliac disease are typical examples of complex genetic diseases caused by a combination of genetic and non-genetic risk factors. Insight into the genetic risk factors (single nucleotide polymorphisms (SNPs)) has increased since genome-wide association studies (GWAS) became possible in 2007 and, for individual diseases, SNPs can now explain some 15-50% of genetic risk. GWAS have also shown that some 50% of the genetic risk factors for individual autoimmune diseases overlap between different diseases. Thus, shared risk factors may converge to pathways that, when perturbed by genetic variation, predispose to autoimmunity in general. This raises the question of what determines disease specificity, and suggests that identical risk factors may have different effects in various autoimmune diseases. Addressing this question requires translation of genetic risk factors to causal genes and then to molecular and cellular pathways. Since >90% of the genetic risk factors are found in the non-coding part of the genome (i.e. outside the exons of protein-coding genes) and can have an impact on gene regulation, there is an urgent need to better understand the non-coding part of the genome. Here, we will outline the methods being used to unravel the gene regulatory networks perturbed in autoimmune diseases and the importance of doing this in the relevant cell types. We will highlight findings in coeliac disease, which manifests in the small intestine, to demonstrate how cell type and disease context can impact on the consequences of genetic risk factors.
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Affiliation(s)
- Iris H. Jonkers
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
- Department of Immunology, K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, 0424 Oslo, Norway
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7
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Escudero-Hernández C, Peña AS, Bernardo D. Immunogenetic Pathogenesis of Celiac Disease and Non-celiac Gluten Sensitivity. Curr Gastroenterol Rep 2017; 18:36. [PMID: 27216895 DOI: 10.1007/s11894-016-0512-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Celiac disease is the most common oral intolerance in Western countries. It results from an immune response towards gluten proteins from certain cereals in genetically predisposed individuals (HLA-DQ2 and/or HLA-DQ8). Its pathogenesis involves the adaptive (HLA molecules, transglutaminase 2, dendritic cells, and CD4(+) T-cells) and the innate immunity with an IL-15-mediated response elicited in the intraepithelial compartment. At present, the only treatment is a permanent strict gluten-free diet (GFD). Multidisciplinary studies have provided a deeper insight of the genetic and immunological factors and their interaction with the microbiota in the pathogenesis of the disease. Similarly, a better understanding of the composition of the toxic gluten peptides has improved the ways to detect them in food and drinks and how to monitor GFD compliance via non-invasive approaches. This review, therefore, addresses the major findings obtained in the last few years including the re-discovery of non-celiac gluten sensitivity.
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Affiliation(s)
- Celia Escudero-Hernández
- Mucosal Immunology Laboratory, IBGM, Facultad de Medicina, Dpto. Pediatría e Inmunología, University of Valladolid-Consejo Superior de Investigaciones Científicas, (4th floor) Av. Ramón y Cajal 7, 47005, Valladolid, Spain
| | - Amado Salvador Peña
- VU Medical Center Amsterdam, Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, De Boelelaan 1108 Room 10E65, 1081 HZ, Amsterdam, The Netherlands
| | - David Bernardo
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, 28006, Spain.
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8
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Gabrielsen ISM, Amundsen SS, Helgeland H, Flåm ST, Hatinoor N, Holm K, Viken MK, Lie BA. Genetic risk variants for autoimmune diseases that influence gene expression in thymus. Hum Mol Genet 2016; 25:3117-3124. [PMID: 27199374 DOI: 10.1093/hmg/ddw152] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 04/08/2016] [Accepted: 05/13/2016] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have boosted our knowledge of genetic risk variants in autoimmune diseases (AIDs). Most risk variants are located within or near genes with immunological functions, and the majority is found to be non-coding, pointing towards a regulatory role. In this study, we performed a cis expression quantitative trait locus (eQTL) screen restricted to 353 AID associated risk variants selected from the GWAS catalog to investigate whether these single nucleotide polymorphisms (SNPs) influence gene expression in thymus. Genotypes were obtained by Immunochip (Ichip) and tested against expression of surrounding genes (±1 Mb) in human thymic tissue (n = 42). We identified eight significant eQTLs located within seven genetic regions (FCRL3, RNASET2, C2orf74, NPIPB8, SIRPG, SYS1 and AJ006998.2) where the expression was associated with AID risk SNPs at a study-wide level of significance (P < 2.7 × 10-5). In NPIPB8 and AJ006998.2, the eQTL signals appeared to be thymus-specific. Furthermore, many AID risk SNPs from GWAS have been subsequently fine-mapped in recent Ichip projects, and fine-mapped AID SNPs overlapped with the thymic eQTLs within RNASET2 and SIRPG Finally, in all the eQTL regions, except C2orf74, SNPs underlying the thymic eQTLs were predicted to interfere with transcription factors important in T cell development. Our study therefore reveals autoimmune risk variants that act as eQTLs in thymus, and suggest that thymic gene regulation may play a functional role at some AID risk loci.
