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Dashti M, Nizam R, Jacob S, Al-Kandari H, Al Ozairi E, Thanaraj TA, Al-Mulla F. Association between alleles, haplotypes, and amino acid variations in HLA class II genes and type 1 diabetes in Kuwaiti children. Front Immunol 2023; 14:1238269. [PMID: 37638053 PMCID: PMC10457110 DOI: 10.3389/fimmu.2023.1238269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Type 1 diabetes (T1D) is a complex autoimmune disorder that is highly prevalent globally. The interactions between genetic and environmental factors may trigger T1D in susceptible individuals. HLA genes play a significant role in T1D pathogenesis, and specific haplotypes are associated with an increased risk of developing the disease. Identifying risk haplotypes can greatly improve the genetic scoring for early diagnosis of T1D in difficult to rank subgroups. This study employed next-generation sequencing to evaluate the association between HLA class II alleles, haplotypes, and amino acids and T1D, by recruiting 95 children with T1D and 150 controls in the Kuwaiti population. Significant associations were identified for alleles at the HLA-DRB1, HLA-DQA1, and HLA-DQB1 loci, including DRB1*03:01:01, DQA1*05:01:01, and DQB1*02:01:01, which conferred high risk, and DRB1*11:04:01, DQA1*05:05:01, and DQB1*03:01:01, which were protective. The DRB1*03:01:01~DQA1*05:01:01~DQB1*02:01:01 haplotype was most strongly associated with the risk of developing T1D, while DRB1*11:04-DQA1*05:05-DQB1*03:01 was the only haplotype that rendered protection against T1D. We also identified 66 amino acid positions across the HLA-DRB1, HLA-DQA1, and HLA-DQB1 genes that were significantly associated with T1D, including novel associations. These results validate and extend our knowledge on the associations between HLA genes and T1D in Kuwaiti children. The identified risk alleles, haplotypes, and amino acid variations may influence disease development through effects on HLA structure and function and may allow early intervention via population-based screening efforts.
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Affiliation(s)
- Mohammed Dashti
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Rasheeba Nizam
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Sindhu Jacob
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Hessa Al-Kandari
- Department of Population Health, Dasman Diabetes Institute, Dasman, Kuwait
- Department of Pediatrics, Farwaniya Hospital, Ministry of Health, Sabah Al Nasser, Kuwait
| | - Ebaa Al Ozairi
- Clinical Care Research and Trials, Dasman Diabetes Institute, Dasman, Kuwait
- Faculty of Medicine, Kuwait University, Jabriya, Kuwait
| | | | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
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Thomas NJ, Dennis JM, Sharp SA, Kaur A, Misra S, Walkey HC, Johnston DG, Oliver NS, Hagopian WA, Weedon MN, Patel KA, Oram RA. DR15-DQ6 remains dominantly protective against type 1 diabetes throughout the first five decades of life. Diabetologia 2021; 64:2258-2265. [PMID: 34272580 PMCID: PMC8423681 DOI: 10.1007/s00125-021-05513-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 03/24/2021] [Indexed: 12/05/2022]
Abstract
AIMS/HYPOTHESIS Among white European children developing type 1 diabetes, the otherwise common HLA haplotype DR15-DQ6 is rare, and highly protective. Adult-onset type 1 diabetes is now known to represent more overall cases than childhood onset, but it is not known whether DR15-DQ6 is protective in older-adult-onset type 1 diabetes. We sought to quantify DR15-DQ6 protection against type 1 diabetes as age of onset increased. METHODS In two independent cohorts we assessed the proportion of type 1 diabetes cases presenting through the first 50 years of life with DR15-DQ6, compared with population controls. In the After Diabetes Diagnosis Research Support System-2 (ADDRESS-2) cohort (n = 1458) clinician-diagnosed type 1 diabetes was confirmed by positivity for one or more islet-specific autoantibodies. In UK Biobank (n = 2502), we estimated type 1 diabetes incidence rates relative to baseline HLA risk for each HLA group using Poisson regression. Analyses were restricted to white Europeans and were performed in three groups according to age at type 1 diabetes onset: 0-18 years, 19-30 years and 31-50 years. RESULTS DR15-DQ6 was protective against type 1 diabetes through to age 50 years (OR < 1 for each age group, all p < 0.001). The following ORs for type 1 diabetes, relative to a neutral HLA genotype, were observed in ADDRESS-2: age 5-18 years OR 0.16 (95% CI 0.08, 0.31); age 19-30 years OR 0.10 (0.04, 0.23); and age 31-50 years OR 0.37 (0.21, 0.68). DR15-DQ6 also remained highly protective at all ages in UK Biobank. Without DR15-DQ6, the presence of major type 1 diabetes high-risk haplotype (either DR3-DQ2 or DR4-DQ8) was associated with increased risk of type 1 diabetes. CONCLUSIONS/INTERPRETATION HLA DR15-DQ6 confers dominant protection from type 1 diabetes across the first five decades of life.
