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McGrail C, Sears TJ, Kudtarkar P, Carter H, Gaulton K. Genetic association and machine learning improves discovery and prediction of type 1 diabetes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.31.24311310. [PMID: 39132494 PMCID: PMC11312647 DOI: 10.1101/2024.07.31.24311310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Type 1 diabetes (T1D) has a large genetic component, and expanded genetic studies of T1D can lead to novel biological and therapeutic discovery and improved risk prediction. In this study, we performed genetic association and fine-mapping analyses in 817,718 European ancestry samples genome-wide and 29,746 samples at the MHC locus, which identified 165 independent risk signals for T1D of which 19 were novel. We used risk variants to train a machine learning model (named T1GRS) to predict T1D, which highly differentiated T1D from non-disease and type 2 diabetes (T2D) in Europeans as well as African Americans at or beyond the level of current standards. We identified extensive non-linear interactions between risk loci in T1GRS, for example between HLA-DQB1*57 and INS, coding and non-coding HLA alleles, and DEXI, INS and other beta cell loci, that provided mechanistic insight and improved risk prediction. T1D individuals formed distinct clusters based on genetic features from T1GRS which had significant differences in age of onset, HbA1c, and renal disease severity. Finally, we provided T1GRS in formats to enhance accessibility of risk prediction to any user and computing environment. Overall, the improved genetic discovery and prediction of T1D will have wide clinical, therapeutic, and research applications.
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Zhao LP, Papadopoulos GK, Skyler JS, Pugliese A, Parikh HM, Kwok WW, Lybrand TP, Bondinas GP, Moustakas AK, Wang R, Pyo CW, Nelson WC, Geraghty DE, Lernmark Å. HLA Class II (DR, DQ, DP) Genes Were Separately Associated With the Progression From Seroconversion to Onset of Type 1 Diabetes Among Participants in Two Diabetes Prevention Trials (DPT-1 and TN07). Diabetes Care 2024; 47:826-834. [PMID: 38498185 PMCID: PMC11043228 DOI: 10.2337/dc23-1947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024]
Abstract
OBJECTIVE To explore associations of HLA class II genes (HLAII) with the progression of islet autoimmunity from asymptomatic to symptomatic type 1 diabetes (T1D). RESEARCH DESIGN AND METHODS Next-generation targeted sequencing was used to genotype eight HLAII genes (DQA1, DQB1, DRB1, DRB3, DRB4, DRB5, DPA1, DPB1) in 1,216 participants from the Diabetes Prevention Trial-1 and Randomized Diabetes Prevention Trial with Oral Insulin sponsored by TrialNet. By the linkage disequilibrium, DQA1 and DQB1 are haplotyped to form DQ haplotypes; DP and DR haplotypes are similarly constructed. Together with available clinical covariables, we applied the Cox regression model to assess HLAII immunogenic associations with the disease progression. RESULTS First, the current investigation updated the previously reported genetic associations of DQA1*03:01-DQB1*03:02 (hazard ratio [HR] = 1.25, P = 3.50*10-3) and DQA1*03:03-DQB1*03:01 (HR = 0.56, P = 1.16*10-3), and also uncovered a risk association with DQA1*05:01-DQB1*02:01 (HR = 1.19, P = 0.041). Second, after adjusting for DQ, DPA1*02:01-DPB1*11:01 and DPA1*01:03-DPB1*03:01 were found to have opposite associations with progression (HR = 1.98 and 0.70, P = 0.021 and 6.16*10-3, respectively). Third, DRB1*03:01-DRB3*01:01 and DRB1*03:01-DRB3*02:02, sharing the DRB1*03:01, had opposite associations (HR = 0.73 and 1.44, P = 0.04 and 0.019, respectively), indicating a role of DRB3. Meanwhile, DRB1*12:01-DRB3*02:02 and DRB1*01:03 alone were found to associate with progression (HR = 2.6 and 2.32, P = 0.018 and 0.039, respectively). Fourth, through enumerating all heterodimers, it was found that both DQ and DP could exhibit associations with disease progression. CONCLUSIONS These results suggest that HLAII polymorphisms influence progression from islet autoimmunity to T1D among at-risk subjects with islet autoantibodies.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- School of Public Health, University of Washington, Seattle, WA
| | - George K. Papadopoulos
- Laboratory of Biophysics, Biochemistry, Biomaterials and Bioprocessing, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece
| | - Jay S. Skyler
- Diabetes Research Institute and Division of Endocrinology, Diabetes & Metabolism, University of Miami Miler School of Medicine, Miami, FL
| | - Alberto Pugliese
- Department of Diabetes Immunology, City of Hope, South Pasadena, CA
| | - Hemang M. Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | | | | | - George P. Bondinas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, Argostoli, Cephalonia, Greece
| | - Antonis K. Moustakas
- Department of Food Science and Technology, Faculty of Environmental Sciences, Ionian University, Argostoli, Cephalonia, Greece
| | - Ruihan Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Wyatt C. Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University CRC, Skåne University Hospital, Malmö, Sweden
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Padoan B, Casar C, Krause J, Schultheiss C, Baumdick ME, Niehrs A, Zecher BF, Pujantell M, Yuki Y, Martin M, Remmerswaal EBM, Dekker T, van der Bom-Baylon ND, Noble JA, Carrington M, Bemelman FJ, van Lier RAW, Binder M, Gagliani N, Bunders MJ, Altfeld M. NKp44/HLA-DP-dependent regulation of CD8 effector T cells by NK cells. Cell Rep 2024; 43:114089. [PMID: 38615318 DOI: 10.1016/j.celrep.2024.114089] [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: 10/30/2023] [Revised: 03/03/2024] [Accepted: 03/26/2024] [Indexed: 04/16/2024] Open
Abstract
Although natural killer (NK) cells are recognized for their modulation of immune responses, the mechanisms by which human NK cells mediate immune regulation are unclear. Here, we report that expression of human leukocyte antigen (HLA)-DP, a ligand for the activating NK cell receptor NKp44, is significantly upregulated on CD8+ effector T cells, in particular in human cytomegalovirus (HCMV)+ individuals. HLA-DP+ CD8+ T cells expressing NKp44-binding HLA-DP antigens activate NKp44+ NK cells, while HLA-DP+ CD8+ T cells not expressing NKp44-binding HLA-DP antigens do not. In line with this, frequencies of HLA-DP+ CD8+ T cells are increased in individuals not encoding for NKp44-binding HLA-DP haplotypes, and contain hyper-expanded CD8+ T cell clones, compared to individuals expressing NKp44-binding HLA-DP molecules. These findings identify a molecular interaction facilitating the HLA-DP haplotype-specific editing of HLA-DP+ CD8+ T cell effector populations by NKp44+ NK cells and preventing the generation of hyper-expanded T cell clones, which have been suggested to have increased potential for autoimmunity.
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Affiliation(s)
- Benedetta Padoan
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Christian Casar
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Jenny Krause
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Center for Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Christoph Schultheiss
- Division of Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland; Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, 4031 Basel, Switzerland
| | - Martin E Baumdick
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Annika Niehrs
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Britta F Zecher
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Maria Pujantell
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany
| | - Yuko Yuki
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Maureen Martin
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ester B M Remmerswaal
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Tamara Dekker
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Nelly D van der Bom-Baylon
- Department of Experimental Immunology, Amsterdam Infection and Immunity Institute, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | - Janelle A Noble
- Department of Pediatrics UCSF, Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Frederike J Bemelman
- Renal Transplant Unit, Division of Internal Medicine, Academic Medical Centre, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands
| | | | - Mascha Binder
- Division of Medical Oncology, University Hospital Basel, 4031 Basel, Switzerland; Laboratory of Translational Immuno-Oncology, Department of Biomedicine, University and University Hospital Basel, 4031 Basel, Switzerland
| | - Nicola Gagliani
- I. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Madeleine J Bunders
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; III. Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany
| | - Marcus Altfeld
- Research Department Virus Immunology, Leibniz Institute of Virology, 20251 Hamburg, Germany; Hamburg Center for Translational Immunology (HCTI), Hamburg, Germany.
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McGrail C, Chiou J, Elgamal R, Luckett AM, Oram RA, Benaglio P, Gaulton KJ. Genetic discovery and risk prediction for type 1 diabetes in individuals without high-risk HLA-DR3/DR4 haplotypes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.11.23298405. [PMID: 37986756 PMCID: PMC10659516 DOI: 10.1101/2023.11.11.23298405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Over 10% of type 1 diabetes (T1D) cases do not have high-risk HLA-DR3 or DR4 haplotypes with distinct clinical features such as later onset and reduced insulin dependence. To identify genetic drivers of T1D in the absence of DR3/DR4, we performed association and fine-mapping analyses in 12,316 non-DR3/DR4 samples. Risk variants at the MHC and other loci genome-wide had heterogeneity in effects on T1D dependent on DR3/DR4, and non-DR3/DR4 T1D had evidence for a greater polygenic burden. T1D-assocated variants in non-DR3/DR4 were more enriched for loci, regulatory elements, and pathways for antigen presentation, innate immunity, and beta cells, and depleted in T cells, compared to DR3/DR4. Non-DR3/DR4 T1D cases were poorly classified based on an existing genetic risk score GRS2, and we created a new GRS which highly discriminated non-DR3/DR4 T1D from both non-diabetes and T2D. In total we identified heterogeneity in T1D genetic risk and disease mechanisms dependent on high-risk HLA haplotype and which enabled accurate classification of T1D across HLA background.
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Affiliation(s)
- Carolyn McGrail
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla, CA
| | - Joshua Chiou
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla, CA
| | - Ruth Elgamal
- Biomedical Sciences Graduate Program, UC San Diego, La Jolla, CA
| | - Amber M Luckett
- University of Exeter College of Medicine and Health, Exeter, UK
| | - Richard A Oram
- University of Exeter College of Medicine and Health, Exeter, UK
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
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Stamellou E, Seikrit C, Tang SCW, Boor P, Tesař V, Floege J, Barratt J, Kramann R. IgA nephropathy. Nat Rev Dis Primers 2023; 9:67. [PMID: 38036542 DOI: 10.1038/s41572-023-00476-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
IgA nephropathy (IgAN), the most prevalent primary glomerulonephritis worldwide, carries a considerable lifetime risk of kidney failure. Clinical manifestations of IgAN vary from asymptomatic with microscopic or intermittent macroscopic haematuria and stable kidney function to rapidly progressive glomerulonephritis. IgAN has been proposed to develop through a 'four-hit' process, commencing with overproduction and increased systemic presence of poorly O-glycosylated galactose-deficient IgA1 (Gd-IgA1), followed by recognition of Gd-IgA1 by antiglycan autoantibodies, aggregation of Gd-IgA1 and formation of polymeric IgA1 immune complexes and, lastly, deposition of these immune complexes in the glomerular mesangium, leading to kidney inflammation and scarring. IgAN can only be diagnosed by kidney biopsy. Extensive, optimized supportive care is the mainstay of therapy for patients with IgAN. For those at high risk of disease progression, the 2021 KDIGO Clinical Practice Guideline suggests considering a 6-month course of systemic corticosteroid therapy; however, the efficacy of systemic steroid treatment is under debate and serious adverse effects are common. Advances in understanding the pathophysiology of IgAN have led to clinical trials of novel targeted therapies with acceptable safety profiles, including SGLT2 inhibitors, endothelin receptor blockers, targeted-release budesonide, B cell proliferation and differentiation inhibitors, as well as blockade of complement components.
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Affiliation(s)
- Eleni Stamellou
- Department of Nephrology, School of Medicine, University of Ioannina, Ioannina, Greece
- Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Claudia Seikrit
- Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Sydney C W Tang
- Division of Nephrology, Department of Medicine, University of Hong Kong, Hong Kong, China
| | - Peter Boor
- Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
- Department of Pathology, RWTH Aachen University, Aachen, Germany
| | - Vladimir Tesař
- Department of Nephrology, 1st Faculty of Medicine and General University Hospital, Charles University, Prague, Czech Republic
| | - Jürgen Floege
- Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany
| | - Jonathan Barratt
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rafael Kramann
- Department of Nephrology and Clinical Immunology, RWTH Aachen University Hospital, Aachen, Germany.
- Department of Internal Medicine, Nephrology and Transplantation, Erasmus Medical Center, Rotterdam, Netherlands.