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Affiliation(s)
- Ingvild S M Gabrielsen
- Department of Medical Genetics, Oslo University Hospital .,K. G. Jebsen Inflammation Research Centre
| | | | - Hanna Helgeland
- Department of Medical Genetics, Oslo University Hospital.,K. G. Jebsen Inflammation Research Centre
| | - Siri Tennebø Flåm
- Department of Medical Genetics, Oslo University Hospital.,K. G. Jebsen Inflammation Research Centre
| | - Nimo Hatinoor
- Department of Medical Genetics, Oslo University Hospital.,Faculty of Health Sciences, Oslo University College, 0130 Oslo, Norway
| | - Kristian Holm
- Norwegian PSC Research Center, Division of Cancer Medicine, Surgery and Transplantation
| | - Marte K Viken
- Department of Medical Genetics, Oslo University Hospital.,Department of Immunology, Oslo University Hospital, University of Oslo, 0424 Oslo, Norway and
| | - Benedicte A Lie
- Department of Medical Genetics, Oslo University Hospital.,K. G. Jebsen Inflammation Research Centre
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9
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Withoff S, Li Y, Jonkers I, Wijmenga C. Understanding Celiac Disease by Genomics. Trends Genet 2016; 32:295-308. [PMID: 26972670 DOI: 10.1016/j.tig.2016.02.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 02/06/2023]
Abstract
Celiac disease (CeD) is a complex immune-mediated disease. Genetic studies have implicated 43 predisposing loci that collectively explain some 50% of the genetic variance in CeD. More than ∼90% of CeD-associated single nucleotide polymorphisms (SNPs) localize to the non-coding genome, which we need to better understand to translate genetic knowledge into clinical practice. New genomic technologies and resources are permitting a systematic analysis of the functional elements in the non-coding part of the genome. Here we explain how investigating the regulatory and epigenomic landscape will help to pinpoint the cell types involved in CeD, and the driver genes and gene regulatory networks that are affected by CeD-associated SNPs.
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Affiliation(s)
- Sebo Withoff
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands.
| | - Yang Li
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Iris Jonkers
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
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10
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Dieli-Crimi R, Cénit MC, Núñez C. The genetics of celiac disease: A comprehensive review of clinical implications. J Autoimmun 2015; 64:26-41. [DOI: 10.1016/j.jaut.2015.07.003] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 07/01/2015] [Indexed: 02/09/2023]
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11
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Ricaño-Ponce I, Wijmenga C, Gutierrez-Achury J. Genetics of celiac disease. Best Pract Res Clin Gastroenterol 2015; 29:399-412. [PMID: 26060105 DOI: 10.1016/j.bpg.2015.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/26/2015] [Indexed: 01/31/2023]
Abstract
New insights into the underlying molecular pathophysiology of celiac disease (CeD) over the last few years have been guided by major advances in the fields of genetics and genomics. The development and use of the Immunochip genotyping platform paved the way for the discovery of 39 non-HLA loci associated to CeD, and for follow-up functional genomics studies that pinpointed new disease genes, biological pathways and regulatory elements. By combining information from genetics with gene expression data, it has become clear that CeD is a disease with a dysregulated immune response, which can probably occur in a variety of immune cells. This type of information is crucial for our understanding of the disease and for providing leads for developing alternative therapies to the current gluten-free diet. In this review, we place these genetic findings in a wider context and suggest how they can assist the clinical care of CeD patients.