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Affiliation(s)
- Nicholas J Thomas
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
- Department of Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.
| | - John M Dennis
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Seth A Sharp
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Akaal Kaur
- Faculty of Medicine, Imperial College, London, UK
| | | | | | | | | | | | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
| | - Kashyap A Patel
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK
- Department of Diabetes and Endocrinology, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Richard A Oram
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Exeter, UK.
- Renal Department, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK.
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Denyer AL, Massey JP, Davison LJ, Ollier WER, Catchpole B, Kennedy LJ. Dog leucocyte antigen (DLA) class II haplotypes and risk of canine diabetes mellitus in specific dog breeds. Canine Med Genet 2020; 7:15. [PMID: 33292601 PMCID: PMC7603736 DOI: 10.1186/s40575-020-00093-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
Background Canine diabetes mellitus (DM) is a common endocrine disease in domestic dogs. A number of pathological mechanisms are thought to contribute to the aetiopathogenesis of relative or absolute insulin deficiency, including immune-mediated destruction of pancreatic beta cells. DM risk varies considerably between different dog breeds, suggesting that genetic factors are involved and contribute susceptibility or protection. Associations of particular dog leucocyte antigen (DLA) class II haplotypes with DM have been identified, but investigations to date have only considered all breeds pooled together. The aim of this study was to analyse an expanded data set so as to identify breed-specific diabetes-associated DLA haplotypes. Methods The 12 most highly represented breeds in the UK Canine Diabetes Register were selected for study. DLA-typing data from 646 diabetic dogs and 912 breed-matched non-diabetic controls were analysed to enable breed-specific analysis of the DLA. Dogs were genotyped for allelic variation at DLA-DRB1, -DQA1, -DQB1 loci using DNA sequence-based typing. Genotypes from all three loci were combined to reveal three-locus DLA class II haplotypes, which were evaluated for statistical associations with DM. This was performed for each breed individually and for all breeds pooled together. Results Five dog breeds were identified as having one or more DLA haplotype associated with DM susceptibility or protection. Four DM-associated haplotypes were identified in the Cocker Spaniel breed, of which one haplotype was shared with Border Terriers. In the three breeds known to be at highest risk of DM included in the study (Samoyed, Tibetan Terrier and Cairn Terrier), no DLA haplotypes were found to be associated with DM. Conclusions Novel DLA associations with DM in specific dog breeds provide further evidence that immune response genes contribute susceptibility to this disease in some cases. It is also apparent that DLA may not be contributing obvious or strong risk for DM in some breeds, including the seven breeds analysed for which no associations were identified.
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Affiliation(s)
- A L Denyer
- Department of Pathology and Pathogen Biology, Royal Veterinary College, Hatfield, UK
| | - J P Massey
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - L J Davison
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Department of Clinical Sciences and Services, Royal Veterinary College, Hatfield, UK
| | - W E R Ollier
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK
| | - B Catchpole
- Department of Pathology and Pathogen Biology, Royal Veterinary College, Hatfield, UK
| | - L J Kennedy
- Centre for Integrated Genomic Medical Research, University of Manchester, Stopford Building, Oxford Road, Manchester, M13 9PT, UK.
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Abstract
Underlying type 1 diabetes is a genetic aetiology dominated by the influence of specific HLA haplotypes involving primarily the class II DR-DQ region. In genetically predisposed children with the DR4-DQ8 haplotype, exogenous factors, yet to be identified, are thought to trigger an autoimmune reaction against insulin, signalled by insulin autoantibodies as the first autoantibody to appear. In children with the DR3-DQ2 haplotype, the triggering reaction is primarily against GAD signalled by GAD autoantibodies (GADA) as the first-appearing autoantibody. The incidence rate of insulin autoantibodies as the first-appearing autoantibody peaks during the first years of life and declines thereafter. The incidence rate of GADA as the first-appearing autoantibody peaks later but does not decline. The first autoantibody may variably be followed, in an apparently non-HLA-associated pathogenesis, by a second, third or fourth autoantibody. Although not all persons with a single type of autoantibody progress to diabetes, the presence of multiple autoantibodies seems invariably to be followed by loss of functional beta cell mass and eventually by dysglycaemia and symptoms. Infiltration of mononuclear cells in and around the islets appears to be a late phenomenon appearing in the multiple-autoantibody-positive with dysglycaemia. As our understanding of the aetiology and pathogenesis of type 1 diabetes advances, the improved capability for early prediction should guide new strategies for the prevention of type 1 diabetes.