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Jensen TSR, Fugleholm K, Ekstrøm CT, Bruunsgaard H. Inflammatory human leucocyte antigen genotypes are not a risk factor in chronic subdural hematoma development. Acta Neurochir (Wien) 2023; 165:2399-2405. [PMID: 37550524 DOI: 10.1007/s00701-023-05745-w] [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: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/09/2023]
Abstract
BACKGROUND Chronic subdural hematoma (CSDH) pathophysiology has undergone a paradigm shift from being regarded as solely traumatic to be driven mainly by inflammation. Human leucocyte antigen (HLA) is a gene complex involved in antigen processing and presentation to T lymphocytes, thereby mediating the adaptive immune responses. As specific HLA profiles are associated with inflammatory diseases, patients with a specific HLA profile may have a lower threshold for subdural inflammation, and therefore are predisposed for CSDH development. We hypothesized that (1) CSDH patients have a specific HLA profile compared to a Danish background population, and (2) patients with recurrent CSDH have a specific HLA profile compared to CSDH patients without recurrent CSDH. METHODS Three specific HLA class II haplotypes known to drive inflammatory-mediated diseases were determined in 68 patients with CSDH. The distribution of these three haplotypes in our CSDH population was compared to a Danish population of blood donors using Monte Carlo Pearson's chi-square test. Furthermore, the distribution of the haplotypes was compared between CSDH patients with and without recurrent CSDH. RESULTS We found no significant association between either of the haplotypes and the risk of CSDH, and neither of the haplotypes were associated with increased risk of CSDH recurrence. CONCLUSION This study did not show an association between selected HLA class II haplotypes and the risk of CSDH or recurrence of CSDH compared with a healthy background population.
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Affiliation(s)
- Thorbjørn Søren Rønn Jensen
- Department of Neurosurgery, The Neuroscience Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen Ø, Denmark.
| | - Kåre Fugleholm
- Department of Neurosurgery, The Neuroscience Centre, Copenhagen University Hospital, Rigshospitalet, Inge Lehmanns Vej 6, 2100, Copenhagen Ø, Denmark
| | - Claus Thorn Ekstrøm
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Helle Bruunsgaard
- Department of Clinical Immunology 7631, University Hospital of Copenhagen - Rigshospitalet and Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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7
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Hu Q, Burns C, Christian D, Yang G, Berka N. Discovery of three novel HLA-DPA1 alleles, HLA-DPA1*01:147N, 01:03:47, and 02:106 using next-generation sequencing. HLA 2023. [PMID: 37315941 DOI: 10.1111/tan.15125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023]
Abstract
Characterization of three novel HLA-DPA1 alleles bearing null, synonymous, and non-synonymous mutations.
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Affiliation(s)
- Qian Hu
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Caitlyn Burns
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Canada
| | - Danielle Christian
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Canada
| | - Guang Yang
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Canada
| | - Noureddine Berka
- Histocompatibility and Immunogenetics Laboratory, Alberta Precision Laboratories, Calgary, Canada
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
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Hu Y, Yu Y, Dong H, Jiang W. Identifying C1QB, ITGAM, and ITGB2 as potential diagnostic candidate genes for diabetic nephropathy using bioinformatics analysis. PeerJ 2023; 11:e15437. [PMID: 37250717 PMCID: PMC10225123 DOI: 10.7717/peerj.15437] [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: 12/15/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023] Open
Abstract
Background Diabetic nephropathy (DN), the most intractable complication in diabetes patients, can lead to proteinuria and progressive reduction of glomerular filtration rate (GFR), which seriously affects the quality of life of patients and is associated with high mortality. However, the lack of accurate key candidate genes makes diagnosis of DN very difficult. This study aimed to identify new potential candidate genes for DN using bioinformatics, and elucidated the mechanism of DN at the cellular transcriptional level. Methods The microarray dataset GSE30529 was downloaded from the Gene Expression Omnibus Database (GEO), and the differentially expressed genes (DEGs) were screened by R software. We used Gene Ontology (GO), gene set enrichment analysis (GSEA), and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis to identify the signal pathways and genes. Protein-protein interaction (PPI) networks were constructed using the STRING database. The GSE30122 dataset was selected as the validation set. Receiver operating characteristic (ROC) curves were applied to evaluate the predictive value of genes. An area under curve (AUC) greater than 0.85 was considered to be of high diagnostic value. Several online databases were used to predict miRNAs and transcription factors (TFs) capable of binding hub genes. Cytoscape was used for constructing a miRNA-mRNA-TF network. The online database 'nephroseq' predicted the correlation between genes and kidney function. The serum level of creatinine, BUN, and albumin, and the urinary protein/creatinine ratio of the DN rat model were detected. The expression of hub genes was further verified through qPCR. Data were analyzed statistically using Student's t-test by the 'ggpubr' package. Results A total of 463 DEGs were identified from GSE30529. According to enrichment analysis, DEGs were mainly enriched in the immune response, coagulation cascades, and cytokine signaling pathways. Twenty hub genes with the highest connectivity and several gene cluster modules were ensured using Cytoscape. Five high diagnostic hub genes were selected and verified by GSE30122. The MiRNA-mRNA-TF network suggested a potential RNA regulatory relationship. Hub gene expression was positively correlated with kidney injury. The level of serum creatinine and BUN in the DN group was higher than in the control group (unpaired t test, t = 3.391, df = 4, p = 0.0275, r = 0.861). Meanwhile, the DN group had a higher urinary protein/creatinine ratio (unpaired t test, t = 17.23, df = 16, p < 0.001, r = 0.974). QPCR results showed that the potential candidate genes for DN diagnosis included C1QB, ITGAM, and ITGB2. Conclusions We identified C1QB, ITGAM and ITGB2 as potential candidate genes for DN diagnosis and therapy and provided insight into the mechanisms of DN development at transcriptome level. We further completed the construction of miRNA-mRNA-TF network to propose potential RNA regulatory pathways adjusting disease progression in DN.
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Affiliation(s)
- Yongzheng Hu
- Department of Nephrology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Yani Yu
- Department of Nephrology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Hui Dong
- Health Management Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wei Jiang
- Department of Nephrology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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Ganekal P, Vastrad B, Vastrad C, Kotrashetti S. Identification of biomarkers, pathways, and potential therapeutic targets for heart failure using next-generation sequencing data and bioinformatics analysis. Ther Adv Cardiovasc Dis 2023; 17:17539447231168471. [PMID: 37092838 PMCID: PMC10134165 DOI: 10.1177/17539447231168471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Heart failure (HF) is the most common cardiovascular diseases and the leading cause of cardiovascular diseases related deaths. Increasing molecular targets have been discovered for HF prognosis and therapy. However, there is still an urgent need to identify novel biomarkers. Therefore, we evaluated biomarkers that might aid the diagnosis and treatment of HF. METHODS We searched next-generation sequencing (NGS) dataset (GSE161472) and identified differentially expressed genes (DEGs) by comparing 47 HF samples and 37 normal control samples using limma in R package. Gene ontology (GO) and pathway enrichment analyses of the DEGs were performed using the g: Profiler database. The protein-protein interaction (PPI) network was plotted with Human Integrated Protein-Protein Interaction rEference (HiPPIE) and visualized using Cytoscape. Module analysis of the PPI network was done using PEWCC1. Then, miRNA-hub gene regulatory network and TF-hub gene regulatory network were constructed by Cytoscape software. Finally, we performed receiver operating characteristic (ROC) curve analysis to predict the diagnostic effectiveness of the hub genes. RESULTS A total of 930 DEGs, 464 upregulated genes and 466 downregulated genes, were identified in HF. GO and REACTOME pathway enrichment results showed that DEGs mainly enriched in localization, small molecule metabolic process, SARS-CoV infections, and the citric acid tricarboxylic acid (TCA) cycle and respiratory electron transport. After combining the results of the PPI network miRNA-hub gene regulatory network and TF-hub gene regulatory network, 10 hub genes were selected, including heat shock protein 90 alpha family class A member 1 (HSP90AA1), arrestin beta 2 (ARRB2), myosin heavy chain 9 (MYH9), heat shock protein 90 alpha family class B member 1 (HSP90AB1), filamin A (FLNA), epidermal growth factor receptor (EGFR), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), cullin 4A (CUL4A), YEATS domain containing 4 (YEATS4), and lysine acetyltransferase 2B (KAT2B). CONCLUSIONS This discovery-driven study might be useful to provide a novel insight into the diagnosis and treatment of HF. However, more experiments are needed in the future to investigate the functional roles of these genes in HF.
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Affiliation(s)
- Prashanth Ganekal
- Department of General Medicine, Basaveshwara Medical College, Chitradurga, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, #253, Bharthinagar, Dharwad 580001, India
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10
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Pagliuca S, Gurnari C, Awada H, Kishtagari A, Kongkiatkamon S, Terkawi L, Zawit M, Guan Y, LaFramboise T, Jha BK, Patel BJ, Hamilton BK, Majhail NS, Lundgren S, Mustjoki S, Saunthararajah Y, Visconte V, Chan TA, Yang CY, Lenz TL, Maciejewski JP. The similarity of class II HLA genotypes defines patterns of autoreactivity in idiopathic bone marrow failure disorders. Blood 2021; 138:2781-2798. [PMID: 34748628 PMCID: PMC8718627 DOI: 10.1182/blood.2021012900] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023] Open
Abstract
Idiopathic aplastic anemia (IAA) is a rare autoimmune bone marrow failure (BMF) disorder initiated by a human leukocyte antigen (HLA)-restricted T-cell response to unknown antigens. As in other autoimmune disorders, the predilection for certain HLA profiles seems to represent an etiologic factor; however, the structure-function patterns involved in the self-presentation in this disease remain unclear. Herein, we analyzed the molecular landscape of HLA complexes of a cohort of 300 IAA patients and almost 3000 healthy and disease controls by deeply dissecting their genotypic configurations, functional divergence, self-antigen binding capabilities, and T-cell receptor (TCR) repertoire specificities. Specifically, analysis of the evolutionary divergence of HLA genotypes (HED) showed that IAA patients carried class II HLA molecules whose antigen-binding sites were characterized by a high level of structural homology, only partially explained by specific risk allele profiles. This pattern implies reduced HLA binding capabilities, confirmed by binding analysis of hematopoietic stem cell (HSC)-derived self-peptides. IAA phenotype was associated with the enrichment in a few amino acids at specific positions within the peptide-binding groove of DRB1 molecules, affecting the interface HLA-antigen-TCR β and potentially constituting the basis of T-cell dysfunction and autoreactivity. When analyzing associations with clinical outcomes, low HED was associated with risk of malignant progression and worse survival, underlying reduced tumor surveillance in clearing potential neoantigens derived from mechanisms of clonal hematopoiesis. Our data shed light on the immunogenetic risk associated with IAA etiology and clonal evolution and on general pathophysiological mechanisms potentially involved in other autoimmune disorders.
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Affiliation(s)
- Simona Pagliuca
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
- University of Paris, Paris, France
| | - Carmelo Gurnari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Hassan Awada
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Ashwin Kishtagari
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Sunisa Kongkiatkamon
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Laila Terkawi
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Misam Zawit
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Yihong Guan
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH
| | - Babal K Jha
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Bhumika J Patel
- Leukemia Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Betty K Hamilton
- Blood and Marrow Transplant Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Navneet S Majhail
- Blood and Marrow Transplant Program, Department of Hematology and Oncology, Cleveland Clinic, Cleveland, OH
| | - Sofie Lundgren
- Hematology Research Unit Helsinki, University of Helsinki-Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, University of Helsinki-Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
- ICAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Yogen Saunthararajah
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Valeria Visconte
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH
| | - Chao-Yie Yang
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany; and
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Jaroslaw P Maciejewski
- Translational Hematology and Oncology Research Department, Cleveland Clinic, Cleveland, OH
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11
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Nygård L, Laine AP, Kiviniemi M, Toppari J, Härkönen T, Knip M, Veijola R, Lempainen J, Ilonen J. Tri-SNP polymorphism in the intron of HLA-DRA1 affects type 1 diabetes susceptibility in the Finnish population. Hum Immunol 2021; 82:912-916. [PMID: 34311991 DOI: 10.1016/j.humimm.2021.07.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/22/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Genes in the HLA class II region include the most important inherited risk factors for type 1 diabetes (T1D) although also polymorphisms outside the HLA region modulate the predisposition to T1D. This study set out to confirm a recent observation in which a novel expression quantitative trait locus was formed by three single nucleotide polymorphisms (SNP) in the intron of HLA-DRA1 in DR3-DQ2 haplotypes. The SNPs significantly increased the risk for T1D in DR3-DQ2 homozygous individuals and we intended to further explore this association, in the Finnish population, by comparing two DR3-DQ2 positive genotypes. Cohorts with DR3-DQ2/DR3-DQ2 (N = 570) and DR3-DQ2/DR1-DQ5 (N = 1035) genotypes were studied using TaqMan analysis that typed for rs3135394, rs9268645 and rs3129877. The tri-SNP haplotype was significantly more common in cases than controls in the DR3-DQ2/DR3-DQ2 cohort (OR = 1.70 CI 95% = 1.15-2.51P = 0.007). However, no significant associations could be observed in the DR3-DQ2/DR1-DQ5 cohort.
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Affiliation(s)
- Lucas Nygård
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland; Faculty of Science and Engineering, Cell Biology, Åbo Akademi, Turku, Finland
| | - Antti-Pekka Laine
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Minna Kiviniemi
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jorma Toppari
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland; Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and Centre for Population Health Research, University of Turku, Turku, Finland
| | - Taina Härkönen
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland; Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Riitta Veijola
- Department of Paediatrics, PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu, Finland
| | - Johanna Lempainen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland.
