1
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Amdare NP, Shultz LD, Greiner DL, DiLorenzo TP. Human insulin as both antigen and protector in type 1 diabetes. Eur J Immunol 2024:e2350949. [PMID: 38778498 DOI: 10.1002/eji.202350949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/25/2024]
Abstract
Type 1 diabetes (T1D) is characterized by T-cell responses to islet antigens. Investigations in humans and the nonobese diabetic (NOD) mouse model of T1D have revealed that T-cell reactivity to insulin plays a central role in the autoimmune response. As there is no convenient NOD-based model to study human insulin (hIns) or its T-cell epitopes in the context of spontaneous T1D, we developed a NOD mouse strain transgenically expressing hIns in islets under the control of the human regulatory region. Female NOD.hIns mice developed T1D at approximately the same rate and overall incidence as NOD mice. Islet-infiltrating T cells from NOD.hIns mice recognized hIns peptides; both CD8 and CD4 T-cell epitopes were identified. We also demonstrate that islet-infiltrating T cells from HLA-transgenic NOD.hIns mice can be used to identify potentially patient-relevant hIns T-cell epitopes. Besides serving as an antigen, hIns was expressed in the thymus of NOD.hIns mice and could serve as a protector against T1D under certain circumstances, as previously suggested by genetic studies in humans. NOD.hIns mice and related strains facilitate human-relevant epitope discovery efforts and the investigation of fundamental questions that cannot be readily addressed in humans.
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Affiliation(s)
- Nitin P Amdare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Dale L Greiner
- Program in Molecular Medicine, Diabetes Center of Excellence, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Medicine (Division of Endocrinology and Diabetes), Albert Einstein College of Medicine, Bronx, New York, USA
- Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA
- The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York, USA
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2
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Patil AR, Schug J, Liu C, Lahori D, Descamps HC, Naji A, Kaestner KH, Faryabi RB, Vahedi G. Modeling type 1 diabetes progression using machine learning and single-cell transcriptomic measurements in human islets. Cell Rep Med 2024; 5:101535. [PMID: 38677282 PMCID: PMC11148720 DOI: 10.1016/j.xcrm.2024.101535] [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: 08/09/2023] [Revised: 01/22/2024] [Accepted: 04/07/2024] [Indexed: 04/29/2024]
Abstract
Type 1 diabetes (T1D) is a chronic condition in which beta cells are destroyed by immune cells. Despite progress in immunotherapies that could delay T1D onset, early detection of autoimmunity remains challenging. Here, we evaluate the utility of machine learning for early prediction of T1D using single-cell analysis of islets. Using gradient-boosting algorithms, we model changes in gene expression of single cells from pancreatic tissues in T1D and non-diabetic organ donors. We assess if mathematical modeling could predict the likelihood of T1D development in non-diabetic autoantibody-positive donors. While most autoantibody-positive donors are predicted to be non-diabetic, select donors with unique gene signatures are classified as T1D. Our strategy also reveals a shared gene signature in distinct T1D-associated models across cell types, suggesting a common effect of the disease on transcriptional outputs of these cells. Our study establishes a precedent for using machine learning in early detection of T1D.
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Affiliation(s)
- Abhijeet R Patil
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jonathan Schug
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chengyang Liu
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Deeksha Lahori
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Hélène C Descamps
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ali Naji
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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3
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Liang D, Liu L, Qi Y, Nan F, Huang J, Tang S, Tang J, Chen N. Jin-Gui-Shen-Qi Wan alleviates fibrosis in mouse diabetic nephropathy via MHC class II. JOURNAL OF ETHNOPHARMACOLOGY 2024; 324:117745. [PMID: 38228231 DOI: 10.1016/j.jep.2024.117745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/18/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Jin-Gui-Shen-Qi Wan (JGSQW) is a traditional Chinese medicine formula that has been traditionally used to alleviate urinary system ailments such as frequent urination and polyuria. Clinical studies have indicated that when combined with hypoglycaemic drugs, JGSQW exhibits a synergistic effect and can improve diabetic nephropathy (DN), yet its underlying mechanism and targets remain unclear. AIM OF THE STUDY This study aims to investigate the therapeutic efficacy of JGSQW and its underlying mechanisms using a DN db/db mouse model. MATERIALS AND METHODS Ultrahigh-performance liquid chromatography coupled with mass spectrometry was utilized to analyse the primary active compounds, blood levels, and pharmacokinetics of JGSQW. Additionally, the therapeutic effects of JGSQW and metformin on blood glucose levels, lipid levels, renal function, and renal pathology in diabetic nephropathy mice were investigated using a db/db mouse model. Proteomic analysis was carried out to identify the primary target of JGSQW in treating DN. The mechanism of action was verified by western blotting, immunohistochemistry, and immunofluorescence. Then, molecular docking and molecular dynamics, transfection, drug affinity responsive target stability (DARTS) assay and cell thermal migration assay (CETSA) further validated the targeted binding effect. RESULTS JGSQW combined with metformin significantly improved the blood glucose levels, blood lipids, renal function, and renal pathology of DN mice. JGSQW mainly exerted its therapeutic effect on DN by targeting major histocompatibility complex class II (MHC class II) molecules. Immunohistochemistry results showed that JGSQW inhibited the expression of collagen I, fibronectin, and alpha smooth muscle actin (α-SMA) expression. Immunofluorescence and Western blot results showed that JGSQW inhibited the expression of H2-Ab1 and H2-Aa, which are MHC class II molecules, thereby suppressing CD4+ T-cell infiltration and improving diabetic kidney fibrosis. The binding ability of paeoniflorin to H2-Aa was predicted and verified by molecular, DARTS, and CETSA assays. Treatment with 80 μM paeoniflorin effectively alleviated high glucose-induced injury in the MPC-5 injury model. H2-Aa was overexpressed at this model concentration, and Western blotting further confirmed that paeoniflorin reduced glomerular podocyte fibrosis by regulating H2-Aa. CONCLUSIONS JGSQW combined with metformin may have a synergistic effect to alleviates renal fibrosis in diabetic nephropathy by downregulating immune complex MHC class II molecules and attenuating the antigen presentation effect of MHC class II on CD4.
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Affiliation(s)
- Dan Liang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Lu Liu
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Yulin Qi
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Feng Nan
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Ju Huang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Shiyun Tang
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Jianyuan Tang
- TCM Regulating Metabolic Diseases Key Laboratory of Sichuan Province, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China.
| | - Nianzhi Chen
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, China.
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4
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Wang G, Warrington NM, Evans DM. Partitioning genetic effects on birthweight at classical human leukocyte antigen loci into maternal and fetal components, using structural equation modelling. Int J Epidemiol 2024; 53:dyad142. [PMID: 37831898 PMCID: PMC10859143 DOI: 10.1093/ije/dyad142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/03/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Single nucleotide polymorphisms in the human leukocyte antigen (HLA) region in both maternal and fetal genomes have been robustly associated with birthweight (BW) in previous genetic association studies. However, no study to date has partitioned the association between BW and classical HLA alleles into maternal and fetal components. METHODS We used structural equation modelling (SEM) to estimate the maternal and fetal effects of classical HLA alleles on BW. Our SEM leverages the data structure of the UK Biobank (UKB), which includes ∼270 000 participants' own BW and/or the BW of their firstborn child. RESULTS We show via simulation that our model yields asymptotically unbiased estimates of the maternal and fetal allelic effects on BW and appropriate type I error rates, in contrast to simple regression models. Asymptotic power calculations show that we have sufficient power to detect moderate-sized maternal or fetal allelic effects of common HLA alleles on BW in the UKB. Applying our SEM to imputed classical HLA alleles and own and offspring BW from the UKB replicated the previously reported association at the HLA-C locus and revealed strong evidence for maternal (HLA-A*03:01, B*35:01, B*39:06, P <0.001) and fetal allelic effects (HLA-B*39:06, P <0.001) of non-HLA-C alleles on BW. CONCLUSIONS Our model yields asymptotically unbiased estimates, appropriate type I error rates and appreciable power to estimate maternal and fetal effects on BW. These novel allelic associations between BW and classical HLA alleles provide insight into the immunogenetics of fetal growth in utero.