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Affiliation(s)
- Simon E Regnell
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Jan Waldenströms gata 35, SE-20502, Malmö, Sweden.
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Lowe JR, Perry DJ, Salama AKS, Mathews CE, Moss LG, Hanks BA. Genetic risk analysis of a patient with fulminant autoimmune type 1 diabetes mellitus secondary to combination ipilimumab and nivolumab immunotherapy. J Immunother Cancer 2016; 4:89. [PMID: 28031819 PMCID: PMC5170902 DOI: 10.1186/s40425-016-0196-z] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 11/17/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Checkpoint inhibitor immunotherapy is becoming an effective treatment modality for an increasing number of malignancies. As a result, autoinflammatory side-effects are also being observed more commonly in the clinic. We are currently unable to predict which patients will develop more severe toxicities associated with these treatment regimens. CASE PRESENTATION We present a patient with stage IV melanoma that developed rapid onset autoimmune type 1 diabetes (T1D) in response to combination ipilimumab and nivolumab immunotherapy. At the time of the patient's presentation with diabetes ketoacidosis, a confirmed anti-GAD antibody seroconversion was noted. Longer-term follow-up of this patient has demonstrated a durable complete response based on PET CT imaging along with a persistently undetectable C-peptide level. Single nucleotide polymorphism gene sequencing and HLA risk allele analysis has revealed the patient to lack any established genetic predisposition to the development of autoimmune T1D. CONCLUSIONS While larger studies are necessary to better understand the role of genetic risk factors for the development of autoimmune toxicities in those patients undergoing checkpoint inhibitor immunotherapy, these results suggest that pre-screening patients for known T1D risk alleles may not be indicated. Additional investigation is needed to determine whether an approach such as T cell receptor clonotypic analysis to identify the presence of autoreactive T cell clones may be an effective approach for predicting which patients are at risk for the development of autoinflammatory toxicities while undergoing checkpoint inhibitor immunotherapy.
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Affiliation(s)
- Jared R. Lowe
- Department of Medicine, Duke University Medical Center, Durham, NC 27710 USA
| | - Daniel J. Perry
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610 USA
| | - April K. S. Salama
- Department of Medicine, Division of Medical Oncology, Melanoma Program, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710 USA
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL 32610 USA
| | - Larry G. Moss
- Department of Medicine, Division of Endocrinology, Metabolism, & Nutrition, Duke University Medical Center, Duke Molecular Physiology Institute and Sarah W. Stedman Nutrition and Metabolism Center, Durham, NC 27701 USA
| | - Brent A. Hanks
- Department of Medicine, Division of Medical Oncology, Melanoma Program, Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710 USA
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Pugliese A, Boulware D, Yu L, Babu S, Steck AK, Becker D, Rodriguez H, DiMeglio L, Evans-Molina C, Harrison LC, Schatz D, Palmer JP, Greenbaum C, Eisenbarth GS, Sosenko JM. HLA-DRB1*15:01-DQA1*01:02-DQB1*06:02 Haplotype Protects Autoantibody-Positive Relatives From Type 1 Diabetes Throughout the Stages of Disease Progression. Diabetes 2016; 65:1109-19. [PMID: 26822082 PMCID: PMC4806662 DOI: 10.2337/db15-1105] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 01/15/2016] [Indexed: 12/18/2022]
Abstract
The HLA-DRB1*15:01-DQA1*01:02-DQB1*06:02 haplotype is linked to protection from the development of type 1 diabetes (T1D). However, it is not known at which stages in the natural history of T1D development this haplotype affords protection. We examined a cohort of 3,358 autoantibody-positive relatives of T1D patients in the Pathway to Prevention (PTP) Study of the Type 1 Diabetes TrialNet. The PTP study examines risk factors for T1D and disease progression in relatives. HLA typing revealed that 155 relatives carried this protective haplotype. A comparison with 60 autoantibody-negative relatives suggested protection from autoantibody development. Moreover, the relatives with DRB1*15:01-DQA1*01:02-DQB1*06:02 less frequently expressed autoantibodies associated with higher T1D risk, were less likely to have multiple autoantibodies at baseline, and rarely converted from single to multiple autoantibody positivity on follow-up. These relatives also had lower frequencies of metabolic abnormalities at baseline and exhibited no overall metabolic worsening on follow-up. Ultimately, they had a very low 5-year cumulative incidence of T1D. In conclusion, the protective influence of DRB1*15:01-DQA1*01:02-DQB1*06:02 spans from autoantibody development through all stages of progression, and relatives with this allele only rarely develop T1D.