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12
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Tay GK, Al Naqbi H, Mawart A, Baalfaqih Z, Almaazmi A, Deeb A, Alsafar H. Segregation Analysis of Genotyped and Family-Phased, Long Range MHC Classical Class I and Class II Haplotypes in 5 Families With Type 1 Diabetes Proband in the United Arab Emirates. Front Genet 2021; 12:670844. [PMID: 34276777 PMCID: PMC8278101 DOI: 10.3389/fgene.2021.670844] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
The classical Human Leucocyte Antigen (HLA) class II haplotypes of the Major Histocompatibility Complex (MHC) that are associated with type 1 diabetes (T1D) were identified in five families from the United Arab Emirates (UAE). Segregation analyses were performed on these 5 families with the disease, 3 with one child and 2 with 2 children diagnosed with T1D. Three HLA-DR4 haplotypes were identified: HLA- DRB1∗04:01:01-DQB1∗03:02:01:01; HLA- DRB1∗04:02:01- DQB1∗03:02:01; and HLA -DRB1∗04:05:01-DQB1∗02:02:01:02. All have previously been identified to be associated with T1D in studies of the Arabian population. In the 10 parents from the 5 families, 9 had at least one HLA-DR4 and HLA-DR3 haplotype which potentially increases the risk of T1D. Of these 9 parents, 3 were heterozygous for HLA-DR4/HLA-DR3 and one was homozygous for HLA-DR3. Two haplotypes that were identified here extend to the HLA class I region were previously designated AH8.2 (HLA -A∗26-B∗08-DRB1∗03) and AH50.2 (HLA -C∗06-B∗50-DRB1∗03:01-DQ∗02) and associated with diabetes in neighboring North Indian populations. This study provides examples of MHC haplotype analysis in pedigrees to improve our understanding of the genetics of T1D in the understudied population of the UAE.
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Affiliation(s)
- Guan K Tay
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Halima Al Naqbi
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Aurélie Mawart
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Zahrah Baalfaqih
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Anoud Almaazmi
- College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Asma Deeb
- Department of Endocrinology, Mafraq Hospital, Abu Dhabi, United Arab Emirates
| | - Habiba Alsafar
- Center for Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,Department of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.,College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
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13
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Xia Y, Li X, Huang G, Lin J, Luo S, Xie Z, Zhou Z. The association of HLA-DP loci with autoimmune diabetes in Chinese. Diabetes Res Clin Pract 2021; 173:108582. [PMID: 33307130 DOI: 10.1016/j.diabres.2020.108582] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 11/16/2020] [Accepted: 11/23/2020] [Indexed: 02/07/2023]
Abstract
AIMS To determine if HLA-DP loci independently contribute to classic type 1 diabetes (T1D) of all ages, childhood-onset T1D and latent autoimmune diabetes in adults (LADA) among Chinese Han population. METHODS A total of 518 patients with classic T1D (Among them 180 participants manifested T1D between 1 and 14 years), 519 patients with LADA and 527 normal controls were genotyped for both HLA-DPA1 and -DPB1 loci. The frequencies of DP alleles and haplotypes in patients were directly compared to those in controls, followed by adjustment for linkage disequilibrium (LD) with DR-DQ haplotypes. RESULTS In the direct comparison, DPA1*01:03, DPB1*04:01 and DPA1*01:03-DPB1*04:01 showed disease-predisposing effects in both the overall T1D group and the childhood-onset T1D group mainly due to their conjunction with the known susceptible DR3 haplotype. Conditioning on DR-DQ haplotypes, only DPA1*02:02-DPB1*02:02 significantly increased T1D risk among those diagnosed during childhood (OR = 2.02, 95% CI = 1.35-3.01). Whether or not adjusted for LD, no statistically significant HLA-DP association could be observed for LADA. CONCLUSION HLA-DP is implicated in the pathogenesis of childhood-onset T1D in Chinese, independent of the predominant DR-DQ loci and might serve as additional markers in genetic models for the recognition of those genetically at-risk individuals.
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Affiliation(s)
- Ying Xia
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.
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14
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Mishra R, Åkerlund M, Cousminer DL, Ahlqvist E, Bradfield JP, Chesi A, Hodge KM, Guy VC, Brillon DJ, Pratley RE, Rickels MR, Vella A, Ovalle F, Harris RI, Melander O, Varvel S, Hakonarson H, Froguel P, Lonsdale JT, Mauricio D, Schloot NC, Khunti K, Greenbaum CJ, Yderstræde KB, Tuomi T, Voight BF, Schwartz S, Boehm BO, Groop L, Leslie RD, Grant SFA. Genetic Discrimination Between LADA and Childhood-Onset Type 1 Diabetes Within the MHC. Diabetes Care 2020; 43:418-425. [PMID: 31843946 PMCID: PMC6971787 DOI: 10.2337/dc19-0986] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 11/16/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE The MHC region harbors the strongest loci for latent autoimmune diabetes in adults (LADA); however, the strength of association is likely attenuated compared with that for childhood-onset type 1 diabetes. In this study, we recapitulate independent effects in the MHC class I region in a population with type 1 diabetes and then determine whether such conditioning in LADA yields potential genetic discriminators between the two subtypes within this region. RESEARCH DESIGN AND METHODS Chromosome 6 was imputed using SNP2HLA, with conditional analysis performed in type 1 diabetes case subjects (n = 1,985) and control subjects (n = 2,219). The same approach was applied to a LADA cohort (n = 1,428) using population-based control subjects (n = 2,850) and in a separate replication cohort (656 type 1 diabetes case, 823 LADA case, and 3,218 control subjects). RESULTS The strongest associations in the MHC class II region (rs3957146, β [SE] = 1.44 [0.05]), as well as the independent effect of MHC class I genes, on type 1 diabetes risk, particularly HLA-B*39 (β [SE] = 1.36 [0.17]), were confirmed. The conditional analysis in LADA versus control subjects showed significant association in the MHC class II region (rs3957146, β [SE] = 1.14 [0.06]); however, we did not observe significant independent effects of MHC class I alleles in LADA. CONCLUSIONS In LADA, the independent effects of MHC class I observed in type 1 diabetes were not observed after conditioning on the leading MHC class II associations, suggesting that the MHC class I association may be a genetic discriminator between LADA and childhood-onset type 1 diabetes.
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Affiliation(s)
- Rajashree Mishra
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Graduate Group in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mikael Åkerlund
- Lund University Diabetes Centre, Department of Clinical Sciences Malmö, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Diana L Cousminer
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Emma Ahlqvist
- Lund University Diabetes Centre, Department of Clinical Sciences Malmö, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Jonathan P Bradfield
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Alessandra Chesi
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Kenyaita M Hodge
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Vanessa C Guy
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA
| | | | - Richard E Pratley
- Translational Research Institute for Metabolism and Diabetes, Florida Hospital, FL
| | - Michael R Rickels
- Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | | | | | - Olle Melander
- Lund University Diabetes Centre, Department of Clinical Sciences Malmö, Lund University, Skåne University Hospital, Malmö, Sweden
| | | | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Phillippe Froguel
- CNRS 8199, Université Lille Nord de France, Pasteur Institute, Lille, France.,Department of Genomics of Common Disease, Imperial College London, London, U.K
| | | | - Didac Mauricio
- Hospital de la Santa Creu i Sant Pau, CIBERDEM, Barcelona, Spain
| | | | - Kamlesh Khunti
- Diabetes Research Centre, University of Leicester, Leicester, U.K
| | | | | | - Tiinamaija Tuomi
- Department of Endocrinology, Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Centre, Helsinki, Finland, and Research Programs Unit, Clinical and Molecular Metabolism, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Benjamin F Voight
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Systems, Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | | | - Bernhard O Boehm
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, and Imperial College London, London, U.K.,Department of Internal Medicine I, Ulm University Medical Centre, Ulm, Germany
| | - Leif Groop
- Lund University Diabetes Centre, Department of Clinical Sciences Malmö, Lund University, Skåne University Hospital, Malmö, Sweden.,Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Richard David Leslie
- Department of Immunobiology, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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15
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Zabeen B, Govender D, Hassan Z, Noble JA, Lane JA, Mack SJ, Atkinson MA, Azad K, Wasserfall CH, Ogle GD. Clinical features, biochemistry and HLA-DRB1 status in children and adolescents with diabetes in Dhaka, Bangladesh. Diabetes Res Clin Pract 2019; 158:107894. [PMID: 31669629 PMCID: PMC6988504 DOI: 10.1016/j.diabres.2019.107894] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 10/22/2019] [Indexed: 11/30/2022]
Abstract
AIMS Little information is published on diabetes in young people in Bangladesh. We aimed to investigate the demographic, clinical, and biochemical features, and HLA-DRB1 alleles in new cases of diabetes affecting Bangladeshi children and adolescents <22 years of age. METHODS The study was conducted at Bangladesh Institute of Research and Rehabilitation of Diabetes, Endocrine and Metabolic Disorders (BIRDEM) in Dhaka. One hundred subjects aged <22 years at diagnosis were enrolled. Demographic characteristics, clinical information, biochemical parameters (blood glucose, HbA1c, C-peptide, and autoantibodies against glutamic acid decarboxylase 65 (GADA) and islet antigen-2 (IA-2A) were measured. High-resolution DNA genotyping was performed for HLA-DRB1. RESULTS Eighty-four subjects were clinically diagnosed as type 1 diabetes (T1D), seven as type 2 diabetes (T2D), and nine as fibrocalculous pancreatic disease (FCPD). Of the 84 with T1D, 37 (44%) were males and 47 (56%) females, with median age at diagnosis 13 years (y) (range 1.6-21.7) and peak age at onset 12-15 years. 85% of subjects were assessed within one month of diagnosis and all within eleven months. For subjects diagnosed with T1D, mean C-peptide was 0.46 ± 0.22 nmol/L (1.40 ± 0.59 ng/mL), with 9 (10.7%) IA-2A positive, 22 (26%) GADA positive, and 5 (6%) positive for both autoantibodies. Analysis of HLA-DRB1 genotypes revealed locus-level T1D association (p = 6.0E-05); DRB1*04:01 appeared predisposing (p < 3.0E-06), and DRB1*14:01 appeared protective (p = 1.7E-02). CONCLUSIONS Atypical forms of T1D appear to be more common in young people in Bangladesh than in European populations. This will be helpful in guiding more specific assessment at onset and potentially, expanding treatment options.
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Affiliation(s)
- Bedowra Zabeen
- Department of Changing Diabetes in Children, Bangladesh Institute of Research and Rehabilitation of Diabetes, Endocrine and Metabolic Disorders, Dhaka, Bangladesh
| | - Denira Govender
- Life for a Child Program, Diabetes NSW, Glebe, NSW 2037, Australia; Sydney Medical School, University of Sydney, NSW 2006, Australia.
| | - Zahid Hassan
- Dept of Physiology and Molecular Biology, Bangladesh University of Health Sciences (BUHS), Mirpur-1, Dhaka, Bangladesh & Dept of Physiology, Tairunnessa Memorial Medical College, Gazipur, Bangladesh.
| | | | - Julie A Lane
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
| | - Steven John Mack
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
| | - Mark Alvin Atkinson
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA; Department of Pediatrics, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Kishwar Azad
- Department of Changing Diabetes in Children, Bangladesh Institute of Research and Rehabilitation of Diabetes, Endocrine and Metabolic Disorders, Dhaka, Bangladesh.
| | - Clive Henry Wasserfall
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, Diabetes Institute, University of Florida, Gainesville, FL 32610, USA.
| | - Graham David Ogle
- Sydney Medical School, University of Sydney, NSW 2006, Australia; Diabetes NSW, Sydney, Australia.
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16
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Human Leukocyte Antigen (HLA) and Islet Autoantibodies Are Tools to Characterize Type 1 Diabetes in Arab Countries: Emphasis on Kuwait. DISEASE MARKERS 2019; 2019:9786078. [PMID: 31827651 PMCID: PMC6886320 DOI: 10.1155/2019/9786078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/15/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
The incidence rate of type 1 diabetes in Kuwait had been increasing exponentially and has doubled in children ≤ 14 years old within almost two decades. Therefore, there is a dire need for a careful systematic familial cohort study. Several immunogenetic factors affect the pathogenesis of the disease. The human leukocyte antigen (HLA) accounts for the major genetic susceptibility to the disease. The triggering agents initiate disease onset by type 1 destruction of pancreatic β-cells. Both HLA and anti-islet antibodies can be used to characterize, predict susceptibility to the disease, innovate, or delay the β-cell destruction. Evidence from prospective longitudinal studies suggested that the underlying disease process represents a continuum that begins before the symptoms are clinically evident. Autoimmunity of the functional pancreatic β-cells results in symptomatic type 1 diabetes and lifelong insulin dependence. The autoantibodies against glutamic acid decarboxylase (GADA), insulinoma antigen-2 (IA-2A), insulin (IAA), and zinc transporter-8 (ZnT-8A) comprise the most reliable biomarkers for type 1 diabetes in both children and adults. Although Kuwait is the second among the top 10 countries with a high incidence rate of type 1 diabetes, there have been no proper diagnostic and prediction tools as per the World Health Organization. The Kuwaiti Type 1 Diabetes Study (KADS) was initiated to understand the disease pathogenesis as well as the HLA and anti-islet autoantibody profile of type 1 diabetes in Kuwait. Understanding the disease sequela in a homogenous gene pool and highly consanguineous population of Kuwaitis could help solve the challenges and pathogenesis, as well as hasten the prevention, of type 1 diabetes.