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Affiliation(s)
- Geng Wang
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Nicole M Warrington
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, Norwegian University of Science and Technology, Trondheim, Norway
| | - David M Evans
- Frazer Institute, Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
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5
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Noble JA, Besançon S, Sidibé AT, Rozemuller EH, Rijkers M, Dadkhodaie F, de Bruin H, Kooij J, Martin HRN, Ogle GD, Mack SJ. Complete HLA genotyping of type 1 diabetes patients and controls from Mali reveals both expected and novel disease associations. HLA 2024; 103:e15319. [PMID: 38226399 PMCID: PMC10863981 DOI: 10.1111/tan.15319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 11/27/2023] [Indexed: 01/17/2024]
Abstract
HLA genotyping was performed on 99 type 1 diabetes (T1D) patients and 200 controls from Mali. Next-generation sequencing of the classical HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQA1, -DQB1, -DPA1, and -DPB1 loci revealed strong T1D association for all loci except HLA-C and -DPA1. Class II association is stronger than class I association, with most observed associations predisposing or protective as expected based on previous studies. For example, HLA-DRB1*03:01, HLA-DRB1*09:01, and HLA-DRB1*04:05 predispose for T1D, whereas HLA-DRB1*15:03 is protective. HLA-DPB1*04:02 (OR = 12.73, p = 2.92 × 10-05 ) and HLA-B*27:05 (OR = 21.36, p = 3.72 × 10-05 ) appear highly predisposing, although previous studies involving multiple populations have reported HLA-DPB1*04:02 as T1D-protective and HLA-B*27:05 as neutral. This result may reflect the linkage disequilibrium between alleles on the extended HLA-A*24:02~HLA-B*27:05~HLA-C*02:02~HLA-DRB1*04:05~HLA-DRB4*01:03~HLA-DQB1*02:02~HLA-DQA1*02:01~HLA-DPB1*04:02~HLA-DPA1*01:03 haplotype in this population rather than an effect of either allele itself. Individual amino acid (AA) analyses are consistent with most T1D association attributable to HLA class II rather than class I in this data set. AA-level analyses reveal previously undescribed differences of the HLA-C locus from the HLA-A and HLA-B loci, with more polymorphic positions, spanning a larger portion of the gene. This may reflect additional mechanisms for HLA-C to influence T1D risk, for example, through expression differences or through its role as the dominant ligand for killer cell immunoglobulin-like receptors (KIR). Comparison of these data to those from larger studies and on other populations may facilitate T1D prediction and help elucidate elusive mechanisms of how HLA contributes to T1D risk and autoimmunity.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, California, USA
- Department of Pediatrics, University of California, San Francisco, Oakland, California, USA
| | | | | | | | | | | | | | | | - Harper R N Martin
- Children's Hospital Oakland Research Institute, Oakland, California, USA
| | - Graham D Ogle
- Life for a Child Program, Diabetes Australia, Glebe, New South Wales, Australia
- Sydney Medical School, University of Sydney, Sydney, New South Wales, Australia
| | - Steven J Mack
- Department of Pediatrics, University of California, San Francisco, Oakland, California, USA
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Forbes S, Halpin A, Lam A, Grynoch D, Parker R, Hidalgo L, Bigam D, Anderson B, Dajani K, Kin T, O'Gorman D, Senior PA, Campbell P, Shapiro AJ. Islet transplantation outcomes in type 1 diabetes and transplantation of HLA-DQ8/DR4: results of a single-centre retrospective cohort in Canada. EClinicalMedicine 2024; 67:102333. [PMID: 38169703 PMCID: PMC10758748 DOI: 10.1016/j.eclinm.2023.102333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 01/05/2024] Open
Abstract
Background In solid organ transplantation, HLA matching between donor and recipient is associated with superior outcomes. In islet transplantation, an intervention for Type 1 diabetes, HLA matching between donor and recipient is not performed as part of allocation. Susceptibility to Type 1 diabetes is associated with the presence of certain HLA types. This study was conducted to determine the impact of these susceptibility antigens on islet allograft survival. Methods This is a single-centre retrospective cohort study. This cohort of transplant recipients (n = 268) received islets from 661 donor pancreases between March 11th, 1999 and August 29th, 2018 at the University of Alberta Hospital (Edmonton, AB, Canada). The frequency of the Type 1 diabetes susceptibility HLA antigens (HLA-A24, -B39, -DQ8, -DQ2 and-DQ2-DQA1∗05) in recipients and donors were determined. Recipient and donor HLA antigens were examined in relation to time to first C-peptide negative status/graft failure or last observation point. Taking into account multiple transplants per patient, we fitted a Gaussian frailty survival analysis model with baseline hazard function stratified by transplant number, adjusted for cumulative islet dose and other confounders. Findings Across all transplants recipients of donors positive for HLA-DQ8 had significantly better graft survival (adjusted HRs 0.33 95% CI 0.17-0.66; p = 0.002). At first transplant only, donors positive for HLA-DQ2-DQA1∗05 had inferior graft survival (adjusted HR 1.96 95% CI 1.10-3.46); p = 0.02), although this was not significant in the frailty analysis taking multiple transplants into account (adjusted HR 1.46 95% CI 0.77-2.78; p = 0.25). Other HLA antigens were not associated with graft survival after adjustment for confounders. Interpretation Our findings suggest islet transplantation from HLA-DQ8 donors is associated with superior graft outcomes. A donor positive for HLA-DQ2-DQA1∗05 at first transplant was associated with inferior graft survival but not when taking into account multiple transplants per recipient. The relevance of HLA-antigens on organ allocation needs further evaluation and inclusion in islet transplant registries and additional observational and interventional studies to evaluate the role of HLA-DQ8 in islet graft survival are required. Funding None.
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Affiliation(s)
- Shareen Forbes
- Clinical Islet Transplant Programme, University of Alberta, Edmonton, Canada
- Department of Surgery, University of Alberta, Edmonton, Canada
- Queen's Medical Research Institute, BHF Centre for Cardiovascular Science, University of Edinburgh, Scotland, UK
| | - Anne Halpin
- Alberta Precision Laboratories, University of Alberta, Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Anna Lam
- Clinical Islet Transplant Programme, University of Alberta, Edmonton, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, University of Alberta, Edmonton, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Don Grynoch
- Alberta Precision Laboratories, University of Alberta, Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - Richard Parker
- Edinburgh Clinical Trials Unit, Usher Institute, University of Edinburgh, Scotland, UK
| | - Luis Hidalgo
- Department of Surgery, University of Wisconsin, Madison, WI, USA
| | - David Bigam
- Department of Surgery, University of Alberta, Edmonton, Canada
| | - Blaire Anderson
- Department of Surgery, University of Alberta, Edmonton, Canada
| | - Khaled Dajani
- Department of Surgery, University of Alberta, Edmonton, Canada
| | - Tatsuya Kin
- Clinical Islet Transplant Programme, University of Alberta, Edmonton, Canada
| | - Doug O'Gorman
- Clinical Islet Transplant Programme, University of Alberta, Edmonton, Canada
| | - Peter A. Senior
- Clinical Islet Transplant Programme, University of Alberta, Edmonton, Canada
- Division of Endocrinology and Metabolism, Department of Medicine, University of Alberta, Edmonton, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
| | - Patricia Campbell
- Alberta Precision Laboratories, University of Alberta, Laboratory Medicine and Pathology, University of Alberta, Edmonton, Canada
| | - A.M. James Shapiro
- Clinical Islet Transplant Programme, University of Alberta, Edmonton, Canada
- Department of Surgery, University of Alberta, Edmonton, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, Canada
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Gilles A, Hu L, Virdis F, Sant’Angelo DB, Dimitrova N, Hedrick JA, Denzin LK. The MHC Class II Antigen-Processing and Presentation Pathway Is Dysregulated in Type 1 Diabetes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1630-1642. [PMID: 37811896 PMCID: PMC10872857 DOI: 10.4049/jimmunol.2300213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023]
Abstract
Peptide loading of MHC class II (MHCII) molecules is facilitated by HLA-DM (DM), which catalyzes CLIP release, stabilizes empty MHCII, and edits the MHCII-bound peptide repertoire. HLA-DO (DO) binds to DM and modulates its activity, resulting in an altered set of peptides presented at the cell surface. MHCII-peptide presentation in individuals with type 1 diabetes (T1D) is abnormal, leading to a breakdown in tolerance; however, no direct measurement of the MHCII pathway activity in T1D patients has been performed. In this study, we measured MHCII Ag-processing pathway activity in humans by determining MHCII, MHCII-CLIP, DM, and DO levels by flow cytometry for peripheral blood B cells, dendritic cells, and monocytes from 99 T1D patients and 97 controls. Results showed that MHCII levels were similar for all three APC subsets. In contrast, MHCII-CLIP levels, independent of sex, age at blood draw, disease duration, and diagnosis age, were significantly increased for all three APCs, with B cells showing the largest increase (3.4-fold). DM and DO levels, which usually directly correlate with MHCII-CLIP levels, were unexpectedly identical in T1D patients and controls. Gene expression profiling on PBMC RNA showed that DMB mRNA was significantly elevated in T1D patients with residual C-peptide. This resulted in higher levels of DM protein in B cells and dendritic cells. DO levels were also increased, suggesting that the MHCII pathway maybe differentially regulated in individuals with residual C-peptide. Collectively, these studies show a dysregulation of the MHCII Ag-processing pathway in patients with T1D.