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Affiliation(s)
- Alberto Pugliese
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL
| | - David Boulware
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL
| | - Liping Yu
- Division of Bioinformatics and Biostatistics, University of South Florida, Tampa, FL
| | - Sunanda Babu
- Division of Bioinformatics and Biostatistics, University of South Florida, Tampa, FL
| | - Andrea K Steck
- Division of Bioinformatics and Biostatistics, University of South Florida, Tampa, FL
| | - Dorothy Becker
- Barbara Davis Center for Childhood Diabetes, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Henry Rodriguez
- Department of Pediatrics at the Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Linda DiMeglio
- Department of Pediatrics, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Carmella Evans-Molina
- Department of Pediatric Endocrinology, Riley Hospital for Children at Indiana University Health, Indianapolis, IN
| | - Leonard C Harrison
- Department of Medicine, Indiana University School of Medicine and the Richard L. Roudebush VA Medical Center, Indianapolis, IN
| | - Desmond Schatz
- Department of Medical Biology, The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, Parkville, Victoria, Australia
| | - Jerry P Palmer
- Department of Pediatrics, University of Florida, Gainesville, FL
| | - Carla Greenbaum
- VA Puget Sound Health Care System and University of Washington, Seattle, WA
| | - George S Eisenbarth
- Division of Bioinformatics and Biostatistics, University of South Florida, Tampa, FL
| | - Jay M Sosenko
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL Benaroya Research Institute, Seattle, WA
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7
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Abstract
Type 1 diabetes (T1D) is one of the most widely studied complex genetic disorders, and the genes in HLA are reported to account for approximately 40-50% of the familial aggregation of T1D. The major genetic determinants of this disease are polymorphisms of class II HLA genes encoding DQ and DR. The DR-DQ haplotypes conferring the highest risk are DRB1*03:01-DQA1*05:01-DQB1*02:01 (abbreviated "DR3") and DRB1*04:01/02/04/05/08-DQA1*03:01-DQB1*03:02/04 (or DQB1*02; abbreviated "DR4"). The risk is much higher for the heterozygote formed by these two haplotypes (OR = 16.59; 95% CI, 13.7-20.1) than for either of the homozygotes (DR3/DR3, OR = 6.32; 95% CI, 5.12-7.80; DR4/DR4, OR = 5.68; 95% CI, 3.91). In addition, some haplotypes confer strong protection from disease, such as DRB1*15:01-DQA1*01:02-DQB1*06:02 (abbreviated "DR2"; OR = 0.03; 95% CI, 0.01-0.07). After adjusting for the genetic correlation with DR and DQ, significant associations can be seen for HLA class II DPB1 alleles, in particular, DPB1*04:02, DPB1*03:01, and DPB1*02:02. Outside of the class II region, the strongest susceptibility is conferred by class I allele B*39:06 (OR =10.31; 95% CI, 4.21-25.1) and other HLA-B alleles. In addition, several loci in the class III region are reported to be associated with T1D, as are some loci telomeric to class I. Not surprisingly, current approaches for the prediction of T1D in screening studies take advantage of genotyping HLA-DR and HLA-DQ loci, which is then combined with family history and screening for autoantibodies directed against islet-cell antigens. Inclusion of additional moderate HLA risk haplotypes may help identify the majority of children with T1D before the onset of the disease.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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8
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Brandao LC, Vatta S, Guimaraes R, Segat L, Araujo J, De Lima Filho JL, Arraes LC, Not T, Crovella S. Rapid genetic screening for major human leukocyte antigen risk haplotypes in patients with type 1 diabetes from Northeastern Brazil. Hum Immunol 2010; 71:277-80. [DOI: 10.1016/j.humimm.2009.12.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2009] [Revised: 12/01/2009] [Accepted: 12/17/2009] [Indexed: 12/16/2022]