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17
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Ilonen J, Lempainen J, Veijola R. The heterogeneous pathogenesis of type 1 diabetes mellitus. Nat Rev Endocrinol 2019; 15:635-650. [PMID: 31534209 DOI: 10.1038/s41574-019-0254-y] [Citation(s) in RCA: 213] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/13/2019] [Indexed: 12/14/2022]
Abstract
Type 1 diabetes mellitus (T1DM) results from the destruction of pancreatic β-cells that is mediated by the immune system. Multiple genetic and environmental factors found in variable combinations in individual patients are involved in the development of T1DM. Genetic risk is defined by the presence of particular allele combinations, which in the major susceptibility locus (the HLA region) affect T cell recognition and tolerance to foreign and autologous molecules. Multiple other loci also regulate and affect features of specific immune responses and modify the vulnerability of β-cells to inflammatory mediators. Compared with the genetic factors, environmental factors that affect the development of T1DM are less well characterized but contact with particular microorganisms is emerging as an important factor. Certain infections might affect immune regulation, and the role of commensal microorganisms, such as the gut microbiota, are important in the education of the developing immune system. Some evidence also suggests that nutritional factors are important. Multiple islet-specific autoantibodies are found in the circulation from a few weeks to up to 20 years before the onset of clinical disease and this prediabetic phase provides a potential opportunity to manipulate the islet-specific immune response to prevent or postpone β-cell loss. The latest developments in understanding the heterogeneity of T1DM and characterization of major disease subtypes might help in the development of preventive treatments.
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Affiliation(s)
- Jorma Ilonen
- Institue of Biomedicine, University of Turku and Clinical Microbiology, Turku University Hospital, Turku, Finland.
| | - Johanna Lempainen
- Institue of Biomedicine, University of Turku and Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Paediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Riitta Veijola
- Department of Paediatrics, University of Oulu and Oulu University Hospital, Oulu, Finland
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18
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Tamouza R, Fernell E, Eriksson MA, Anderlid BM, Manier C, Mariaselvam CM, Boukouaci W, Leboyer M, Gillberg C. HLA Polymorphism in Regressive and Non-Regressive Autism: A Preliminary Study. Autism Res 2019; 13:182-186. [PMID: 31593375 DOI: 10.1002/aur.2217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/27/2019] [Accepted: 09/12/2019] [Indexed: 12/16/2022]
Abstract
Autism spectrum disorders (ASD) comprises heterogeneous neurodevelopmental conditions with symptom onset usually during infancy. However, about 10%-30% of affected cases experience a loss of language and social skills around 18-30 months, so-called regressive autism. In this subset with regression, immune dysfunctions including inflammation and autoimmunity have been proposed to be at risk factors. Given the implication of the human histocompatibility antigens (HLA) system in various aspects of immune responses, including autoimmunity, and in ASD, we investigate here the distribution of the HLA Class I and Class II haplotypes in 131 children with ASD meeting DSM-IV TR criteria, with and without regression. We found that 62 of the 98 non-regressive ASD patients carry the HLA-DPA1*01-DPB1*04 sub-haplotype as compared to 14 of the 33 patients with regression (63% vs. 43% respectively, Pc = 0.02), suggesting that this HLA haplotype may exert a protective effect against regression. Similarly, the HLA-DPA1*01-DPB1*04 has also been found to be more represented in healthy controls as compared to patients affected with common nonpsychiatric autoimmune disorders. Overall our findings suggest a possible involvement of HLA polymorphism in the context of regressive ASD. Autism Res 2020, 13: 182-186. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc. LAY SUMMARY: Immune dysfunctions including inflammatory and autoimmune processes have been reported in autism, particularly in regressive forms. In this study, we analyzed the distribution of HLA haplotypes among children with autism spectrum disorder (ASD), with and without regression from Sweden and observed that HLA-DPA1*01-DPB1*04 sub-haplotype was less represented in patients with regressive autism as compared with those without regression. Such possible protective effect, also observed in other common autoimmune disorders, may constitute a link between HLA-mediated immune processes and regressive ASD.
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Affiliation(s)
- Ryad Tamouza
- Translational Psychiatry Laboratory, Mondor Institute of Biomedical Research, INSERM U955, Créteil, France.,DHU PePSY, AP-HP, Pôle de Psychiatrie, Hôpitaux Universitaires Henri Mondor, Université Paris-Est-Créteil, Créteil, France.,Fondation FondaMental, Créteil, France
| | - Elisabeth Fernell
- Gillberg Neuropsychiatry Centre, Institute of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden.,Sahlgren University Hospital, Gothenburg, Sweden
| | - Mats Anders Eriksson
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Britt-Marie Anderlid
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Céline Manier
- Translational Psychiatry Laboratory, Mondor Institute of Biomedical Research, INSERM U955, Créteil, France
| | - Christina Mary Mariaselvam
- Translational Psychiatry Laboratory, Mondor Institute of Biomedical Research, INSERM U955, Créteil, France
| | - Wahid Boukouaci
- Translational Psychiatry Laboratory, Mondor Institute of Biomedical Research, INSERM U955, Créteil, France
| | - Marion Leboyer
- Translational Psychiatry Laboratory, Mondor Institute of Biomedical Research, INSERM U955, Créteil, France.,DHU PePSY, AP-HP, Pôle de Psychiatrie, Hôpitaux Universitaires Henri Mondor, Université Paris-Est-Créteil, Créteil, France.,Fondation FondaMental, Créteil, France
| | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, Institute of Neuroscience and Physiology, University of Gothenburg, Sahlgrenska Academy, Gothenburg, Sweden.,Sahlgren University Hospital, Gothenburg, Sweden
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19
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Aydemir Ö, Noble JA, Bailey JA, Lernmark Å, Marsh P, Andersson Svärd A, Bearoff F, Blankenhorn EP, Mordes JP. Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes. Diabetes 2019; 68:1523-1527. [PMID: 30962219 PMCID: PMC6609989 DOI: 10.2337/db18-1128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
Type 1 diabetes (T1D) involves the interaction of multiple gene variants, environmental factors, and immunoregulatory dysfunction. Major T1D genetic risk loci encode HLA-DR and -DQ. Genetic heterogeneity and linkage disequilibrium in the highly polymorphic HLA region confound attempts to identify additional T1D susceptibility loci. To minimize HLA heterogeneity, T1D patients (N = 365) and control subjects (N = 668) homozygous for the HLA-DR3 high-risk haplotype were selected from multiple large T1D studies and examined to identify new T1D susceptibility loci using molecular inversion probe sequencing technology. We report that risk for T1D in HLA-DR3 homozygotes is increased significantly by a previously unreported haplotype of three single nucleotide polymorphisms (SNPs) within the first intron of HLA-DRA1. The homozygous risk haplotype has an odds ratio of 4.65 relative to the protective homozygous haplotype in our sample. Individually, these SNPs reportedly function as "expression quantitative trait loci," modulating HLA-DR and -DQ expression. From our analysis of available data, we conclude that the tri-SNP haplotype within HLA-DRA1 may modulate class II expression, suggesting that increased T1D risk could be attributable to regulated expression of class II genes. These findings could help clarify the role of HLA in T1D susceptibility and improve diabetes risk assessment, particularly in high-risk HLA-DR3 homozygous individuals.
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Affiliation(s)
- Özkan Aydemir
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | | | - Jeffrey A Bailey
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Patrick Marsh
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Agnes Andersson Svärd
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Frank Bearoff
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - John P Mordes
- Division of Endocrinology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
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20
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Molineros JE, Looger LL, Kim K, Okada Y, Terao C, Sun C, Zhou XJ, Raj P, Kochi Y, Suzuki A, Akizuki S, Nakabo S, Bang SY, Lee HS, Kang YM, Suh CH, Chung WT, Park YB, Choe JY, Shim SC, Lee SS, Zuo X, Yamamoto K, Li QZ, Shen N, Porter LL, Harley JB, Chua KH, Zhang H, Wakeland EK, Tsao BP, Bae SC, Nath SK. Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians. PLoS Genet 2019; 15:e1008092. [PMID: 31022184 PMCID: PMC6504188 DOI: 10.1371/journal.pgen.1008092] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 05/07/2019] [Accepted: 03/13/2019] [Indexed: 11/18/2022] Open
Abstract
Human leukocyte antigen (HLA) is a key genetic factor conferring risk of systemic lupus erythematosus (SLE), but precise independent localization of HLA effects is extremely challenging. As a result, the contribution of specific HLA alleles and amino-acid residues to the overall risk of SLE and to risk of specific autoantibodies are far from completely understood. Here, we dissected (a) overall SLE association signals across HLA, (b) HLA-peptide interaction, and (c) residue-autoantibody association. Classical alleles, SNPs, and amino-acid residues of eight HLA genes were imputed across 4,915 SLE cases and 13,513 controls from Eastern Asia. We performed association followed by conditional analysis across HLA, assessing both overall SLE risk and risk of autoantibody production. DR15 alleles HLA-DRB1*15:01 (P = 1.4x10-27, odds ratio (OR) = 1.57) and HLA-DQB1*06:02 (P = 7.4x10-23, OR = 1.55) formed the most significant haplotype (OR = 2.33). Conditioned protein-residue signals were stronger than allele signals and mapped predominantly to HLA-DRB1 residue 13 (P = 2.2x10-75) and its proxy position 11 (P = 1.1x10-67), followed by HLA-DRB1-37 (P = 4.5x10-24). After conditioning on HLA-DRB1, novel associations at HLA-A-70 (P = 1.4x10-8), HLA-DPB1-35 (P = 9.0x10-16), HLA-DQB1-37 (P = 2.7x10-14), and HLA-B-9 (P = 6.5x10-15) emerged. Together, these seven residues increased the proportion of explained heritability due to HLA to 2.6%. Risk residues for both overall disease and hallmark autoantibodies (i.e., nRNP: DRB1-11, P = 2.0x10-14; DRB1-13, P = 2.9x10-13; DRB1-30, P = 3.9x10-14) localized to the peptide-binding groove of HLA-DRB1. Enrichment for specific amino-acid characteristics in the peptide-binding groove correlated with overall SLE risk and with autoantibody presence. Risk residues were in primarily negatively charged side-chains, in contrast with rheumatoid arthritis. We identified novel SLE signals in HLA Class I loci (HLA-A, HLA-B), and localized primary Class II signals to five residues in HLA-DRB1, HLA-DPB1, and HLA-DQB1. These findings provide insights about the mechanisms by which the risk residues interact with each other to produce autoantibodies and are involved in SLE pathophysiology. The Human leukocyte antigen (HLA) region is a key genetic factor conferring risk of systemic lupus erythematosus (SLE). In spite of multiple SLE association signals identified in the HLA region, only amino-acid residues within HLA-DRB1 have been specifically described previously. In this study, we performed an imputation-based analysis on individuals with East Asian ancestry, and characterized SLE risk within the HLA region for all involved independent genes (HLA-DRB1, HLA-DPB1, HLA-DQB1, HLA-A, and HLA-B). Furthermore, we identified a characteristic SLE risk residue signature as well as a pattern of specific nRNP and Ro/La autoantibody residues located in the peptide-binding grooves, suggesting their key involvement in autoantibody production.
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Affiliation(s)
- Julio E. Molineros
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Loren L. Looger
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - Kwangwoo Kim
- Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Chikashi Terao
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
- Division of Genetics, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Celi Sun
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Xu-jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Shuji Akizuki
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuichiro Nakabo
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
| | - Young Mo Kang
- School of Medicine, Kyungpook National University Hospital, Daegu, Korea
| | - Chang-Hee Suh
- Department of Rheumatology, Ajou University Hospital, Suwon, Korea
| | - Won Tae Chung
- Dong-A University Hospital, Department of Internal Medicine, Busan, Korea
| | - Yong-Beom Park
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Jung-Yoon Choe
- Department of Rheumatology, Catholic University of Daegu School of Medicine, Daegu, Korea
| | - Seung-Cheol Shim
- Daejeon Rheumatoid & Degenerative Arthritis Center, Chungnam National University Hospital, Daejeon, Korea
| | - Shin-Seok Lee
- Department of Rheumatology, Chonnam National University Medical School and Hospital, Gwangju, Korea
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, China
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Quan-Zhen Li
- Department of Immunology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Nan Shen
- Department of Rheumatology and Shanghai Institute of Rheumatology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
| | - Lauren L. Porter
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, United States of America
| | - John B. Harley
- Center for Autoimmune Genomics and Etiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, United States of America
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Hong Zhang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Edward K. Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Betty P. Tsao
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- * E-mail: (SCB); (SKN)
| | - Swapan K. Nath
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
- * E-mail: (SCB); (SKN)
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21
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Lees JR. Targeting antigen presentation in autoimmunity. Cell Immunol 2018; 339:4-9. [PMID: 30554782 DOI: 10.1016/j.cellimm.2018.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023]
Abstract
Autoimmune diseases are heterogeneous group of disorders that together represent an enormous societal and medical problem. CD4+ T cells have critical roles in the initiation and pathogenesis of autoimmune disease. As such, modulation of T cell activity has proven to have significant therapeutic effects in multiple autoimmune settings. T cell activation is a complex process with multiple potential therapeutic targets, many of which have been successfully utilized to treat human disease. Current pharmacological treatment largely targets T cell intrinsic activities as a means of treating various autoimmune disorders. Here I review extant and potential therapeutic approaches that instead specifically target antigen presentation to CD4+ T cells as a critical checkpoint in autoimmune responses. In addition, the contribution of antigen modulation components in current therapeutic approaches is considered along with the impact of new antigen targeted treatment modalities. Finally, potential challenges are considered in the context of the potential for antigen specific targeting of the antigen presentation process.