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Affiliation(s)
- Ambroise Gilles
- Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, Current address: Division of Plastic Surgery, Department of Surgery, Penn State Health Milton S. Hershey Medical Center, Hershey, PA
| | - Lan Hu
- Oncology Informatics & Genomics, Philips North America, Cambridge, MA, 02141
| | - Francesca Virdis
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901, Current address: Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Monserrato, Cagliari, Italy
| | - Derek B. Sant’Angelo
- Child Health Institute of New Jersey, Department of Pediatrics and Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, and Graduate School of Biomedical Sciences, The State University of NJ, New Brunswick, NJ, 08901
| | - Nevenka Dimitrova
- Oncology Informatics and Genomics, Philips North America, Valhalla, NY 10598, Current address: Memorial Sloan-Kettering Cancer Center, New York, NY, 10065
| | | | - Lisa K. Denzin
- Child Health Institute of New Jersey, Department of Pediatrics and Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, and Graduate School of Biomedical Sciences, The State University of NJ, New Brunswick, NJ, 08901
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Liao WL, Huang YN, Chang YW, Liu TY, Lu HF, Tiao ZY, Su PH, Wang CH, Tsai FJ. Combining polygenic risk scores and human leukocyte antigen variants for personalized risk assessment of type 1 diabetes in the Taiwanese population. Diabetes Obes Metab 2023; 25:2928-2936. [PMID: 37455666 DOI: 10.1111/dom.15187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
AIMS To analyse the genome-wide association study (GWAS) data of patients with type 1 diabetes mellitus (T1D) in order to develop a risk score for the genetic effects on T1D risk and age at diagnosis in the Taiwanese population. MATERIALS AND METHODS We selected 610 patients with T1D and 2511 healthy individuals from an electronic medical record database of more than 300 000 individuals with genetic information, analysed their GWAS data, and developed a polygenic risk score (PRS). RESULTS The PRS, based on 149 selected single-nucleotide polymorphisms, could effectively predict T1D risk. A PRS increase was associated with increased T1D risk (odds ratio [OR] 2.09, 95% confidence interval [CI] 1.72-2.55). Moreover, a 1-unit increase in standardized T1D PRS decreased the age at diagnosis by 0.74 years. Combined PRS and human leukocyte antigen (HLA) DQA1*03:02-DQA1*05:01 genotypes could accurately predict T1D risk. In multivariable models, HLA variants and PRS were independent risk factors for T1D risk (OR 3.76 [95% CI 1.54-9.16] and 1.71 [95% CI 1.37-2.13] for HLA DQA1*03:02-DQA1*05:01 and PRS, respectively). In a limited study population of those aged ≤18 years, PRS remained significantly associated with T1D risk. The association between T1D PRS and age at diagnosis was more obvious among males and patients aged ≤18 years. CONCLUSIONS Polygenic risk score and HLA variations enable personalized risk estimates, enhance newborn screening efficiency for ketoacidosis prevention, and addresses the gap in data on T1D prediction in isolated Asian populations.
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Affiliation(s)
- Wen-Ling Liao
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Nan Huang
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, Taichung, Taiwan
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Ya-Wen Chang
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan
- Department of Medical Research, Genetic Center, China Medical University Hospital, Taichung, Taiwan
| | - Ting-Yuan Liu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Hsing-Fang Lu
- Center for Precision Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Zih-Yu Tiao
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Pen-Hua Su
- Department of Pediatrics, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Chung-Hsing Wang
- Division of Genetics and Metabolism, Children's Hospital of China Medical University, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Fuu-Jen Tsai
- Department of Medical Research, Genetic Center, China Medical University Hospital, Taichung, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
- Division of Medical Genetics, China Medical University Children's Hospital, Taichung, Taiwan
- Department of Biotechnology and Bioinformatics, Asia University, Taichung, Taiwan
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9
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Jiang Y, Du Y, Su R, Wei L, Gao P, Zhang J, Zhou X, Zhu S, Zhang H, Chen Y, Fang C, Wang S, Yu J, Ding W, Feng L. Analysis, validation, and discussion of key genes in placenta of patients with gestational diabetes mellitus. Exp Biol Med (Maywood) 2023; 248:1806-1817. [PMID: 37873933 PMCID: PMC10792417 DOI: 10.1177/15353702231199077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/27/2023] [Indexed: 10/25/2023] Open
Abstract
Gestational diabetes mellitus (GDM) is a common complication during pregnancy, which can have harmful health consequences for both the mother and the fetus. Given the placenta's crucial role as an endocrine organ during pregnancy, exploring and validating key genes in the placenta hold significant potential in the realm of GDM prevention and treatment. In this study, differentially expressed genes (DEGs) were identified from two databases, GSE70493 and PRJNA646212, and verified by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) in placenta tissues. DEGs expression was detected in normal or high-glucose-treated HTR8/SVneo cells. We also investigated the relationship between DEGs and glucose levels in GDM patients. By selecting the intersection of the two databases, we screened 20 DEGs, which were validated in GDM patients. We observed an up-regulation of SLAMF, ALDH1A2, and CHI3L2, and a down-regulation of HLA-E, MYH11, HLA-DRB5, ITGAX, GZMB, NAIP, TMEM74B, RANBP3L, PAEP, WT-1, and CEP170. We conducted further investigations into the expression of DEGs in HTR8/SVneo cells exposed to high glucose, revealing a significant upregulation in the expression of SERPINA3, while the expressions of HLA-E, BCL6, NAIP, PAEP, MUC16, WT-1, and CEP170 were decreased. Moreover, some DEGs were confirmed to have a positive or negative correlation with blood glucose levels of GDM patients through correlation analysis. The identified DEGs are anticipated to exert potential implications in the prevention and management of GDM, thereby offering potential benefits for improving pregnancy outcomes and long-term prognosis of fetuses among individuals affected by GDM.