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Genetic variation within the HLA class III influences T1D susceptibility conferred by high-risk HLA haplotypes. Genes Immun 2010; 11:209-18. [PMID: 20054343 PMCID: PMC2858242 DOI: 10.1038/gene.2009.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Human leukocyte antigen (HLA) class II DRB1 and DQB1 represent the major type I diabetes (T1D) genetic susceptibility loci; however, other genes in the HLA region are also involved in T1D risk. We analyzed 1411 pedigrees (2865 affected individuals) from the type I diabetes genetics consortium genotyped for HLA classical loci and for 12 single-nucleotide polymorphisms (SNPs) in the class III region previously shown to be associated with T1D in a subset of 886 pedigrees. Using the transmission disequilibrium test, we compared the proportion of SNP alleles transmitted from within the high-risk DR3 and DR4 haplotypes to affected offspring. Markers rs4151659 (mapping to CFB) and rs7762619 (mapping 5' of LTA) were the most strongly associated with T1D on DR3 (P=1.2 x 10(-9) and P=2 x 10(-12), respectively) and DR4 (P=4 x 10(-15) and P=8 x 10(-8), respectively) haplotypes. They remained significantly associated after stratifying individuals in analyses for B*1801, A*0101-B*0801, DPB1*0301, DPB1*0202, DPB1*0401 or DPB1*0402. Rs7762619 and rs4151659 are in strong linkage disequilibrium (LD) (r(2)=0.82) with each other, but a joint analysis showed that the association for each SNP was not solely because of LD. Our data support a role for more than one locus in the class III region contributing to risk of T1D.
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10
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Valdes AM, Thomson G. Several loci in the HLA class III region are associated with T1D risk after adjusting for DRB1-DQB1. Diabetes Obes Metab 2009; 11 Suppl 1:46-52. [PMID: 19143814 PMCID: PMC2755069 DOI: 10.1111/j.1463-1326.2008.01002.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIM Several studies have indicated that genes in the human leucocyte antigen (HLA) region additional to the HLA class II DRB1-DQB1 contribute to type 1 diabetes (T1D) susceptibility. The aim of this study was to assess if markers in the class III Major Histocompatibility Complex (MHC) region are associated with T1D after accounting for linkage disequilibrium (LD) with DRB1-DQB1. METHODS We investigated 356 single nucleotide polymorphisms (SNPs) in the class III region covering 1.1 megabases in two subsets of data: 289 Human Biological Data Interchange (HBDI) Caucasian families and 597 additional Caucasian families collected by the Type 1 Diabetes Genetics Consortium (T1DGC). Analysis conditioning on DRB1-DQB1 was performed using the overall conditional genotype method. RESULTS Thirteen SNPs replicated in both subsets of the data and showed evidence of an additional effect on disease risk. Although some of the SNPs are in tight LD with each other, at least six of the associations were not because of LD with other class III markers. The strongest association within class III markers was with rs2395106 that maps 5' to the NOTCH4 gene, which has also been implicated in susceptibility to rheumatoid arthritis. The second association was with rs707915 mapping to the MSH5 gene, in a block of six markers significantly associated with T1D after adjusting for LD with DR-DQ. In total, six-independent associations within class III were observed although results were not adjusted for LD with class I. CONCLUSIONS Our data confirm that the class III region is involved in T1D susceptibility and suggest that more than one gene in the region is involved.
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Affiliation(s)
- A M Valdes
- Twin Research Unit, King's College London, St Thomas' Hospital, London, UK.
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11
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Baschal EE, Eisenbarth GS. Extreme genetic risk for type 1A diabetes in the post-genome era. J Autoimmun 2008; 31:1-6. [PMID: 18450419 DOI: 10.1016/j.jaut.2008.03.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Revised: 03/19/2008] [Accepted: 03/19/2008] [Indexed: 02/07/2023]
Abstract
A series of genes and loci influencing the genetic risk of type 1A (immune-mediated) diabetes are now well characterized. These include genes of the major histocompatibility complex (MHC), polymorphisms 5' of the insulin gene, and PTPN22, as well as more recently defined loci from genome-wide association studies. By far the major determinants of risk for type 1A diabetes are genes within or linked to the MHC and in particular alleles of class II genes (HLA-DR, DQ, and DP). There is evidence that MHC class I alleles contribute and there are additional MHC-linked influences such that for a major subset of relatives of patients there is a risk as high as 80% for siblings, and for the general population a risk as high as 20% can be defined at birth just by analyzing the MHC. We believe the search for additional MHC loci will require analysis of the remarkable long-range identity (up to 9 million base pairs) of extended MHC haplotypes. Current prediction algorithms will likely be greatly improved for the general population when the additional contributing loci of the MHC are defined.