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Affiliation(s)
- Jason R Lees
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.
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22
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Zheng Z, Zheng F. A complex auxiliary: IL-17/Th17 signaling during type 1 diabetes progression. Mol Immunol 2018; 105:16-31. [PMID: 30472513 DOI: 10.1016/j.molimm.2018.11.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/03/2018] [Accepted: 11/09/2018] [Indexed: 02/08/2023]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease centered around the loss of the beta cells of the islets of Langerhans, and consequent inability of the islets to produce the insulin necessary to maintain glycemic control. While most therapeutic approaches have been centered on insulin replacement, newer approaches to target the underlying immune response have become an area of focus. However, the immune landscape in T1D is extremely complex, and the roles played by individual cytokines during disease progression are incompletely understood, making the development of immunotherapies very difficult. In this review, we discuss the complex auxiliary role played by IL-17, both around the islet and in peripheral tissues such as the gut and kidney, which might influence T1D progression. Through our re-analysis of the key factors involved IL-17 signaling in recently published single-cell sequencing and sorted-cell bulk sequencing datasets, we find supporting evidence for the general existence of the signaling apparatus in islet endocrine cells. We also explore the emerging evidence of IL-17 serving as an influential factor in diabetic complications that affect distal tissues. While anti-IL-17 therapies are emerging as an option for psoriasis and other autoimmune disorders, we highlight here a number of questions that would need to be addressed before their potential applicability to treating T1D can be fully evaluated.
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Affiliation(s)
- Zihan Zheng
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, Liaoning Province, PR China; Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Feng Zheng
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, Liaoning Province, PR China.
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23
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Han S, Yang H, Han Y, Zhang H. Genes and transcription factors related to the adverse effects of maternal type I diabetes mellitus on fetal development. Mol Cell Probes 2018; 43:64-71. [PMID: 30447278 DOI: 10.1016/j.mcp.2018.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/15/2018] [Accepted: 11/13/2018] [Indexed: 11/24/2022]
Abstract
PURPOSE Maternal type I diabetes mellitus (T1DM) increases the risk of adverse pregnancy outcomes, but the corresponding mechanism is unclear. This study aims to investigate the mechanism underlying the adverse pregnancy outcomes of maternal T1DM. METHODS Gene expression microarray (GSE51546) was down-loaded from the Gene Expression Omnibus. This dataset included 12 umbilical cord samples from the newborns of T1DM mothers (T1DM group, N = six) and non-diabetic mothers (control group, N = six). RESULTS Consequently, 1051 differentially expressed genes (DEGs) were found between the two groups. The up-regulated DEGs enriched in 30 KEGG pathways. HLA-DPA1, HLA-DMA, HLA-DMB, HLA-DQA1, HLA-DQA2 and HLA-DRA enriched in "Type I diabetes mellitus". This pathway was strongly related to 14 pathways, most of which were associated with diseases. Then, a protein-protein interaction network was constructed, and 45 potential key DEGs were identified. The 45 DEGs enriched in pathways such as "Rheumatoid arthritis", "Chemokine signaling pathway" and "Cytokine-cytokine receptor interaction" (e.g. CXCL12 and CCL5). Transcription factors (TFs) of key DEGs were predicted, and a TF-DEG regulatory network was constructed. CONCLUSIONS Some genes (e.g. CXCL12 and CCL5) and their TFs were significantly and abnormally regulated in the umbilical cord tissue from the pregnancies of T1DM mothers compared to that from non-T1DM mothers.
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Affiliation(s)
- Shuyi Han
- Department of Clinical Laboratory, Ji'nan Central Hospital Affiliated to Shandong University, Ji'nan, 250013, China
| | - Huili Yang
- Department of Obstetrics, Ji'nan Central Hospital Affiliated to Shandong University, Ji'nan, 250013, China.
| | - Yunhui Han
- Department of Obstetrics, Ji'nan Central Hospital Affiliated to Shandong University, Ji'nan, 250013, China
| | - Hongzhi Zhang
- Department of Gynecology, Ji'nan Central Hospital Affiliated to Shandong University, Ji'nan, 250013, China
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24
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Ma F, Sun T, Wu M, Wang W, Xu Z. Identification of key genes for diabetic kidney disease using biological informatics methods. Mol Med Rep 2017; 16:7931-7938. [PMID: 28990106 PMCID: PMC5779875 DOI: 10.3892/mmr.2017.7666] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 06/11/2017] [Indexed: 01/15/2023] Open
Abstract
Diabetic kidney disease (DKD) is a common complication of diabetes, which is characterized by albuminuria, impaired glomerular filtration rate or a combination of the two. The aim of the present study was to identify the potential key genes involved in DKD progression and to subsequently investigate the underlying mechanism involved in DKD development. The array data of GSE30528 including 9 DKD and 13 control samples was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in DKD glomerular and tubular kidney biopsy tissues were compared with normal tissues, and were analyzed using the limma package. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for DEGs using the GO Function software in Bioconductor. The protein‑protein interaction (PPI) network was then constructed using Cytoscape software. A total of 426 genes (115 up‑ and 311 downregulated) were differentially expressed between the DKD and normal tissue samples. The PPI network was constructed with 184 nodes and 335 edges. Vascular endothelial growth factor A (VEGFA), α‑actinin‑4 (ACTN4), proto‑oncogene, Src family tyrosine kinase (FYN), collagen, type 1, α2 (COL1A2) and insulin‑like growth factor 1 (IGF1) were hub proteins. Major histocompatibility complex, class II, DP α1 (HLA‑DPA1) was the common gene enriched in the rheumatoid arthritis and systemic lupus erythematosus pathways, and the immune response was a GO term enriched in module A. VEGFA, ACTN4, FYN, COL1A2, IGF1 and HLA‑DPA1 may be potential key genes associated with the progression of DKD, and immune mechanisms may serve a part in DKD development.
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Affiliation(s)
- Fuzhe Ma
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Tao Sun
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Meiyan Wu
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wanning Wang
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Zhonggao Xu
- Department of Nephrology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
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25
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Ilonen J, Kiviniemi M, Lempainen J, Simell O, Toppari J, Veijola R, Knip M. Genetic susceptibility to type 1 diabetes in childhood - estimation of HLA class II associated disease risk and class II effect in various phases of islet autoimmunity. Pediatr Diabetes 2016; 17 Suppl 22:8-16. [PMID: 27411431 DOI: 10.1111/pedi.12327] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/10/2015] [Accepted: 09/17/2015] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVE The HLA-DR/DQ region remains the major determinant of susceptibility to type 1 diabetes (T1D) despite the more than 50 risk affecting loci outside human leukocyte antigen (HLA) region that have been identified. We aimed at developing a simple risk estimation based on HLA class II genotyping, which was also tested by analyzing HLA class II effect on the autoantibody seroconversion and further progression to diabetes. SUBJECTS AND METHODS A total of 2991 trio families with a diabetic child from the Finnish Pediatric Diabetes Register were genotyped and the risk contributed by each DR-DQ haplotype calculated through transmission analysis. The genotype risk was estimated based on the summary effect of haplotypes. Genotype grouping was further tested in a subcohort of the Finnish Type 1 Diabetes Prediction and Prevention (DIPP) Study RESULTS The summary effect of haplotypes was generally seen in genotypes, while the expected synergistic effect of DR3-DQ2 and DR4-DQ8 (DRB1*04:03 excluded) combination was also clear in the T1D risk association analysis. This highest risk DR/DQ genotype was found in 21.6% of patients and 2.0% of controls, odds ratio (OR) = 13.2 (10.1-17.2), whereas the lowest risk genotype contained only 0.8% of patients and 28.0% of controls, OR = 0.02 (0.01-0.03). In the subcohort from the DIPP study the risk grades correlated clearly with seroconversion for islet autoantibodies and T1D development. In contrast, DR/DQ risk groups did not associate with the progression rate from advanced autoimmunity to clinical diabetes. CONCLUSIONS Class II HLA genotype groups improve the estimation of T1D risk. Class II effect is limited to the early phase of the disease process characterized by seroconversion for islet autoantibodies.
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Affiliation(s)
- J Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, Finland
| | - M Kiviniemi
- Immunogenetics Laboratory, University of Turku, Turku, Finland
| | - J Lempainen
- Immunogenetics Laboratory, University of Turku, Turku, Finland
| | - O Simell
- Department of Pediatrics, University of Turku, Turku, Finland.,Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - J Toppari
- Department of Pediatrics, University of Turku, Turku, Finland.,Department of Pediatrics, Turku University Hospital, Turku, Finland.,Department of Physiology, University of Turku, Turku, Finland
| | - R Veijola
- Department of Pediatrics, University of Oulu, PEDEGO Research Unit, MRC Oulu, Oulu, Finland.,Department of Pediatrics, Oulu University Hospital, Oulu, Finland
| | - M Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland.,Department of Pediatrics, Tampere University Hospital, Tampere, Finland
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26
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First report on HLA-DPA1 gene allelic distribution in the general Lebanese population. Meta Gene 2016; 8:11-3. [PMID: 27014585 PMCID: PMC4792896 DOI: 10.1016/j.mgene.2016.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/28/2015] [Accepted: 01/13/2016] [Indexed: 01/20/2023] Open
Abstract
Aims HLA-DPA1 is an important marker in bone marrow and organ transplantation and a highly emerging screening parameter in histocompatibility laboratories. Being highly polymorphic, it has another significant value in detecting population origins and migrations. This is the first study to assess DPA1 allele frequencies in an Arab population. Methods The HLA DPA1 alleles were identified using the One-Lambda assays on a Luminex reverse SSO DNA typing system. Our study included 101 individuals coming from different Lebanese geographical areas representing the different communities and religious sects of the country. Results We compared the results of this study to 16 different populations and found very interesting similarities and differences between Lebanese people and individuals of European ancestry. Conclusion This study is the first to describe the different allelic frequencies of HLA-DPA1 in the Lebanese population and will serve as a template that can be later used for disease association studies both at the level of the country and internationally.
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Silva HPV, Ururahy MAG, Souza KSC, Loureiro MB, Oliveira YMC, Oliveira GHM, Luchessi AD, Carvalho KTC, Freitas JCOC, Donadi EA, Hirata RDC, Almeida MG, Arrais RF, Hirata MH, Rezende AA. The association between the HLA-G 14-bp insertion/deletion polymorphism and type 1 diabetes. Genes Immun 2015; 17:13-8. [DOI: 10.1038/gene.2015.45] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/07/2015] [Accepted: 09/08/2015] [Indexed: 11/09/2022]
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Wenzlau JM, Fain PR, Gardner TJ, Frisch LM, Annibale B, Hutton JC. ATPase4A Autoreactivity and Its Association With Autoimmune Phenotypes in the Type 1 Diabetes Genetics Consortium Study. Diabetes Care 2015; 38 Suppl 2:S29-36. [PMID: 26405069 PMCID: PMC4582907 DOI: 10.2337/dcs15-2006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Autoantibodies targeting the H+/K+-ATPase proton pump of the gastric parietal cell (parietal cell antibodies [PCA]) are diagnostic of atrophic body gastritis (ABG) leading to pernicious anemia (PA). PCA, ABG, and PA occur in increased frequency in patients with type 1 diabetes and their relatives and are considered "minor" components of forms of autoimmune polyglandular syndrome (APS). A customized radioimmunoprecipitation assay was applied to 6,749 samples from the Type 1 Diabetes Genetics Consortium to measure ATP4A autoreactivity. Autoantibody prevalence was correlated with variants in HLA class II, PTPN22, and CTLA4 genes. With an ATP4A radioimmunoprecipitation assay, PCA were detected in sera from 20.9% of affected individuals. PCA prevalence increased with age and was greater in females (25.3%) than males (16.5%) and among Hispanics (36.3%) and blacks (26.2%) compared with non-Hispanic whites (20.8%) and Asians (16.7%). PCA and other organ-specific autoantibodies GAD65, IA-2, thyroid peroxidase (TPO), 21-hydroxylase (21-OH), and transglutaminase (TG) clustered within families with heritability estimates from 71 to 95%. PCA clustered with TPO, 21-OH, and persistent GAD65 autoantibodies but not with celiac (TG) or IA-2 autoantibodies. PCA-positive subjects showed an increased frequency of DRB1*0404, DPB1*0201, and PTPN22 R620W (rs2476601-T) and a decreased frequency of DRB1*0101, DPB1*0301, and CTLA4 CT60 (rs3087243-T). Genetic variants accounted for 4-5% of the heritable risk for PCA. The same alleles were associated with other autoantibody phenotypes in a consistent pattern. Whereas most of the heritable risk for PCA and other antibodies reflects genetic effects that are tissue specific, parietal cell autoimmunity is a major pathogenetic contributor in APS2.