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Affiliation(s)
- Yi Jiang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuanyuan Du
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Rui Su
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lijie Wei
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Peng Gao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingyi Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xuan Zhou
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shenglan Zhu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huiting Zhang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuting Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenyun Fang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shaoshuai Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Yu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wencheng Ding
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ling Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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10
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Sarkar S, Elliott EC, Henry HR, Ludovico ID, Melchior JT, Frazer-Abel A, Webb-Robertson BJ, Davidson WS, Holers VM, Rewers MJ, Metz TO, Nakayasu ES. Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response. Clin Proteomics 2023; 20:38. [PMID: 37735622 PMCID: PMC10512508 DOI: 10.1186/s12014-023-09429-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) results from an autoimmune attack of the pancreatic β cells that progresses to dysglycemia and symptomatic hyperglycemia. Current biomarkers to track this evolution are limited, with development of islet autoantibodies marking the onset of autoimmunity and metabolic tests used to detect dysglycemia. Therefore, additional biomarkers are needed to better track disease initiation and progression. Multiple clinical studies have used proteomics to identify biomarker candidates. However, most of the studies were limited to the initial candidate identification, which needs to be further validated and have assays developed for clinical use. Here we curate these studies to help prioritize biomarker candidates for validation studies and to obtain a broader view of processes regulated during disease development. METHODS This systematic review was registered with Open Science Framework ( https://doi.org/10.17605/OSF.IO/N8TSA ). Using PRISMA guidelines, we conducted a systematic search of proteomics studies of T1D in the PubMed to identify putative protein biomarkers of the disease. Studies that performed mass spectrometry-based untargeted/targeted proteomic analysis of human serum/plasma of control, pre-seroconversion, post-seroconversion, and/or T1D-diagnosed subjects were included. For unbiased screening, 3 reviewers screened all the articles independently using the pre-determined criteria. RESULTS A total of 13 studies met our inclusion criteria, resulting in the identification of 266 unique proteins, with 31 (11.6%) being identified across 3 or more studies. The circulating protein biomarkers were found to be enriched in complement, lipid metabolism, and immune response pathways, all of which are found to be dysregulated in different phases of T1D development. We found 2 subsets: 17 proteins (C3, C1R, C8G, C4B, IBP2, IBP3, ITIH1, ITIH2, BTD, APOE, TETN, C1S, C6A3, SAA4, ALS, SEPP1 and PI16) and 3 proteins (C3, CLUS and C4A) have consistent regulation in at least 2 independent studies at post-seroconversion and post-diagnosis compared to controls, respectively, making them strong candidates for clinical assay development. CONCLUSIONS Biomarkers analyzed in this systematic review highlight alterations in specific biological processes in T1D, including complement, lipid metabolism, and immune response pathways, and may have potential for further use in the clinic as prognostic or diagnostic assays.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Emily C Elliott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hayden R Henry
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ivo Díaz Ludovico
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - John T Melchior
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Ashley Frazer-Abel
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - W Sean Davidson
- Department of Pathology and Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - V Michael Holers
- Division of Rheumatology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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11
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Carré A, Zhou Z, Perez-Hernandez J, Samassa F, Lekka C, Manganaro A, Oshima M, Liao H, Parker R, Nicastri A, Brandao B, Colli ML, Eizirik DL, Göransson M, Morales OB, Anderson A, Landry L, Kobaisi F, Scharfmann R, Marselli L, Marchetti P, You S, Nakayama M, Hadrup SR, Kent SC, Richardson SJ, Ternette N, Mallone R. Interferon-α promotes neo-antigen formation and preferential HLA-B-restricted antigen presentation in pancreatic β-cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.15.557918. [PMID: 37745505 PMCID: PMC10516036 DOI: 10.1101/2023.09.15.557918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Interferon (IFN)-α is the earliest cytokine signature observed in individuals at risk for type 1 diabetes (T1D), but its effect on the repertoire of HLA Class I (HLA-I)-bound peptides presented by pancreatic β-cells is unknown. Using immunopeptidomics, we characterized the peptide/HLA-I presentation in in-vitro resting and IFN-α-exposed β-cells. IFN-α increased HLA-I expression and peptide presentation, including neo-sequences derived from alternative mRNA splicing, post-translational modifications - notably glutathionylation - and protein cis-splicing. This antigenic landscape relied on processing by both the constitutive and immune proteasome. The resting β-cell immunopeptidome was dominated by HLA-A-restricted ligands. However, IFN-α only marginally upregulated HLA-A and largely favored HLA-B, translating into a major increase in HLA-B-restricted peptides and into an increased activation of HLA-B-restricted vs. HLA-A-restricted CD8+ T-cells. A preferential HLA-B hyper-expression was also observed in the islets of T1D vs. non-diabetic donors, and we identified islet-infiltrating CD8+ T-cells from T1D donors reactive to HLA-B-restricted granule peptides. Thus, the inflammatory milieu of insulitis may skew the autoimmune response toward epitopes presented by HLA-B, hence recruiting a distinct T-cell repertoire that may be relevant to T1D pathogenesis.
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Affiliation(s)
- Alexia Carré
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Zhicheng Zhou
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Javier Perez-Hernandez
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Department of Nutrition and Health, Valencian International University (VIU), Valencia, Spain
| | | | - Christiana Lekka
- Islet Biology Group, Exeter Centre of Excellence in Diabetes Research, University of Exeter Medical School, Exeter, UK
| | - Anthony Manganaro
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Masaya Oshima
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Hanqing Liao
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Robert Parker
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Annalisa Nicastri
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Barbara Brandao
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | - Maikel L. Colli
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Decio L. Eizirik
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium
| | - Marcus Göransson
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | | | - Amanda Anderson
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Laurie Landry
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Farah Kobaisi
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
| | | | - Lorella Marselli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Sylvaine You
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
| | - Maki Nakayama
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sine R. Hadrup
- Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Sally C. Kent
- Diabetes Center of Excellence, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Sarah J. Richardson
- Islet Biology Group, Exeter Centre of Excellence in Diabetes Research, University of Exeter Medical School, Exeter, UK
| | - Nicola Ternette
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, UK
| | - Roberto Mallone
- Université Paris Cité, Institut Cochin, CNRS, INSERM, Paris, France
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Assistance Publique Hôpitaux de Paris, Service de Diabétologie et Immunologie Clinique, Cochin Hospital, Paris, France
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12
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Krawczyk M, Burzynska-Pedziwiatr I, Wozniak LA, Bukowiecka-Matusiak M. Impact of Polyphenols on Inflammatory and Oxidative Stress Factors in Diabetes Mellitus: Nutritional Antioxidants and Their Application in Improving Antidiabetic Therapy. Biomolecules 2023; 13:1402. [PMID: 37759802 PMCID: PMC10526737 DOI: 10.3390/biom13091402] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/10/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Diabetes mellitus is a chronic metabolic disorder characterized by hyperglycaemia and oxidative stress. Oxidative stress plays a crucial role in the development and progression of diabetes and its complications. Nutritional antioxidants derived from dietary sources have gained significant attention due to their potential to improve antidiabetic therapy. This review will delve into the world of polyphenols, investigating their origins in plants, metabolism in the human body, and relevance to the antioxidant mechanism in the context of improving antidiabetic therapy by attenuating oxidative stress, improving insulin sensitivity, and preserving β-cell function. The potential mechanisms of, clinical evidence for, and future perspectives on nutritional antioxidants as adjuvant therapy in diabetes management are discussed.
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13
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Nakayasu ES, Bramer LM, Ansong C, Schepmoes AA, Fillmore TL, Gritsenko MA, Clauss TR, Gao Y, Piehowski PD, Stanfill BA, Engel DW, Orton DJ, Moore RJ, Qian WJ, Sechi S, Frohnert BI, Toppari J, Ziegler AG, Lernmark Å, Hagopian W, Akolkar B, Smith RD, Rewers MJ, Webb-Robertson BJM, Metz TO. Plasma protein biomarkers predict the development of persistent autoantibodies and type 1 diabetes 6 months prior to the onset of autoimmunity. Cell Rep Med 2023; 4:101093. [PMID: 37390828 PMCID: PMC10394168 DOI: 10.1016/j.xcrm.2023.101093] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 07/02/2023]
Abstract
Type 1 diabetes (T1D) results from autoimmune destruction of β cells. Insufficient availability of biomarkers represents a significant gap in understanding the disease cause and progression. We conduct blinded, two-phase case-control plasma proteomics on the TEDDY study to identify biomarkers predictive of T1D development. Untargeted proteomics of 2,252 samples from 184 individuals identify 376 regulated proteins, showing alteration of complement, inflammatory signaling, and metabolic proteins even prior to autoimmunity onset. Extracellular matrix and antigen presentation proteins are differentially regulated in individuals who progress to T1D vs. those that remain in autoimmunity. Targeted proteomics measurements of 167 proteins in 6,426 samples from 990 individuals validate 83 biomarkers. A machine learning analysis predicts if individuals would remain in autoimmunity or develop T1D 6 months before autoantibody appearance, with areas under receiver operating characteristic curves of 0.871 and 0.918, respectively. Our study identifies and validates biomarkers, highlighting pathways affected during T1D development.