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Affiliation(s)
- Erin E Baschal
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, Aurora, CO 80045-6511, USA
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12
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Erlich H, Valdes AM, Noble J, Carlson JA, Varney M, Concannon P, Mychaleckyj JC, Todd JA, Bonella P, Fear AL, Lavant E, Louey A, Moonsamy P. HLA DR-DQ haplotypes and genotypes and type 1 diabetes risk: analysis of the type 1 diabetes genetics consortium families. Diabetes 2008; 57:1084-92. [PMID: 18252895 PMCID: PMC4103420 DOI: 10.2337/db07-1331] [Citation(s) in RCA: 533] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The Type 1 Diabetes Genetics Consortium has collected type 1 diabetic families worldwide for genetic analysis. The major genetic determinants of type 1 diabetes are alleles at the HLA-DRB1 and DQB1 loci, with both susceptible and protective DR-DQ haplotypes present in all human populations. The aim of this study is to estimate the risk conferred by specific DR-DQ haplotypes and genotypes. RESEARCH DESIGN AND METHODS Six hundred and seven Caucasian families and 38 Asian families were typed at high resolution for the DRB1, DQA1, and DQB1 loci. The association analysis was performed by comparing the frequency of DR-DQ haplotypes among the chromosomes transmitted to an affected child with the frequency of chromosomes not transmitted to any affected child. RESULTS A number of susceptible, neutral, and protective DR-DQ haplotypes have been identified, and a statistically significant hierarchy of type 1 diabetes risk has been established. The most susceptible haplotypes are the DRB1*0301-DQA1*0501-DQB1*0201 (odds ratio [OR] 3.64) and the DRB1*0405-DQA1*0301-DQB1*0302, DRB1*0401-DQA1*0301-DQB*0302, and DRB1*0402-DQA1*0301-DQB1*0302 haplotypes (ORs 11.37, 8.39, and 3.63), followed by the DRB1*0404-DQA1*0301-DQB1*0302 (OR 1.59) and the DRB1*0801-DQB1*0401-DQB1*0402 (OR 1.25) haplotypes. The most protective haplotypes are DRB1*1501-DQA1*0102-DQB1*0602 (OR 0.03), DRB1*1401-DQA1*0101-DQB1*0503 (OR 0.02), and DRB1*0701-DQA1*0201-DQB1*0303 (OR 0.02). CONCLUSIONS Specific combinations of alleles at the DRB1, DQA1, and DQB1 loci determine the extent of haplotypic risk. The comparison of closely related DR-DQ haplotype pairs with different type 1 diabetes risks allowed identification of specific amino acid positions critical in determining disease susceptibility. These data also indicate that the risk associated with specific HLA haplotypes can be influenced by the genotype context and that the trans-complementing heterodimer encoded by DQA1*0501 and DQB1*0302 confers very high risk.
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Affiliation(s)
- Henry Erlich
- Roche Molecular Systems, 1145 Atlantic Ave., Alameda, CA 94501, USA.
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13
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Abstract
Our aim is to review methods to optimize detection of all disease genes in a genetic region. As a starting point, we assume there is sufficient evidence from linkage and/or association studies, based on significance levels or replication studies, for the involvement in disease risk of the genetic region under study. For closely linked markers, there will often be multiple associations with disease, and linkage analyses identify a region rather than the specific disease-predisposing gene. Hence, the first task is to identify the primary (major) disease-predisposing gene or genes in a genetic region, and single nucleotide polymorphisms thereof, that is, how to distinguish true associations from those that are just due to linkage disequilibrium with the actual disease-predisposing variants. Then, how do we detect additional disease genes in this genetic region? These two issues are of course very closely interrelated. No existing programs, either individually or in aggregate, can handle the magnitude and complexity of the analyses needed using currently available methods. Further, even with modern computers, one cannot study every possible combination of genetic markers and their haplotypes across the genome, or even within a genetic region. Although we must rely heavily on computers, in the final analysis of multiple effects in a genetic region and/or interaction or independent effects between unlinked genes, manipulation of the data by the individual investigator will play a crucial role. We recommend a multistrategy approach using a variety of complementary methods described below.