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Affiliation(s)
- Janet M Wenzlau
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Pamela R Fain
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Thomas J Gardner
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Lisa M Frisch
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
| | - Bruno Annibale
- Digestive and Liver Disease Unit, University "La Sapienza," Sant'Andrea Hospital, Rome, Italy
| | - John C Hutton
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Aurora, CO
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Noble JA. Immunogenetics of type 1 diabetes: A comprehensive review. J Autoimmun 2015; 64:101-12. [PMID: 26272854 DOI: 10.1016/j.jaut.2015.07.014] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/13/2022]
Abstract
Type 1 diabetes (T1D) results from the autoimmune destruction of insulin-producing beta cells in the pancreas. Prevention of T1D will require the ability to detect and modulate the autoimmune process before the clinical onset of disease. Genetic screening is a logical first step in identification of future patients to test prevention strategies. Susceptibility to T1D includes a strong genetic component, with the strongest risk attributable to genes that encode the classical Human Leukocyte Antigens (HLA). Other genetic loci, both immune and non-immune genes, contribute to T1D risk; however, the results of decades of small and large genetic linkage and association studies show clearly that the HLA genes confer the most disease risk and protection and can be used as part of a prediction strategy for T1D. Current predictive genetic models, based on HLA and other susceptibility loci, are effective in identifying the highest-risk individuals in populations of European descent. These models generally include screening for the HLA haplotypes "DR3" and "DR4." However, genetic variation among racial and ethnic groups reduces the predictive value of current models that are based on low resolution HLA genotyping. Not all DR3 and DR4 haplotypes are high T1D risk; some versions, rare in Europeans but high frequency in other populations, are even T1D protective. More information is needed to create predictive models for non-European populations. Comparative studies among different populations are needed to complete the knowledge base for the genetics of T1D risk to enable the eventual development of screening and intervention strategies applicable to all individuals, tailored to their individual genetic background. This review summarizes the current understanding of the genetic basis of T1D susceptibility, focusing on genes of the immune system, with particular emphasis on the HLA genes.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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30
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Rönn T, Volkov P, Gillberg L, Kokosar M, Perfilyev A, Jacobsen AL, Jørgensen SW, Brøns C, Jansson PA, Eriksson KF, Pedersen O, Hansen T, Groop L, Stener-Victorin E, Vaag A, Nilsson E, Ling C. Impact of age, BMI and HbA1c levels on the genome-wide DNA methylation and mRNA expression patterns in human adipose tissue and identification of epigenetic biomarkers in blood. Hum Mol Genet 2015; 24:3792-813. [PMID: 25861810 DOI: 10.1093/hmg/ddv124] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/07/2015] [Indexed: 01/03/2023] Open
Abstract
Increased age, BMI and HbA1c levels are risk factors for several non-communicable diseases. However, the impact of these factors on the genome-wide DNA methylation pattern in human adipose tissue remains unknown. We analyzed the DNA methylation of ∼480 000 sites in human adipose tissue from 96 males and 94 females and related methylation to age, BMI and HbA1c. We also compared epigenetic signatures in adipose tissue and blood. Age was significantly associated with both altered DNA methylation and expression of 1050 genes (e.g. FHL2, NOX4 and PLG). Interestingly, many reported epigenetic biomarkers of aging in blood, including ELOVL2, FHL2, KLF14 and GLRA1, also showed significant correlations between adipose tissue DNA methylation and age in our study. The most significant association between age and adipose tissue DNA methylation was found upstream of ELOVL2. We identified 2825 genes (e.g. FTO, ITIH5, CCL18, MTCH2, IRS1 and SPP1) where both DNA methylation and expression correlated with BMI. Methylation at previously reported HIF3A sites correlated significantly with BMI in females only. HbA1c (range 28-46 mmol/mol) correlated significantly with the methylation of 711 sites, annotated to, for example, RAB37, TICAM1 and HLA-DPB1. Pathway analyses demonstrated that methylation levels associated with age and BMI are overrepresented among genes involved in cancer, type 2 diabetes and cardiovascular disease. Our results highlight the impact of age, BMI and HbA1c on epigenetic variation of candidate genes for obesity, type 2 diabetes and cancer in human adipose tissue. Importantly, we demonstrate that epigenetic biomarkers in blood can mirror age-related epigenetic signatures in target tissues for metabolic diseases such as adipose tissue.
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Affiliation(s)
- Tina Rönn
- Department of Clinical Sciences, Epigenetics and Diabetes and
| | - Petr Volkov
- Department of Clinical Sciences, Epigenetics and Diabetes and
| | - Linn Gillberg
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Milana Kokosar
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 11, Box 434, 405 30 Gothenburg, Sweden
| | | | - Anna Louisa Jacobsen
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Sine W Jørgensen
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark, Steno Diabetes Center, Niels Steensensvej 2, DK-2820 Gentofte, Denmark
| | - Charlotte Brøns
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Per-Anders Jansson
- Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Karl-Fredrik Eriksson
- Department of Clinical Sciences, Vascular Diseases, Lund University, 205 02 Malmö, Sweden
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark and
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Universitetsparken 1, 2100 Copenhagen, Denmark and
| | - Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University Diabetes Centre, CRC, 205 02 Malmö, Sweden
| | - Elisabet Stener-Victorin
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Medicinaregatan 11, Box 434, 405 30 Gothenburg, Sweden, Department of Physiology and Pharmacology, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Allan Vaag
- Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Emma Nilsson
- Department of Clinical Sciences, Epigenetics and Diabetes and Department of Endocrinology, Rigshospitalet, Tagensvej 20, DK-2200 Copenhagen, Denmark
| | - Charlotte Ling
- Department of Clinical Sciences, Epigenetics and Diabetes and
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Ollila H, Ravel JM, Han F, Faraco J, Lin L, Zheng X, Plazzi G, Dauvilliers Y, Pizza F, Hong SC, Jennum P, Knudsen S, Kornum B, Dong X, Yan H, Hong H, Coquillard C, Mahlios J, Jolanki O, Einen M, Arnulf I, Högl B, Frauscher B, Crowe C, Partinen M, Huang Y, Bourgin P, Vaarala O, Désautels A, Montplaisir J, Mack S, Mindrinos M, Fernandez-Vina M, Mignot E, Mignot E. HLA-DPB1 and HLA class I confer risk of and protection from narcolepsy. Am J Hum Genet 2015; 96:136-46. [PMID: 25574827 DOI: 10.1016/j.ajhg.2014.12.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/08/2014] [Indexed: 01/29/2023] Open
Abstract
Type 1 narcolepsy, a disorder caused by a lack of hypocretin (orexin), is so strongly associated with human leukocyte antigen (HLA) class II HLA-DQA1(∗)01:02-DQB1(∗)06:02 (DQ0602) that very few non-DQ0602 cases have been reported. A known triggering factor for narcolepsy is pandemic 2009 influenza H1N1, suggesting autoimmunity triggered by upper-airway infections. Additional effects of other HLA-DQ alleles have been reported consistently across multiple ethnic groups. Using over 3,000 case and 10,000 control individuals of European and Chinese background, we examined the effects of other HLA loci. After careful matching of HLA-DR and HLA-DQ in case and control individuals, we found strong protective effects of HLA-DPA1(∗)01:03-DPB1(∗)04:02 (DP0402; odds ratio [OR] = 0.51 [0.38-0.67], p = 1.01 × 10(-6)) and HLA-DPA1(∗)01:03-DPB1(∗)04:01 (DP0401; OR = 0.61 [0.47-0.80], p = 2.07 × 10(-4)) and predisposing effects of HLA-DPB1(∗)05:01 in Asians (OR = 1.76 [1.34-2.31], p = 4.71 × 10(-05)). Similar effects were found by conditional analysis controlling for HLA-DR and HLA-DQ with DP0402 (OR = 0.45 [0.38-0.55] p = 8.99 × 10(-17)) and DP0501 (OR = 1.38 [1.18-1.61], p = 7.11 × 10(-5)). HLA-class-II-independent associations with HLA-A(∗)11:01 (OR = 1.32 [1.13-1.54], p = 4.92 × 10(-4)), HLA-B(∗)35:03 (OR = 1.96 [1.41-2.70], p = 5.14 × 10(-5)), and HLA-B(∗)51:01 (OR = 1.49 [1.25-1.78], p = 1.09 × 10(-5)) were also seen across ethnic groups in the HLA class I region. These effects might reflect modulation of autoimmunity or indirect effects of HLA class I and HLA-DP alleles on response to viral infections such as that of influenza.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Emmanuel Mignot
- Stanford University Center for Sleep Sciences, Palo Alto, CA 94304, USA.
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Umemura T, Katsuyama Y, Yoshizawa K, Kimura T, Joshita S, Komatsu M, Matsumoto A, Tanaka E, Ota M. Human leukocyte antigen class II haplotypes affect clinical characteristics and progression of type 1 autoimmune hepatitis in Japan. PLoS One 2014; 9:e100565. [PMID: 24956105 PMCID: PMC4067340 DOI: 10.1371/journal.pone.0100565] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 05/25/2014] [Indexed: 12/31/2022] Open
Abstract
Although we earlier demonstrated that the human leukocyte antigen (HLA) DRB1*04:05 allele was associated with susceptibility to autoimmune hepatitis (AIH) in Japan, the precise relationship of HLA haplotype and the role of amino acid alignment with disease susceptibility and progression has not been fully clarified. We reinvestigated HLA class I A, B, and C and HLA class II DRB1, DQB1, and DPB1 alleles and haplotypes in a larger new cohort of 156 Japanese patients with type 1 AIH and compared them with the published data of 210 healthy subjects. The DRB1*04:05-DQB1*04:01 haplotype was significantly associated with AIH susceptibility (30% vs. 11%, P = 1.2×10−10; odds ratio [OR] = 3.51) and correlated with elevated serum IgG (3042 vs. 2606 mg/dL, P = 0.041) and anti-smooth muscle antigen positivity (77% vs. 34%, P = 0.000006). No associations with HLA-DPB1 alleles were found. The HLA A*24:02 and C*01:02 alleles were associated with disease susceptibility (corrected P = 0.0053 and 0.036, respectively), but this likely constituents of a long ranged haplotype including DRB1*04:05-DQB1*04:01 haplotype. Conversely, the DRB1*15:01-DQB1*06:02 haplotype was associated with protection from both disease onset (5% vs. 13%, P = 0.00057; OR = 0.38) and the development of hepatocellular carcinoma (25% vs. 5%, P = 0.017; OR = 6.81). The frequency of the DRB1*08:03-DQB1*06:01 haplotype was significantly higher in patients who developed hepatic failure (22% vs. 6%, P = 0.034; OR = 4.38). In conclusion, this study established the role of HLA haplotypes in determining AIH susceptibility and progression in the Japanese population. Additional sequencing of the entire HLA region is required to more precisely identify the genetic components of AIH.