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Affiliation(s)
- Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Charles Ansong
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Athena A Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marina A Gritsenko
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Therese R Clauss
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Paul D Piehowski
- Environmental and Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Bryan A Stanfill
- Computational Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Dave W Engel
- Computational Analytics Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Daniel J Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Salvatore Sechi
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland; Institute of Biomedicine, Research Centre for Integrative Physiology and Pharmacology and Centre for Population Health Research, University of Turku, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, Munich, Germany; Forschergruppe Diabetes, Technical University of Munich, Klinikum Rechts der Isar, Munich, Germany; Forschergruppe Diabetes e.V. at Helmholtz Zentrum München, Munich, Germany
| | - Åke Lernmark
- Unit for Diabetes and Celiac Disease, Wallenberg/CRC, Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, 21428 Malmö, Sweden
| | | | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Marian J Rewers
- Barbara Davis Center for Diabetes, University of Colorado, Aurora, CO, USA
| | | | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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14
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Talwar JV, Laub D, Pagadala MS, Castro A, Lewis M, Luebeck GE, Gorman BR, Pan C, Dong FN, Markianos K, Teerlink CC, Lynch J, Hauger R, Pyarajan S, Tsao PS, Morris GP, Salem RM, Thompson WK, Curtius K, Zanetti M, Carter H. Autoimmune alleles at the major histocompatibility locus modify melanoma susceptibility. Am J Hum Genet 2023; 110:1138-1161. [PMID: 37339630 PMCID: PMC10357503 DOI: 10.1016/j.ajhg.2023.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 05/20/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
Autoimmunity and cancer represent two different aspects of immune dysfunction. Autoimmunity is characterized by breakdowns in immune self-tolerance, while impaired immune surveillance can allow for tumorigenesis. The class I major histocompatibility complex (MHC-I), which displays derivatives of the cellular peptidome for immune surveillance by CD8+ T cells, serves as a common genetic link between these conditions. As melanoma-specific CD8+ T cells have been shown to target melanocyte-specific peptide antigens more often than melanoma-specific antigens, we investigated whether vitiligo- and psoriasis-predisposing MHC-I alleles conferred a melanoma-protective effect. In individuals with cutaneous melanoma from both The Cancer Genome Atlas (n = 451) and an independent validation set (n = 586), MHC-I autoimmune-allele carrier status was significantly associated with a later age of melanoma diagnosis. Furthermore, MHC-I autoimmune-allele carriers were significantly associated with decreased risk of developing melanoma in the Million Veteran Program (OR = 0.962, p = 0.024). Existing melanoma polygenic risk scores (PRSs) did not predict autoimmune-allele carrier status, suggesting these alleles provide orthogonal risk-relevant information. Mechanisms of autoimmune protection were neither associated with improved melanoma-driver mutation association nor improved gene-level conserved antigen presentation relative to common alleles. However, autoimmune alleles showed higher affinity relative to common alleles for particular windows of melanocyte-conserved antigens and loss of heterozygosity of autoimmune alleles caused the greatest reduction in presentation for several conserved antigens across individuals with loss of HLA alleles. Overall, this study presents evidence that MHC-I autoimmune-risk alleles modulate melanoma risk unaccounted for by current PRSs.
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Affiliation(s)
- James V Talwar
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - David Laub
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Meghana S Pagadala
- Biomedical Science Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA
| | - McKenna Lewis
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Georg E Luebeck
- Public Health Sciences Division, Herbold Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Cuiping Pan
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA
| | - Frederick N Dong
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Booz Allen Hamilton, Inc., McLean, VA 22102, USA
| | - Kyriacos Markianos
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02115, USA
| | - Craig C Teerlink
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Julie Lynch
- Department of Veterans Affairs Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System, Salt Lake City, UT, USA; Department of Internal Medicine, Division of Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Richard Hauger
- VA San Diego Healthcare System, La Jolla, CA, USA; Center for Behavioral Genetics of Aging, University of California San Diego, La Jolla, CA, USA; Center of Excellence for Stress and Mental Health (CESAMH), VA San Diego Healthcare System, San Diego, CA, USA
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Boston Healthcare System, Boston, MA 02130, USA; Department of Medicine, Brigham Women's Hospital, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Philip S Tsao
- Palo Alto Epidemiology Research and Information Center for Genomics, VA Palo Alto, CA, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Gerald P Morris
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Rany M Salem
- Division of Epidemiology, Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA 92093, USA
| | - Wesley K Thompson
- Center for Population Neuroscience and Genetics, Laureate Institute for Brain Research, Tulsa, OK 74136, USA
| | - Kit Curtius
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; Division of Biomedical Informatics, Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Maurizio Zanetti
- Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA; The Laboratory of Immunology, University of California San Diego, La Jolla, CA 92093, USA; Department of Medicine, Division of Hematology and Oncology, University of California San Diego, La Jolla, CA 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA 92093, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92093, USA.
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15
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Jaros RK, Fadason T, Cameron-Smith D, Golovina E, O'Sullivan JM. Comorbidity genetic risk and pathways impact SARS-CoV-2 infection outcomes. Sci Rep 2023; 13:9879. [PMID: 37336921 DOI: 10.1038/s41598-023-36900-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 06/12/2023] [Indexed: 06/21/2023] Open
Abstract
Understanding the genetic risk and mechanisms through which SARS-CoV-2 infection outcomes and comorbidities interact to impact acute and long-term sequelae is essential if we are to reduce the ongoing health burdens of the COVID-19 pandemic. Here we use a de novo protein diffusion network analysis coupled with tissue-specific gene regulatory networks, to examine putative mechanisms for associations between SARS-CoV-2 infection outcomes and comorbidities. Our approach identifies a shared genetic aetiology and molecular mechanisms for known and previously unknown comorbidities of SARS-CoV-2 infection outcomes. Additionally, genomic variants, genes and biological pathways that provide putative causal mechanisms connecting inherited risk factors for SARS-CoV-2 infection and coronary artery disease and Parkinson's disease are identified for the first time. Our findings provide an in depth understanding of genetic impacts on traits that collectively alter an individual's predisposition to acute and post-acute SARS-CoV-2 infection outcomes. The existence of complex inter-relationships between the comorbidities we identify raises the possibility of a much greater post-acute burden arising from SARS-CoV-2 infection if this genetic predisposition is realised.
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Affiliation(s)
- Rachel K Jaros
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Tayaza Fadason
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1010, New Zealand
| | - David Cameron-Smith
- College of Health, Medicine and Wellbeing, The University of Newcastle, Callaghan, 2308, Australia
| | - Evgeniia Golovina
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand
| | - Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland, 1023, New Zealand.
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, 1010, New Zealand.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK.
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Australian Parkinson's Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia.
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16
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Coss SL, Zhou D, Chua GT, Aziz RA, Hoffman RP, Wu YL, Ardoin SP, Atkinson JP, Yu CY. The complement system and human autoimmune diseases. J Autoimmun 2023; 137:102979. [PMID: 36535812 PMCID: PMC10276174 DOI: 10.1016/j.jaut.2022.102979] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022]
Abstract
Genetic deficiencies of early components of the classical complement activation pathway (especially C1q, r, s, and C4) are the strongest monogenic causal factors for the prototypic autoimmune disease systemic lupus erythematosus (SLE), but their prevalence is extremely rare. In contrast, isotype genetic deficiency of C4A and acquired deficiency of C1q by autoantibodies are frequent among patients with SLE. Here we review the genetic basis of complement deficiencies in autoimmune disease, discuss the complex genetic diversity seen in complement C4 and its association with autoimmune disease, provide guidance as to when clinicians should suspect and test for complement deficiencies, and outline the current understanding of the mechanisms relating complement deficiencies to autoimmunity. We focus primarily on SLE, as the role of complement in SLE is well-established, but will also discuss other informative diseases such as inflammatory arthritis and myositis.
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Affiliation(s)
- Samantha L Coss
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
| | - Danlei Zhou
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Gilbert T Chua
- Department of Pediatrics and Adolescent Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Rabheh Abdul Aziz
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Allergy, Immunology and Rheumatology, University of Buffalo, NY, USA
| | - Robert P Hoffman
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Yee Ling Wu
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA; Department of Microbiology and Immunology, Loyola University Chicago, Maywood, IL, USA
| | - Stacy P Ardoin
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - John P Atkinson
- Department of Medicine, Division of Rheumatology, Washington University School of Medicine, St Louis, MO, USA
| | - Chack-Yung Yu
- Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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17
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Limanaqi F, Vicentini C, Saulle I, Clerici M, Biasin M. The role of endoplasmic reticulum aminopeptidases in type 1 diabetes mellitus. Life Sci 2023; 323:121701. [PMID: 37059356 DOI: 10.1016/j.lfs.2023.121701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/16/2023]
Abstract
Type-I diabetes mellitus (T1DM) is generally considered as a chronic, T-cell mediated autoimmune disease. This notwithstanding, both the endogenous characteristics of β-cells, and their response to environmental factors and exogenous inflammatory stimuli are key events in disease progression and exacerbation. As such, T1DM is now recognized as a multifactorial condition, with its onset being influenced by both genetic predisposition and environmental factors, among which, viral infections represent major triggers. In this frame, endoplasmic reticulum aminopeptidase 1 (ERAP1) and 2 (ERAP2) hold center stage. ERAPs represent the main hydrolytic enzymes specialized in trimming of N-terminal antigen peptides to be bound by MHC class I molecules and presented to CD8+ T cells. Thus, abnormalities in ERAPs expression alter the peptide-MHC-I repertoire both quantitatively and qualitatively, fostering both autoimmune and infectious diseases. Although only a few studies succeeded in determining direct associations between ERAPs variants and T1DM susceptibility/outbreak, alterations of ERAPs do impinge on a plethora of biological events which might indeed contribute to the disease development/exacerbation. Beyond abnormal self-antigen peptide trimming, these include preproinsulin processing, nitric oxide (NO) production, ER stress, cytokine responsiveness, and immune cell recruitment/activity. The present review brings together direct and indirect evidence focused on the immunobiological role of ERAPs in T1DM onset and progression, covering both genetic and environmental aspects.