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Thomson G, Valdes AM, Noble JA, Kockum I, Grote MN, Najman J, Erlich HA, Cucca F, Pugliese A, Steenkiste A, Dorman JS, Caillat-Zucman S, Hermann R, Ilonen J, Lambert AP, Bingley PJ, Gillespie KM, Lernmark A, Sanjeevi CB, Rønningen KS, Undlien DE, Thorsby E, Petrone A, Buzzetti R, Koeleman BPC, Roep BO, Saruhan-Direskeneli G, Uyar FA, Günoz H, Gorodezky C, Alaez C, Boehm BO, Mlynarski W, Ikegami H, Berrino M, Fasano ME, Dametto E, Israel S, Brautbar C, Santiago-Cortes A, Frazer de Llado T, She JX, Bugawan TL, Rotter JI, Raffel L, Zeidler A, Leyva-Cobian F, Hawkins BR, Chan SH, Castano L, Pociot F, Nerup J. Relative predispositional effects of HLA class II DRB1-DQB1 haplotypes and genotypes on type 1 diabetes: a meta-analysis. ACTA ACUST UNITED AC 2007; 70:110-27. [PMID: 17610416 DOI: 10.1111/j.1399-0039.2007.00867.x] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The direct involvement of the human leukocyte antigen class II DR-DQ genes in type 1 diabetes (T1D) is well established, and these genes display a complex hierarchy of risk effects at the genotype and haplotype levels. We investigated, using data from 38 studies, whether the DR-DQ haplotypes and genotypes show the same relative predispositional effects across populations and ethnic groups. Significant differences in risk within a population were considered, as well as comparisons across populations using the patient/control (P/C) ratio. Within a population, the ratio of the P/C ratios for two different genotypes or haplotypes is a function only of the absolute penetrance values, allowing ranking of risk effects. Categories of consistent predisposing, intermediate ('neutral'), and protective haplotypes were identified and found to correlate with disease prevalence and the marked ethnic differences in DRB1-DQB1 frequencies. Specific effects were identified, for example for predisposing haplotypes, there was a statistically significant and consistent hierarchy for DR4 DQB1*0302s: DRB1*0405 =*0401 =*0402 > *0404 > *0403, with DRB1*0301 DQB1*0200 (DR3) being significantly less predisposing than DRB1*0402 and more than DRB1*0404. The predisposing DRB1*0401 DQB1*0302 haplotype was relatively increased compared with the protective haplotype DRB1*0401 DQB1*0301 in heterozygotes with DR3 compared with heterozygotes with DRB1*0101 DQB1*0501 (DR1). Our results show that meta-analyses and use of the P/C ratio and rankings thereof can be valuable in determining T1D risk factors at the haplotype and amino acid residue levels.
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Affiliation(s)
- G Thomson
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA.
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15
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van der Slik AR, van den Eng I, Eerligh P, Doxiadis IIN, Koeleman BPC, Roep BO, Giphart MJ. Sequence variation within the major histocompatibility complex subregion centromeric of HLA class II in type 1 diabetes. ACTA ACUST UNITED AC 2007; 69:348-53. [PMID: 17389020 DOI: 10.1111/j.1399-0039.2007.00820.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The extended major histocompatibility complex (xMHC) has been studied intensively with regard to type 1 diabetes (T1D) predisposition. So far, little attention has been given to the subregion centromeric of MHC class II. We selected five single nucleotide polymorphisms in genes with potential immune-related functions in the genomic regions of death-domain-associated protein 6 (DAXX, apoptosis associated), TAP-binding protein (TAPBP, human leukocyte antigen class I loading) and retinoic acid receptor beta (RXRB, vitamin D receptor function) that may bear relevance to the pathogenesis of T1D. A total of 277 unrelated individuals with juvenile-onset T1D and 286 control subjects were genotyped using sequence-specific priming-polymerase chain reaction. The genotype and allelic frequencies of the markers tested were not significantly different between patients and control subjects. Subsequent haplotype analysis showed six DAXX-TAPBP-RXRB haplotypic configurations. No difference was observed between patients and control cohorts when stratified for T1D high-risk DQ2-DR17 and DQ8-DR4 haplotypes. However, the distribution of these haplotypes affected T1D susceptibility encoded by the intermediate risk haplotypes DQ5-DR1 and DQ2-DR7 by increasing and decreasing susceptibility, respectively. We propose that studying genetic variants in the xMHC may be particularly rewarding to define disease pathways in patients displaying intermediate risk DQ-DR haplotypes.