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Affiliation(s)
- Takeji Umemura
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | | | - Kaname Yoshizawa
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan; Department of Gastroenterology, NHO Ueda Medical Center, Ueda, Japan
| | - Takefumi Kimura
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Satoru Joshita
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Michiharu Komatsu
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Akihiro Matsumoto
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Eiji Tanaka
- Department of Medicine, Division of Hepatology and Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masao Ota
- Department of Legal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
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Allorecognition of HLA-DP by CD4+ T cells is affected by polymorphism in its alpha chain. Mol Immunol 2014; 59:19-29. [DOI: 10.1016/j.molimm.2013.12.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 11/18/2013] [Accepted: 12/27/2013] [Indexed: 11/21/2022]
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Voorter CEM, Groeneweg M, Joannis MO, Meertens C, Agis F, Tilanus MGJ. Allele and haplotype frequencies of HLA-DPA1 and -DPB1 in the population of Guadeloupe. ACTA ACUST UNITED AC 2014; 83:147-53. [DOI: 10.1111/tan.12271] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 11/15/2013] [Accepted: 11/28/2013] [Indexed: 11/30/2022]
Affiliation(s)
- C. E. M. Voorter
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - M. Groeneweg
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - M.-O. Joannis
- Laboratoire d'Hématologie-Immunologie; Centre Hospitalier Universitaire de Point-à-Pitre/Abymes; Point-à-Pitre Guadeloupe
| | - C. Meertens
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
| | - F. Agis
- Laboratoire d'Hématologie-Immunologie; Centre Hospitalier Universitaire de Point-à-Pitre/Abymes; Point-à-Pitre Guadeloupe
| | - M. G. J. Tilanus
- Transplantation Immunology, Tissue Typing Laboratory; Maastricht University Medical Center; Maastricht the Netherlands
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Roark CL, Anderson KM, Simon LJ, Schuyler RP, Aubrey MT, Freed BM. Multiple HLA epitopes contribute to type 1 diabetes susceptibility. Diabetes 2014; 63:323-31. [PMID: 24357703 PMCID: PMC3868045 DOI: 10.2337/db13-1153] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Disease susceptibility for type 1 diabetes is strongly associated with the inheritance of specific HLA alleles. However, conventional allele frequency analysis can miss HLA associations because many alleles are rare. In addition, disparate alleles that have similar peptide-binding sites, or shared epitopes, can be missed. To identify the HLA shared epitopes associated with diabetes, we analyzed high-resolution genotyping for class I and class II loci. The HLA epitopes most strongly associated with susceptibility for disease were DQB1 A(57), DQA1 V(76), DRB1 H(13), and DRB1 K(71), whereas DPB1 YD(9,57), HLA-B C(67), and HLA-C YY(9,116) were more weakly associated. The HLA epitopes strongly associated with resistance were DQB1 D(57), DQA1 Y(80), DRB1 R(13), and DRB1 A(71). A dominant resistance phenotype was observed for individuals bearing a protective HLA epitope, even in the presence of a susceptibility epitope. In addition, an earlier age of disease onset correlated with significantly greater numbers of susceptibility epitopes and fewer resistance epitopes (P < 0.0001). The prevalence of both DQ and DR susceptibility epitopes was higher in patients than in control subjects and was not exclusively a result of linkage disequilibrium, suggesting that multiple HLA epitopes may work together to increase the risk of developing diabetes.
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Affiliation(s)
- Christina L. Roark
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Corresponding author: Christina L. Roark,
| | - Kirsten M. Anderson
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lucas J. Simon
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ronald P. Schuyler
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Michael T. Aubrey
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Brian M. Freed
- ClinImmune Labs and Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO
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Valdes AM, Varney MD, Erlich HA, Noble JA. Receiver operating characteristic analysis of HLA, CTLA4, and insulin genotypes for type 1 diabetes. Diabetes Care 2013; 36:2504-7. [PMID: 23628620 PMCID: PMC3747897 DOI: 10.2337/dc12-2284] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE This study assessed the ability to distinguish between type 1 diabetes-affected individuals and their unaffected relatives using HLA and single nucleotide polymorphism (SNP) genotypes. RESEARCH DESIGN AND METHODS Eight models, ranging from only the high-risk DR3/DR4 genotype to all significantly associated HLA genotypes and two SNPs mapping to the cytotoxic T-cell-associated antigen-4 gene (CTLA4) and insulin (INS) genes, were fitted to high-resolution class I and class II HLA genotyping data for patients from the Type 1 Diabetes Genetics Consortium collection. Pairs of affected individuals and their unaffected siblings were divided into a "discovery" (n = 1,015 pairs) and a "validation" set (n = 318 pairs). The discriminating performance of various combinations of genetic information was estimated using receiver operating characteristic (ROC) curve analysis. RESULTS The use of only the presence or absence of the high-risk DR3/DR4 genotype achieved very modest discriminating ability, yielding an area under the curve (AUC) of 0.62 in the discovery set and 0.59 in the validation set. The full model-which included HLA information from the class II loci DPB1, DRB1, and DQB1; selected alleles from HLA class I loci A and B; and SNPs from the CTLA4 and INS genes-increased the AUC to 0.74 in the discovery set and to 0.71 in the validation set. A cost-effective alternative is proposed, using genotype information equivalent to typing four SNPs (DR3, DR4-DQB1*03:02, CTLA-4, and INS), which achieved an AUC of 0.72 in the discovery set and 0.69 in the validation set. CONCLUSIONS Genotyping data sufficient to tag DR3, DR4-DQB1*03:02, CTLA4, and INS were shown to distinguish between subjects with type 1 diabetes and their unaffected siblings adequately to achieve clinically utility to identify children in multiplex families to be considered for early intervention.
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Affiliation(s)
- Ana M Valdes
- Academic Rheumatology, University of Nottingham, Nottingham, UK.
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Abstract
PURPOSE OF REVIEW Most asthma starts early in life. Defining phenotypes of asthma at this age is difficult as many preschool children have asthma-like respiratory symptoms. This review discusses progress in defining early wheezing phenotypes and describes genetic factors associated with the age of onset of asthma. RECENT FINDINGS Latent class analyses confirmed transient and persistent wheezing phenotypes, and identified a novel intermediate-onset wheezing phenotype that was strongly associated with atopy and asthma at age 8 years. However, no single cross-sectional or longitudinal definition of respiratory symptoms in childhood strongly predicts asthma later in life. Genome-wide association (GWA) studies have identified a locus on chromosome 17q12-21 (encoding ORMDL3 and GSDMB) as a risk factor for predominantly childhood-onset asthma, but not for atopy, and overall not for adult-onset asthma. Other loci found by GWA studies appear to increase asthma risk both in children and adults. Atopy genes do not explain early-onset asthma. SUMMARY Although most asthma starts early in life, no valid test is able to identify asthma at that age period. GWA studies have provided more insight into the unique and common genetic origins of adult-onset and childhood-onset asthma. The 17q12-21 locus is predominantly associated with childhood-onset asthma.
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Erlich HA, Valdes AM, McDevitt SL, Simen BB, Blake LA, McGowan KR, Todd JA, Rich SS, Noble JA. Next generation sequencing reveals the association of DRB3*02:02 with type 1 diabetes. Diabetes 2013; 62:2618-22. [PMID: 23462545 PMCID: PMC3712046 DOI: 10.2337/db12-1387] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The primary associations of the HLA class II genes, HLA-DRB1 and HLA-DQB1, and the class I genes, HLA-A and HLA-B, with type 1 diabetes (T1D) are well established. However, the role of polymorphism at the HLA-DRB3, HLA-DRB4, and HLA-DRB5 loci remains unclear. In two separate studies, one of 500 subjects and 500 control subjects and one of 366 DRB1*03:01-positive samples from selected multiplex T1D families, we used Roche 454 sequencing with Conexio Genomics ASSIGN ATF 454 HLA genotyping software analysis to analyze sequence variation at these three HLA-DRB loci. Association analyses were performed on the two HLA-DRB loci haplotypes (DRB1-DRB3, -DRB4, or -DRB5). Three common HLA-DRB3 alleles (*01:01, *02:02, *03:01) were observed. DRB1*03:01 haplotypes carrying DRB3*02:02 conferred a higher T1D risk than did DRB1*03:01 haplotypes carrying DRB3*01:01 in DRB1*03:01/*03:01 homozygotes with two DRB3*01:01 alleles (odds ratio [OR] 3.4 [95% CI 1.46-8.09]), compared with those carrying one or two DRB3*02:02 alleles (OR 25.5 [3.43-189.2]) (P = 0.033). For DRB1*03:01/*04:01 heterozygotes, however, the HLA-DRB3 allele did not significantly modify the T1D risk of the DRB1*03:01 haplotype (OR 7.7 for *02:02; 6.8 for *01:01). These observations were confirmed by sequence analysis of HLA-DRB3 exon 2 in a targeted replication study of 281 informative T1D family members and 86 affected family-based association control (AFBAC) haplotypes. The frequency of DRB3*02:02 was 42.9% in the DRB1*03:01/*03:01 patients and 27.6% in the DRB1*03:01/*04 (P = 0.005) compared with 22.6% in AFBAC DRB1*03:01 chromosomes (P = 0.001). Analysis of T1D-associated alleles at other HLA loci (HLA-A, HLA-B, and HLA-DPB1) on DRB1*03:01 haplotypes suggests that DRB3*02:02 on the DRB1*03:01 haplotype can contribute to T1D risk.
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Abstract
Genetic susceptibility to type 1 diabetes (T1D) has been a subject of intensive study for nearly four decades. This article will present the history of these studies, beginning with observations of the Human Leukocyte Antigen (HLA) association in the 1970s, through the advent of DNA-based genotyping methodologies, through recent large, international collaborations and genome-wide association studies. More than 40 genetic loci have been associated with T1D in multiple studies; however, the HLA region, with its multiple genes and extreme polymorphism at those loci, remains by far the greatest contributor to the genetic susceptibility to T1D. Even after decades of study, the complete story has yet to unfold, and exact mechanisms by which HLA and other associated loci confer T1D susceptibility remain elusive.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA.
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Abstract
Genetic susceptibility to type 1 diabetes (T1D) has been a subject of intensive study for nearly four decades. This article will present the history of these studies, beginning with observations of the Human Leukocyte Antigen (HLA) association in the 1970s, through the advent of DNA-based genotyping methodologies, through recent large, international collaborations and genome-wide association studies. More than 40 genetic loci have been associated with T1D in multiple studies; however, the HLA region, with its multiple genes and extreme polymorphism at those loci, remains by far the greatest contributor to the genetic susceptibility to T1D. Even after decades of study, the complete story has yet to unfold, and exact mechanisms by which HLA and other associated loci confer T1D susceptibility remain elusive.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, California 94609, USA.
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Lipner EM, Tomer Y, Noble JA, Monti MC, Lonsdale JT, Corso B, Stewart WCL, Greenberg DA. HLA class I and II alleles are associated with microvascular complications of type 1 diabetes. Hum Immunol 2013; 74:538-44. [PMID: 23376458 PMCID: PMC3686564 DOI: 10.1016/j.humimm.2013.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 12/13/2012] [Accepted: 01/14/2013] [Indexed: 12/25/2022]
Abstract
Although HLA alleles are associated with type 1 diabetes, association with microvascular complications remains controversial. We tested HLA association with complications in multiplex type 1 diabetes families. Probands from 425 type 1 diabetes families from the Human Biological Data Interchange (HBDI) collection were analyzed. The frequencies of specific HLA alleles in patients with complications were compared with the frequencies in complications-free patients. The complications we examined were: retinopathy, neuropathy, and nephropathy. We used logistic regression models with covariates to estimate odds ratios. We found that the DRB1*03:01 allele is a protective factor for complications (OR=0.58; p=0.03), as is the DQA1*05:01-DQB1*02:01 haplotype found in linkage disequilibrium with DRB1*03:01 (OR=0.59; p=0.031). The DRB1*04:01 allele showed no evidence of association (OR=1.13; p=0.624), although DRB1*04:01 showed suggestive evidence when the carriers of the protective DRB1*03:01 were removed from the analysis. The class II DQA1*03:01-DQB1*03:02 haplotype was not associated with complications, but the class I allele B*39:06 (OR=3.27; p=0.008) suggested a strong positive association with complications. Our results show that in type 1 diabetes patients, specific HLA alleles may be involved in susceptibility to, or protection from, microvascular complications.
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Affiliation(s)
- E M Lipner
- Department of Epidemiology, Columbia University, Mailman School of Public Health, New York, NY, USA
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Affiliation(s)
- Henry A Erlich
- Department of Medicine, University of Ottawa and The Ottawa Hospital, Ottawa, Ontario, Canada.
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Chen D, Juko-Pecirep I, Hammer J, Ivansson E, Enroth S, Gustavsson I, Feuk L, Magnusson PKE, McKay JD, Wilander E, Gyllensten U. Genome-wide association study of susceptibility loci for cervical cancer. J Natl Cancer Inst 2013; 105:624-33. [PMID: 23482656 DOI: 10.1093/jnci/djt051] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cervical carcinoma has a heritable genetic component, but the genetic basis of cervical cancer is still not well understood. METHODS We performed a genome-wide association study of 731 422 single nucleotide polymorphisms (SNPs) in 1075 cervical cancer case subjects and 4014 control subjects and replicated it in 1140 case subjects and 1058 control subjects. The association between top SNPs and cervical cancer was estimated by odds ratios (ORs) and 95% confidence intervals (CIs) with unconditional logistic regression. All statistical tests were two-sided. RESULTS Three independent loci in the major histocompatibility complex (MHC) region at 6p21.3 were associated with cervical cancer: the first is adjacent to the MHC class I polypeptide-related sequence A gene (MICA) (rs2516448; OR = 1.42, 95% CI = 1.31 to 1.54; P = 1.6×10(-18)); the second is between HLA-DRB1 and HLA-DQA1 (rs9272143; OR = 0.67, 95% CI = 0.62 to 0.72; P = 9.3×10(-24)); and the third is at HLA-DPB2 (rs3117027; OR=1.25, 95% CI = 1.15 to 1.35; P = 4.9×10(-8)). We also confirmed previously reported associations of B*0702 and DRB1*1501-DQB1*0602 with susceptibility to and DRB1*1301-DQA1*0103-DQB1*0603 with protection against cervical cancer. The three new loci are statistically independent of these specific human leukocyte antigen alleles/haplotypes. MICA encodes a membrane-bound protein that acts as a ligand for NKG2D to activate antitumor effects. The risk allele of rs2516448 is in perfect linkage disequilibrium with a frameshift mutation (A5.1) of MICA, which results in a truncated protein. Functional analysis shows that women carrying this mutation have lower levels of membrane-bound MICA. CONCLUSIONS Three novel loci in the MHC may affect susceptibility to cervical cancer in situ, including the MICA-A5.1 allele that may cause impaired immune activation and increased risk of tumor development.