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Affiliation(s)
- Isis Ricaño-Ponce
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands.
| | - Javier Gutierrez-Achury
- University of Groningen, University Medical Center Groningen, Department of Genetics, 9700 RB Groningen, The Netherlands
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12
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Pan W, Zhang AQ, Gu W, Gao JW, Du DY, Zhang LY, Zeng L, Du J, Wang HY, Jiang JX. Identification of haplotype tag single nucleotide polymorphisms within the nuclear factor-κB family genes and their clinical relevance in patients with major trauma. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2015; 19:95. [PMID: 25880845 PMCID: PMC4404128 DOI: 10.1186/s13054-015-0836-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/23/2015] [Indexed: 12/25/2022]
Abstract
Introduction Nuclear factor-κB (NF-κB) family plays an important role in the development of sepsis in critically ill patients. Although several single nucleotide polymorphisms (SNPs) have been identified in the NF-κB family genes, only a few SNPs have been studied. Methods A total of 753 patients with major blunt trauma were included in this study. Tag SNPs (tSNPs) were selected from the NF-κB family genes (NFKB1, NFKB2, RELA, RELB and REL) through construction of haplotype blocks. The SNPs selected from genes within the canonical NF-κB pathway (including NFKB1, RELA and REL), which played a critical role in innate immune responses were genotyped using pyrosequencing method and analyzed in relation to the risk of development of sepsis and multiple organ dysfunction (MOD) syndrome. Moreover, the rs842647 polymorphism was analyzed in relation to tumor necrosis factor α (TNF-α) production by peripheral blood leukocytes in response to bacterial lipoprotein stimulation. Results Eight SNPs (rs28362491, rs3774932, rs4648068, rs7119750, rs4803789, rs12609547, rs1560725 and rs842647) were selected from the NF-κB family genes. All of them were shown to be high-frequency SNPs in this study cohort. Four SNPs (rs28362491, rs4648068, rs7119750 and rs842647) within the canonical NF-κB pathway were genotyped, and rs842647 was associated with sepsis morbidity rate and MOD scores. An association was also observed between the rs842647 A allele and lower TNF-α production. Conclusions rs842647 polymorphism might be used as relevant risk estimate for the development of sepsis and MOD syndrome in patients with major trauma. Electronic supplementary material The online version of this article (doi:10.1186/s13054-015-0836-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Pan
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - An Qiang Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Wei Gu
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Jun Wei Gao
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Ding Yuan Du
- Chongqing Emergency Medical Center, Jiankang Road, Chongqing, 400042, China.
| | - Lian Yang Zhang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Ling Zeng
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Juan Du
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Hai Yan Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
| | - Jian Xin Jiang
- State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Surgery Research, Daping Hospital, Third Military Medical University, Gaotanyan Street, Chongqing, 400038, China.
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Mesbah-Uddin M, Elango R, Banaganapalli B, Shaik NA, Al-Abbasi FA. In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections. PLoS One 2015; 10:e0119420. [PMID: 25786114 PMCID: PMC4364731 DOI: 10.1371/journal.pone.0119420] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/13/2015] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWASs) for many complex diseases, including inflammatory bowel disease (IBD), produced hundreds of disease-associated loci—the majority of which are noncoding. The number of GWAS loci is increasing very rapidly, but the process of translating single nucleotide polymorphisms (SNPs) from these loci to genomic medicine is lagging. In this study, we investigated 4,734 variants from 152 IBD associated GWAS loci (IBD associated 152 lead noncoding SNPs identified from pooled GWAS results + 4,582 variants in strong linkage-disequilibrium (LD) (r2 ≥0.8) for EUR population of 1K Genomes Project) using four publicly available bioinformatics tools, e.g. dbPSHP, CADD, GWAVA, and RegulomeDB, to annotate and prioritize putative regulatory variants. Of the 152 lead noncoding SNPs, around 11% are under strong negative selection (GERP++ RS ≥2); and ~30% are under balancing selection (Tajima’s D score >2) in CEU population (1K Genomes Project)—though these regions are positively selected (GERP++ RS <0) in mammalian evolution. The analysis of 4,734 variants using three integrative annotation tools produced 929 putative functional SNPs, of which 18 SNPs (from 15 GWAS loci) are in concordance with all three classifiers. These prioritized noncoding SNPs may contribute to IBD pathogenesis by dysregulating the expression of nearby genes. This study showed the usefulness of integrative annotation for prioritizing fewer functional variants from a large number of GWAS markers.
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Affiliation(s)
- Md. Mesbah-Uddin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (MMU); (FAA)
| | - Ramu Elango
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (MMU); (FAA)
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