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Affiliation(s)
- Fiona Limanaqi
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Chiara Vicentini
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, University of Milan, Via Francesco Sforza, 20122 Milan, Italy; Don C. Gnocchi Foundation, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Foundation, Via A. Capecelatro 66, 20148 Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences, University of Milan, Via G.B. Grassi, 20122 Milan, Italy.
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18
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Ferris ST, Liu T, Chen J, Ohara RA, Ou F, Wu R, Kim S, Murphy TL, Murphy KM. WDFY4 deficiency in NOD mice ameliorates autoimmune diabetes and insulitis. Proc Natl Acad Sci U S A 2023; 120:e2219956120. [PMID: 36940342 PMCID: PMC10068798 DOI: 10.1073/pnas.2219956120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 02/13/2023] [Indexed: 03/22/2023] Open
Abstract
The events that initiate autoimmune diabetes in nonobese diabetic (NOD) mice remain poorly understood. CD4+ and CD8+ T cells are both required to develop disease, but their relative roles in initiating disease are unclear. To test whether CD4+ T cell infiltration into islets requires damage to β cells induced by autoreactive CD8+ T cells, we inactivated Wdfy4 in nonobese diabetic (NOD) mice (NOD.Wdfy4-/--) using CRISPR/Cas9 targeting to eliminate cross-presentation by type 1 conventional dendritic cells (cDC1s). Similar to C57BL/6 Wdfy4-/- mice, cDC1 in NOD.Wdfy4-/- mice are unable to cross-present cell-associated antigens to prime CD8+ T cells, while cDC1 from heterozygous NOD.Wdfy4+/- mice cross-present normally. Further, NOD.Wdfy4-/- mice fail to develop diabetes while heterozygous NOD.Wdfy4+/- mice develop diabetes similarly to wild-type NOD mice. NOD.Wdfy4-/- mice remain capable of processing and presenting major histocompatibility complex class II (MHC-II)-restricted autoantigens and can activate β cell-specific CD4+ T cells in lymph nodes. However, disease in these mice does not progress beyond peri-islet inflammation. These results indicate that the priming of autoreactive CD8+ T cells in NOD mice requires cross-presentation by cDC1. Further, autoreactive CD8+ T cells appear to be required not only to develop diabetes, but to recruit autoreactive CD4+ T cells into islets of NOD mice, perhaps in response to progressive β cell damage.
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Affiliation(s)
- Stephen T. Ferris
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Tiantian Liu
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Jing Chen
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Ray A. Ohara
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Feiya Ou
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Renee Wu
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Sunkyung Kim
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Theresa L. Murphy
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
| | - Kenneth M. Murphy
- Department of Pathology and Immunology, School of Medicine, Washington University in St. Louis, St. Louis, MO63110
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Kang X, Liu S, Roelstraete B, Khalili H, Ludvigsson JF. Type 1 diabetes and microscopic colitis: A nationwide matched case-control study in Sweden. Aliment Pharmacol Ther 2023; 57:1423-1431. [PMID: 36946558 DOI: 10.1111/apt.17473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 03/07/2023] [Indexed: 03/23/2023]
Abstract
BACKGROUND AND AIMS Microscopic colitis (MC) is a colonic inflammatory condition associated with autoimmune dysfunction. Type 1 diabetes (T1D) is a chronic disease induced by autoimmune destruction of pancreatic β-cells. We aimed to examine the association between T1D and MC. METHODS A matched case-control study was conducted using the nationwide ESPRESSO cohort as study base. All biopsy-confirmed MC patients born after 1940 were identified and compared to biopsy-free individuals matched from the general population for T1D diagnosis using the Swedish National Patient Register. The T1D-MC association was estimated as odds ratios (ORs) and 95% confidence intervals (CIs) by conditional logistic models, considering differences by sex and MC subtype. Full sibling comparison and adjustment for MC-associated medications were also performed. RESULTS We identified 352 (3.7%) and 945 (2.0%) T1D diagnoses from 9,600 MC cases and 47,870 matched population controls, respectively, which corresponded to an overall OR of 1.79 (95% CI: 1.56-2.05). The association was stronger for collagenous colitis (OR, 2.15; 95% CI: 1.70-2.71) than lymphocytic colitis (OR, 1.62; 95% CI: 1.37-1.92) and remained statistically significant in full sibling comparison (OR, 1.46; 95%: 1.18-1.81). Medication adjustment attenuated the association to null among females (OR: 1.02; 95% CI: 0.82-1.27) but not among males (OR: 1.45; 95% CI: 1.11-1.90). CONCLUSION T1D diagnosis was almost 80% more prevalent in MC patients compared to general population. This positive association did not seem to be spurious due to residual confounding shared by full siblings but may relate to consumption of medications associated with MC onset.
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Affiliation(s)
- Xiaoying Kang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachussets, USA
| | - Shengxin Liu
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Bjorn Roelstraete
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Hamed Khalili
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Gastroenterology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, Massachussets, USA
| | - Jonas F Ludvigsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Pediatrics, Örebro University Hospital, Örebro, Sweden
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20
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Mehta RS, Cao K, Saliba RM, Al-Atrash G, Alousi AM, Lontos K, Marcoux C, Carmazzi Y, Rondon G, Bashir Q, Hosing CM, Kebriaei P, Khouri I, Marin D, Nieto Y, Oran B, Popat UR, Qazilbash MH, Ramdial J, Rezvani K, Champlin RE, Shpall EJ. HLA Factors versus Non-HLA Factors for Haploidentical Donor Selection. Transplant Cell Ther 2023; 29:189-198. [PMID: 36470579 PMCID: PMC10125001 DOI: 10.1016/j.jtct.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
When multiple haploidentical donors are available for transplantation, those of younger generations are generally selected over those of older generations. However, it is unclear who is the optimal donor when selecting candidates from within a generation, such as father versus mother, son versus daughter, or brother versus sister. Although traditionally male donors are favored over female donors, particularly for male recipients, and significant associations of individual HLA mis(matches) on outcomes are being increasingly recognized, the hierarchy of factors for donor selection is indeterminate. To assess whether HLA factors take precedence over non-HLA factors and to isolate the influence of specific characteristics on outcomes, we analyzed 412 patients stratified by donor relationship: child donor (son [n = 202] versus daughter [n = 96]), parent (father [n = 28] versus mother [n = 29]), and sibling (noninherited maternal [NIMA; n = 29] versus paternal [NIPA; n = 28] mismatched). Among siblings, NIMA mismatch was associated with a lower risk of acute graft-versus-host disease (aGVHD); B-leader mismatch was associated with high nonrelapse mortality (NRM), poor progression-free survival, and a trend toward poor overall survival (OS), whereas A-mismatch was associated with lower aGVHD. Among parent donors, the relationship did not impact any outcome; B-leader mismatch was associated with higher NRM and a trend toward poor OS, whereas A-mismatch was associated with lower NRM and improved progression-free survival and OS. Among child donors, no individual HLA mismatch was predictive of any outcome, and daughter donors were not associated with any adverse outcomes in multivariate analyses. Our data suggest that certain HLA factors may be more significant in some cases and should be given priority over simply selecting a donor based on relationship/sex.