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Affiliation(s)
- Dan Chen
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, 751 85 Uppsala, Sweden
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Munger KL, Levin LI, Massa J, Horst R, Orban T, Ascherio A. Preclinical serum 25-hydroxyvitamin D levels and risk of type 1 diabetes in a cohort of US military personnel. Am J Epidemiol 2013; 177:411-9. [PMID: 23380046 DOI: 10.1093/aje/kws243] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To determine whether serum levels of 25-hydroxyvitamin D (25(OH)D) in young adults are associated with risk of type 1 diabetes mellitus (T1D), we conducted a prospective, nested case-control study among US active-duty military personnel with serum in the US Department of Defense Serum Repository, identifying 310 T1D cases diagnosed between 1997 and 2009 with at least 2 serum samples collected before disease onset and 613 controls matched to cases on age, sex, race/ethnicity, branch of military service, and dates of serum collection. Conditional logistic regression was used to estimate rate ratios and 95% confidence intervals. Among non-Hispanic whites, those with average 25(OH)D levels of ≥ 100 nmol/L had a 44% lower risk of developing T1D than those with average 25(OH)D levels < 75 nmol/L (rate ratio = 0.56, 95% confidence interval: 0.35, 0.90, P for trend = 0.03) over an average follow-up of 5.4 years. In quintile analyses, T1D risk was highest among individuals whose 25(OH)D levels were in the lowest 20% of those measured. There was no association between 25(OH)D levels and risk of T1D among non-Hispanic blacks or Hispanics. Low 25(OH)D levels may predispose healthy, young, non-Hispanic white adults to the development of T1D.
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Affiliation(s)
- Kassandra L Munger
- Department of Nutrition, Harvard School of Public Health, Harvard University, Boston, MA 02115, USA.
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Genetic study confirms association of HLA-DPA1(∗)01:03 subtype with ankylosing spondylitis in HLA-B27-positive populations. Hum Immunol 2013; 74:764-7. [PMID: 23459078 DOI: 10.1016/j.humimm.2013.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 01/15/2013] [Accepted: 02/19/2013] [Indexed: 11/21/2022]
Abstract
The association of human leukocyte antigen (HLA)-B27 with ankylosing spondylitis (AS) has been known for over 38 years. However, it is not the only gene associated with AS. The aim of this study was to confirm the association of HLA markers around HLA-DPA1/DPB1 region with AS in HLA-B27 positive populations. Five SNPs (rs422544, rs6914849, rs92777535, rs3128968 and rs2295119) from the HLA-DPA1/DPB1 region were genotyped in 340 individuals HLA-B27-positive from Portugal (137 AS patients and 203 healthy controls). Characterizations of HLA-DPA1/DPB1 alleles were also performed. rs422544 revealed a significant association with AS (P<0.05) and sliding windows (SW) analysis showed association of some groups of adjacent SNPs within HLA-DPA1/DPB1 region with AS (P<0.05). We also found association of the HLA-DPA1(∗)01:03 allele with AS (P<0.05). This is the first study that confirms the association of HLA markers and haplotypes around HLA-DPA1 and HLA-DPB1 with AS.
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Raha O, Sarkar B, Lakkakula BVKS, Pasumarthy V, Godi S, Chowdhury S, Raychaudhuri P, Vadlamudi RR. HLA class II SNP interactions and the association with type 1 diabetes mellitus in Bengali speaking patients of Eastern India. J Biomed Sci 2013; 20:12. [PMID: 23441825 PMCID: PMC3599455 DOI: 10.1186/1423-0127-20-12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 02/25/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Several studies have demonstrated a fundamental role for the HLA in the susceptibility of, or protection to, type 1 diabetes mellitus (T1DM). However, this has not been adequately studied in Asian Indian populations. To assess the frequency of HLA class II (DPA1, DPB1, DQA1, DQB1 and DRB1) associated to susceptibility or protection toT1DM in a Bengali population of India with diabetes. RESULTS Single nucleotide polymorphism study. The HLA genotyping was performed by a polymerase chain reaction followed by their HLA-DP, DQ, and DRB1 genotypes and haplotypes by sequencing method. The results are studied by Plink software. The χ2 tests were used for the inferential statistics. To our knowledge, this study is the first of a kind which has attempted to check the HLA association with T1DM by SNPs analysis. The study recruited 151 patients with T1DM and same number of ethno-linguistic, sex matched non-diabetic controls. The present study found a significant SNP rs7990 of HLA-DQA1 (p = 0.009) negative correlation, again indicating that risk from HLA is considerably more with T1DM. CONCLUSIONS This study demonstrates that the HLA class-II alleles play a major role in genetic basis of T1DM.
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Affiliation(s)
- Oindrila Raha
- Anthropological Survey of India, Kolkata, West Bengal 700016, India
| | - Biswanath Sarkar
- Anthropological Survey of India, Kolkata, West Bengal 700016, India
| | - Bhaskar VKS Lakkakula
- Department of Biomedical Sciences, Sri Ramachandra University, Chennai 600 116, India
| | - Veerraju Pasumarthy
- Department of Human Genetics, Andhra University, Visakhapatnam 530003, India
| | - Sudhakar Godi
- Department of Human Genetics, Andhra University, Visakhapatnam 530003, India
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Díaz-Peña R, Aransay AM, Bruges-Armas J, López-Vázquez A, Rodríguez-Ezpeleta N, Mendibil I, Sánchez A, Torre-Alonso JC, Bettencourt BF, Mulero J, Collantes E, López-Larrea C. Fine mapping of a major histocompatibility complex in ankylosing spondylitis: association of the HLA-DPA1 and HLA-DPB1 regions. ACTA ACUST UNITED AC 2013; 63:3305-12. [PMID: 21769851 DOI: 10.1002/art.30555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
OBJECTIVE To investigate the potential association of major histocompatibility complex (MHC) markers other than HLA-B27 with ankylosing spondylitis (AS). METHODS A total of 603 patients with AS and 542 healthy control subjects, all of whom were HLA-B27 positive, were selected for this study based on clinical criteria. First, high-density genotyping across the MHC region (2,360 single-nucleotide polymorphisms [SNPs]) was performed in a cohort of 191 patients and 241 control subjects. After a fine-mapping study, 5 SNPs from the HLA-DPA1/DPB1 region were validated in a second cohort of 412 patients with AS and 301 healthy control subjects. RESULTS Seventeen SNPs located within or near the HLA-DPA1 and HLA-DPB1 loci showed association with AS (P = 1.38 × 10⁻⁵ to 0.05). In addition, multimarker tests, both linkage disequilibrium and sliding windows, showed association of some groups of adjacent SNPs within the HLA-DPA1/DPB1 region with AS (P = 1.0 × 10⁻⁴ to 3.96 × 10⁻⁷). We validated the association by genotyping 5 SNPs from the DPA1/DPB1 region in an additional cohort and obtained P values from 6.42 × 10⁻⁵ to 0.01 in the analysis of the combined cohorts. Subtyping analysis of HLA-DPA1 and HLA-DPB1 showed that HLA-DPA1*01:03, A1*02:01, and B1*13:01 were the subtypes most susceptible to AS. CONCLUSION HLA markers and linkage disequilibrium blocks near HLA-DPA1 and HLA-DPB1 are statistically associated with AS. We identified a region located around the HLA-DPA1 and HLA-DPB1 loci associated with AS, another region within the MHC that is different from HLA-B27.
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Raha O, Sarkar B, Veerraju P, Sudhakar G, Raychaudhuri P, Mukhopadhyay S, Rao VR. Role of HLA Class II Loci Polymorphism in the Manifestation of Type 1 Diabetes in a Bengali Indian Patient Population. Genet Test Mol Biomarkers 2013; 17:52-61. [DOI: 10.1089/gtmb.2012.0221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Godi Sudhakar
- Department of Human Genetics, Andhra University, Visakhapatnam, India
| | - Pradip Raychaudhuri
- Endocrinology Department, Calcutta Medical College and Hospital, Kolkata, India
| | - Soma Mukhopadhyay
- Genetics Lab, Netaji Subhash Chandra Bose Cancer Research Institute, Kolkata, India
| | - Vadlamudi Raghavendra Rao
- Biochemical and Molecular Genetics Lab, Department of Anthropology, University of Delhi, Delhi, India
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Valdes AM, Erlich HA, Carlson J, Varney M, Moonsamy PV, Noble JA. Use of class I and class II HLA loci for predicting age at onset of type 1 diabetes in multiple populations. Diabetologia 2012; 55:2394-401. [PMID: 22706720 PMCID: PMC3639291 DOI: 10.1007/s00125-012-2608-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/16/2012] [Indexed: 12/17/2022]
Abstract
AIMS/HYPOTHESIS The study aimed to assess, in multiple populations, the role of HLA alleles on early and late age at onset of type 1 diabetes. METHODS Stepwise linear regression models were used to determine which HLA class I and class II risk alleles to include. High-resolution genotyping data for patients from the Type 1 Diabetes Genetics Consortium (T1DGC) collection (n = 2,278) and four independent cohorts from Denmark, Sardinia and the USA (Human Biological Data Interchange [HBDI] and Joslin Diabetes Center) (n = 1,324) (total n = 3,602) were used to assess the role of HLA variation on age of onset and predict early onset (age ≤ 5 years) and late onset (age ≥ 15 years) of type 1 diabetes. RESULTS In addition to carriage of HLA class I alleles A*24:02, B*39:06, B*44:03 and B*18:01, HLA class II DRB1-DQB1 loci significantly contributed to age at onset, explaining 3.4% of its variance in the combined data. HLA genotypes, together with sex, were able to predict late onset in all cohorts studied, with AUC values ranging from 0.58 to 0.63. Similar AUC values (0.59-0.70) were obtained for early onset for most cohorts, except in the Sardinian study, in which none of the models tested had significant predictive power. CONCLUSIONS/INTERPRETATION HLA associations with age of onset are consistent across most white populations and HLA information can predict some of the risk of early and late onset of type 1 diabetes. Considerable heterogeneity was observed between Sardinian and other populations, particularly with regard to early age of onset.
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Affiliation(s)
- A M Valdes
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, London SE1 7EH, UK.
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50
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Chang DY, Luo H, Zhou XJ, Chen M, Zhao MH. Association of HLA genes with clinical outcomes of ANCA-associated vasculitis. Clin J Am Soc Nephrol 2012; 7:1293-9. [PMID: 22595829 DOI: 10.2215/cjn.13071211] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
BACKGROUND AND OBJECTIVES The HLA system plays a central role in the distinction between self antigens and non-self antigens. This study aimed to investigate the association between HLA genes and the outcomes of patients with ANCA-associated vasculitis (AAV). DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS This study recruited 152 consecutive Chinese patients with AAV. The predictive value of the HLA alleles for renal outcome, response to treatment, and all-cause mortality were analyzed. RESULTS The proportion of patients with treatment failure was significantly higher in DRB1*0405-positive patients than in DRB1*0405-negative patients (41.7% versus 12.9%; P=0.008; corrected P=0.02). After adjusting for the other potential predictors, DRB1*0405 was still an independent predictor for the poor response to treatment (hazard ratio [HR], 5.91; 95% confidence interval [95% CI], 1.23-28.52; P=0.03). Renal survival was significantly worse in patients with DRB1*0405 than those without DRB1*0405 (P<0.001; corrected P<0.001). After adjusting for the other potential predictors, DRB1*0405 was still an independent predictor for ESRD (HR, 5.50; 95% CI, 2.18-13.88; P<0.001). The probability of all-cause mortality in patients with DPB1*0402 was significantly higher than those without DPB1*0402 (P=0.02; corrected P=0.04). After adjusting for the other potential predictors, DPB1*0402 was still an independent predictor for all-cause mortality (HR, 2.52; 95% CI, 1.21-5.28; P=0.01). CONCLUSIONS In AAV patients, DRB1*0405 might be an independent risk factor for the poor response to treatment and the deterioration of renal function, whereas DPB1*0402 might be an independent risk factor for all-cause mortality.
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Affiliation(s)
- Dong-yuan Chang
- Renal Division, Department of Medicine, Peking University First Hospital, Institute of Nephrology, Peking University, Key Laboratory of Renal Disease, Ministry of Health of China, and Key Laboratory of CKD Prevention and Treatment, Ministry of Education of China, Beijing, China
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