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Affiliation(s)
- A R van der Slik
- Department of Immunohaematology and Blood Transfusion, Leiden University Medical Center, Leiden, The Netherlands
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16
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Steenkiste A, Valdes AM, Feolo M, Hoffman D, Concannon P, Noble J, Schoch G, Hansen J, Helmberg W, Dorman JS, Thomson G, Pugliese A. 14th International HLA and Immunogenetics Workshop: report on the HLA component of type 1 diabetes. ACTA ACUST UNITED AC 2007; 69 Suppl 1:214-25. [PMID: 17445204 DOI: 10.1111/j.1399-0039.2006.00772.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The type 1 diabetes (T1D) component of the 13th International Histocompatibility Workshop (IHW) obtained microsatellite (msat) and human leukocyte antigen (HLA)-DR/DQ data on case/control and family samples through an international collaboration. The aim was to detect the effects of susceptibility loci on the HLA complex independent of the primary determinants in the class II region (HLA-DR/DQ). As part of the activity of the 14th International HLA and Immunogenetics Workshop (14th IHIWS), a T1D workshop was held to present analyses of the 13th IHW data and to discuss the current status of knowledge about the genetics of T1D. These data are now available online through dbMHC, a web-based resource established by the National Center for Biotechnology. Continuing work since the 13th IHW has resulted in published work showing heterogeneity of DR3 haplotypes in data sets from the 13th IHW and Human Biological Data Interchange (HBDI). In addition, we identified markers that define DRB1*1501 DQB1*0602 haplotypes conferring reduced protection from diabetes in a Swedish 13th IHW data set. Further analyses of the 13th IHW data set not only showed some significant results but also demonstrated extensive heterogeneity reminiscent of non-HLA genes. The haplotype analysis in HBDI families identified two msats with significant effects on susceptibility and statistically significant age of onset effects at class III markers that are not because of linkage disequilibrium, with class I alleles known to affect age of onset. The above studies underscore the importance of refining our understanding of susceptibility associated with genes in the HLA complex.
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Affiliation(s)
- A Steenkiste
- Department of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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17
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Bibliography. Current world literature. Diabetes and the endocrine pancreas. Curr Opin Endocrinol Diabetes Obes 2007; 14:170-96. [PMID: 17940437 DOI: 10.1097/med.0b013e3280d5f7e9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Abstract
T1D results from autoimmune-mediated destruction of the pancreatic beta cells, a process that is conditioned by multiple genes and environmental factors. The main genetic determinants map to the major histocompatibility complex (MHC), and in particular DR and DQ, although, genes outside the MHC contribute, including the insulin gene, PTPN22, and CTLA-4. There are remarkable differences in genetic susceptibility to T1D between populations. We believe this variation reflects differing frequencies of diabetes causative and protective alleles and haplotypes, and thus remains a major genetic influence linked to the MHC region not accounted for by DR and DQ alleles. In this article, we discuss global variations in genetic susceptibility to T1D in view of current genetic understanding.
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Affiliation(s)
- Mohamed M Jahromi
- Barbara Davis Center for Childhood Diabetes, University of Colorado Health Sciences Center, PO Box 6511, Aurora, CO 80010, USA
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Abstract
Autoimmune diseases such as the diabetes that develops in NOD mice depend on immunologic recognition of specific autoantigens, but recognition can result in a pathogenic or protective T cell response. A study by Du et al. in this issue of the JCI demonstrates that TGF-beta signaling by T cells recognizing the insulin peptide B:9-23 is essential for such protection and that this inhibitory cytokine functions in both a paracrine and an autocrine manner (see the related article beginning on page 1360). We propose that the insulin peptide B:9-23 and a conserved TCR motif form an "immunologic homunculus" underlying the relatively common targeting of insulin by T cells that, as demonstrated by the study of Du and coworkers, results in a protective T cell response, or diabetes, as shown by other investigators, for related T cell receptors.
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Affiliation(s)
- Dirk Homann
- Barbara Davis Center for Childhood Diabetes, University of Colorado at Denver and Health Sciences Center, Aurora, Colorado, USA
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