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Affiliation(s)
- Rohtesh S Mehta
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Kai Cao
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rima M Saliba
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Amin M Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Konstantinos Lontos
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Curtis Marcoux
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yudith Carmazzi
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Qaiser Bashir
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chitra M Hosing
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Issa Khouri
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Marin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yago Nieto
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Betul Oran
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Uday R Popat
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Muzaffar H Qazilbash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeremy Ramdial
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Katayoun Rezvani
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Richard E Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
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21
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Sarkar S, Elliott EC, Henry HR, Ludovico ID, Melchior JT, Frazer-Abel A, Webb-Robertson BJ, Davidson WS, Holers VM, Rewers MJ, Metz TO, Nakayasu ES. Systematic review of type 1 diabetes biomarkers reveals regulation in circulating proteins related to complement, lipid metabolism, and immune response. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.21.23286132. [PMID: 36865103 PMCID: PMC9980237 DOI: 10.1101/2023.02.21.23286132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Aims Type 1 diabetes (T1D) results from an autoimmune attack of the pancreatic β cells that progresses to dysglycemia and symptomatic hyperglycemia. Current biomarkers to track this evolution are limited, with development of islet autoantibodies marking the onset of autoimmunity and metabolic tests used to detect dysglycemia. Therefore, additional biomarkers are needed to better track disease initiation and progression. Multiple clinical studies have used proteomics to identify biomarker candidates. However, most of the studies were limited to the initial candidate identification, which needs to be further validated and have assays developed for clinical use. Here we curate these studies to help prioritize biomarker candidates for validation studies and to obtain a broader view of processes regulated during disease development. Methods This systematic review was registered with Open Science Framework (DOI 10.17605/OSF.IO/N8TSA). Using PRISMA guidelines, we conducted a systematic search of proteomics studies of T1D in the PubMed to identify putative protein biomarkers of the disease. Studies that performed mass spectrometry-based untargeted/targeted proteomic analysis of human serum/plasma of control, pre-seroconversion, post-seroconversion, and/or T1D-diagnosed subjects were included. For unbiased screening, 3 reviewers screened all the articles independently using the pre-determined criteria. Results A total of 13 studies met our inclusion criteria, resulting in the identification of 251 unique proteins, with 27 (11%) being identified across 3 or more studies. The circulating protein biomarkers were found to be enriched in complement, lipid metabolism, and immune response pathways, all of which are found to be dysregulated in different phases of T1D development. We found a subset of 3 proteins (C3, KNG1 & CFAH), 6 proteins (C3, C4A, APOA4, C4B, A2AP & BTD) and 7 proteins (C3, CLUS, APOA4, C6, A2AP, C1R & CFAI) have consistent regulation between multiple studies in samples from individuals at pre-seroconversion, post-seroconversion and post-diagnosis compared to controls, respectively, making them strong candidates for clinical assay development. Conclusions Biomarkers analyzed in this systematic review highlight alterations in specific biological processes in T1D, including complement, lipid metabolism, and immune response pathways, and may have potential for further use in the clinic as prognostic or diagnostic assays.
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22
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Uncovering novel MHC alleles from RNA-Seq data: expanding the spectrum of MHC class I alleles in sheep. BMC Genom Data 2023; 24:1. [PMID: 36597020 PMCID: PMC9809118 DOI: 10.1186/s12863-022-01102-5] [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: 01/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) class I glycoproteins present selected peptides or antigens to CD8 + T cells that control the cytotoxic immune response. The MHC class I genes are among the most polymorphic loci in the vertebrate genome, with more than twenty thousand alleles known in humans. In sheep, only a very small number of alleles have been described to date, making the development of genotyping systems or functional studies difficult. A cost-effective way to identify new alleles could be to use already available RNA-Seq data from sheep. Current strategies for aligning RNA-Seq reads against annotated genome sequences or transcriptomes fail to detect the majority of class I alleles. Here, I combine the alignment of RNA-Seq reads against a specific reference database with de novo assembly to identify alleles. The method allows the comprehensive discovery of novel MHC class I alleles from RNA-Seq data (DinoMfRS). RESULTS Using DinoMfRS, virtually all expressed MHC class I alleles could be determined. From 18 animals 75 MHC class I alleles were identified, of which 69 were novel. In addition, it was shown that DinoMfRS can be used to improve the annotation of MHC genes in the sheep genome sequence. CONCLUSIONS DinoMfRS allows for the first time the annotation of unknown, more divergent MHC alleles from RNA-Seq data. Successful application to RNA-Seq data from 16 animals has approximately doubled the number of known alleles in sheep. By using existing data, alleles can now be determined very inexpensively for populations that have not been well studied. In addition, MHC expression studies or evolutionary studies, for example, can be greatly improved in this way, and the method should be applicable to a broader spectrum of other multigene families or highly polymorphic genes.
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23
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Lemos JRN, Baidal DA, Poggioli R, Fuenmayor V, Chavez C, Alvarez A, Ricordi C, Alejandro R. HLA-B Matching Prolongs Allograft Survival in Islet Cell Transplantation. Cell Transplant 2023; 32:9636897231166529. [PMID: 37526141 PMCID: PMC10395153 DOI: 10.1177/09636897231166529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 08/02/2023] Open
Abstract
Islet cell transplantation (ITx) is an effective therapeutic approach for selected patients with type 1 diabetes with hypoglycemia unawareness and severe hypoglycemia events. In organ transplantation, human leukocyte antigen (HLA) mismatching between donor and recipient negatively impacts transplant outcomes. We aimed to determine whether HLA matching has an impact on islet allograft survival. Forty-eight patients were followed up after islet transplantation at our institution from 2000 to 2020 in a retrospective cohort. Patients underwent intrahepatic ITx or laparoscopic omental approach. Immunosuppression was dependent upon the protocol. We analyzed HLA data restricted to A, B, and DR loci on allograft survival using survival and subsequent multivariable analyses. Patients were aged 42.8 ± 8.4 years, and 64.3% were female. Diabetes duration was 28.6 ± 11.6 years. Patients matching all three HLA loci presented longer graft survival (P = 0.030). Patients with ≥1 HLA-B matching had longer graft survival compared with zero matching (P = 0.025). The number of HLA-B matching was positively associated with time of graft survival (Spearman's rho = 0.590; P = 0.034). Analyses adjusted for confounders showed that ≥1 matching for HLA-B decreased the risk of allograft failure (P = 0.009). Our data suggest that HLA-B matching between recipients and donors improved islet allograft survival. Matching all three HLA loci (A, B, and DR) was also associated with prolonged islet allograft survival. Prospective studies and a larger sample size are warranted to validate our findings.
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Affiliation(s)
- Joana R. N. Lemos
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - David A. Baidal
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Raffaella Poggioli
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Virginia Fuenmayor
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Carmen Chavez
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Ana Alvarez
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Camillo Ricordi
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
- Division of Cellular Transplantation, Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL, USA
| | - Rodolfo Alejandro
- Diabetes Research Institute (DRI) and Clinical Cell Transplant Program, Miller School of Medicine, University of Miami, Miami, FL, USA
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The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α. Nat Commun 2022; 13:6363. [PMID: 36289205 PMCID: PMC9606380 DOI: 10.1038/s41467-022-34069-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/13/2022] [Indexed: 01/05/2023] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that results in the destruction of insulin producing pancreatic β-cells. One of the genes associated with T1D is TYK2, which encodes a Janus kinase with critical roles in type-Ι interferon (IFN-Ι) mediated intracellular signalling. To study the role of TYK2 in β-cell development and response to IFNα, we generated TYK2 knockout human iPSCs and directed them into the pancreatic endocrine lineage. Here we show that loss of TYK2 compromises the emergence of endocrine precursors by regulating KRAS expression, while mature stem cell-islets (SC-islets) function is not affected. In the SC-islets, the loss or inhibition of TYK2 prevents IFNα-induced antigen processing and presentation, including MHC Class Ι and Class ΙΙ expression, enhancing their survival against CD8+ T-cell cytotoxicity. These results identify an unsuspected role for TYK2 in β-cell development and support TYK2 inhibition in adult β-cells as a potent therapeutic target to halt T1D progression.
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25
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TCR CDR3 Sequencing as a Clue to Elucidate the Landscape of Dysimmunity in Patients with Primary Immune Thrombocytopenia. J Clin Med 2022; 11:jcm11195665. [PMID: 36233533 PMCID: PMC9571369 DOI: 10.3390/jcm11195665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Primary immune thrombocytopenia (ITP) is an autoimmune disorder. The existence of autoreactive T cells has long been proposed in ITP. Yet the identification of autoreactive T cells has not been achieved, which is an important step to elucidate the pathogenesis of ITP. Methods: ITP patients’ peripheral blood was collected prior to the treatment and one month after initiating dexamethasone treatment per related therapeutic guideline. Serum cytokines were profiled to examine T cell subtypes imbalance using a protein chip. TCR Vβ analysis in CD8+T cells of ITP patients, and TCR CDR3 DNA sequencing of CD4+T and CD8+T cells were performed to determine the autoreactive T cells’ clones. Results: Cytokine profiling revealed imbalanced distribution of T cells subtypes, which was confirmed by CD4+T and CD8+T cells’ oligoclonal expansion of TCR Vβ analysis and TCR CDR3 DNA sequencing. VDJ segments were found to be more frequently presented in ITP patients, when compared with health controls. There was an individualized CD4+T cell or CD8+T cell CDR3 sequence in each ITP patient. Conclusions: The present study revealed that T cell clones expanded in ITP patients’ peripheral blood, and each clone had an individualized TCR CDR3 sequence. The expanded T cell clones preferred to use some specific VDJ segment. Further studies are warranted to get access to individualized treatment such as Car-T in patients with ITP.
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26
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Rojas M, Heuer LS, Zhang W, Chen YG, Ridgway WM. The long and winding road: From mouse linkage studies to a novel human therapeutic pathway in type 1 diabetes. Front Immunol 2022; 13:918837. [PMID: 35935980 PMCID: PMC9353112 DOI: 10.3389/fimmu.2022.918837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Autoimmunity involves a loss of immune tolerance to self-proteins due to a combination of genetic susceptibility and environmental provocation, which generates autoreactive T and B cells. Genetic susceptibility affects lymphocyte autoreactivity at the level of central tolerance (e.g., defective, or incomplete MHC-mediated negative selection of self-reactive T cells) and peripheral tolerance (e.g., failure of mechanisms to control circulating self-reactive T cells). T regulatory cell (Treg) mediated suppression is essential for controlling peripheral autoreactive T cells. Understanding the genetic control of Treg development and function and Treg interaction with T effector and other immune cells is thus a key goal of autoimmunity research. Herein, we will review immunogenetic control of tolerance in one of the classic models of autoimmunity, the non-obese diabetic (NOD) mouse model of autoimmune Type 1 diabetes (T1D). We review the long (and still evolving) elucidation of how one susceptibility gene, Cd137, (identified originally via linkage studies) affects both the immune response and its regulation in a highly complex fashion. The CD137 (present in both membrane and soluble forms) and the CD137 ligand (CD137L) both signal into a variety of immune cells (bi-directional signaling). The overall outcome of these multitudinous effects (either tolerance or autoimmunity) depends upon the balance between the regulatory signals (predominantly mediated by soluble CD137 via the CD137L pathway) and the effector signals (mediated by both membrane-bound CD137 and CD137L). This immune balance/homeostasis can be decisively affected by genetic (susceptibility vs. resistant alleles) and environmental factors (stimulation of soluble CD137 production). The discovery of the homeostatic immune effect of soluble CD137 on the CD137-CD137L system makes it a promising candidate for immunotherapy to restore tolerance in autoimmune diseases.
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Affiliation(s)
- Manuel Rojas
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
- School of Medicine and Health Sciences, Doctoral Program in Biological and Biomedical Sciences, Universidad del Rosario, Bogota, Colombia
| | - Luke S. Heuer
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Weici Zhang
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Yi-Guang Chen
- The Max McGee Research Center for Juvenile Diabetes, Children’s Research Institute of Children’s Wisconsin, Milwaukee, WI, United States
- Division of Endocrinology, Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI, United States
| | - William M. Ridgway
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
- *Correspondence: William M. Ridgway,
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27
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Cheng W, Ramachandran S, Crawford L. Uncertainty quantification in variable selection for genetic fine-mapping using bayesian neural networks. iScience 2022; 25:104553. [PMID: 35769876 PMCID: PMC9234235 DOI: 10.1016/j.isci.2022.104553] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/09/2022] [Accepted: 06/01/2022] [Indexed: 02/07/2023] Open
Abstract
In this paper, we propose a new approach for variable selection using a collection of Bayesian neural networks with a focus on quantifying uncertainty over which variables are selected. Motivated by fine-mapping applications in statistical genetics, we refer to our framework as an "ensemble of single-effect neural networks" (ESNN) which generalizes the "sum of single effects" regression framework by both accounting for nonlinear structure in genotypic data (e.g., dominance effects) and having the capability to model discrete phenotypes (e.g., case-control studies). Through extensive simulations, we demonstrate our method's ability to produce calibrated posterior summaries such as credible sets and posterior inclusion probabilities, particularly for traits with genetic architectures that have significant proportions of non-additive variation driven by correlated variants. Lastly, we use real data to demonstrate that the ESNN framework improves upon the state of the art for identifying true effect variables underlying various complex traits.
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Affiliation(s)
- Wei Cheng
- Department of Computer Science, Brown University, Providence, RI, USA.,Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Sohini Ramachandran
- Department of Computer Science, Brown University, Providence, RI, USA.,Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Lorin Crawford
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA.,Department of Biostatistics, Brown University, Providence, RI, USA.,Microsoft Research New England, Cambridge, MA, USA
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28
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Pujar M, Vastrad B, Kavatagimath S, Vastrad C, Kotturshetti S. Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis. Sci Rep 2022; 12:9157. [PMID: 35650387 PMCID: PMC9160069 DOI: 10.1038/s41598-022-13291-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein–protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. The top hub genes such as MYC, EGFR, LNX1, YBX1, HSP90AA1, ESR1, FN1, TK1, ANLN and SMAD9 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Receiver operating characteristic curve (ROC) analysis confirmed that these genes were significantly associated with T1DM. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the advancement and progression of T1DM, and certain genes might be used as candidate target molecules to diagnose, monitor and treat T1DM.
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Affiliation(s)
- Madhu Pujar
- Department of Pediatrics, J J M Medical College, Davangere, Karnataka, 577004, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, Karnataka, 582101, India
| | - Satish Kavatagimath
- Department of Pharmacognosy, K.L.E. College of Pharmacy, Belagavi, Karnataka, 590010, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka, 580001, India.
| | - Shivakumar Kotturshetti
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka, 580001, India
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29
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Gootjes C, Zwaginga JJ, Roep BO, Nikolic T. Functional Impact of Risk Gene Variants on the Autoimmune Responses in Type 1 Diabetes. Front Immunol 2022; 13:886736. [PMID: 35603161 PMCID: PMC9114814 DOI: 10.3389/fimmu.2022.886736] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Type 1 diabetes (T1D) is an autoimmune disease that develops in the interplay between genetic and environmental factors. A majority of individuals who develop T1D have a HLA make up, that accounts for 50% of the genetic risk of disease. Besides these HLA haplotypes and the insulin region that importantly contribute to the heritable component, genome-wide association studies have identified many polymorphisms in over 60 non-HLA gene regions that also contribute to T1D susceptibility. Combining the risk genes in a score (T1D-GRS), significantly improved the prediction of disease progression in autoantibody positive individuals. Many of these minor-risk SNPs are associated with immune genes but how they influence the gene and protein expression and whether they cause functional changes on a cellular level remains a subject of investigation. A positive correlation between the genetic risk and the intensity of the peripheral autoimmune response was demonstrated both for HLA and non-HLA genetic risk variants. We also observed epigenetic and genetic modulation of several of these T1D susceptibility genes in dendritic cells (DCs) treated with vitamin D3 and dexamethasone to acquire tolerogenic properties as compared to immune activating DCs (mDC) illustrating the interaction between genes and environment that collectively determines risk for T1D. A notion that targeting such genes for therapeutic modulation could be compatible with correction of the impaired immune response, inspired us to review the current knowledge on the immune-related minor risk genes, their expression and function in immune cells, and how they may contribute to activation of autoreactive T cells, Treg function or β-cell apoptosis, thus contributing to development of the autoimmune disease.
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Affiliation(s)
- Chelsea Gootjes
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Jaap Jan Zwaginga
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Bart O Roep
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
| | - Tatjana Nikolic
- Laboratory of Immunomodulation and Regenerative Cell Therapy, Department of Internal Medicine, Leiden University Medical Center, Leiden, Netherlands
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30
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Hopkins JR, MacLachlan BJ, Harper S, Sewell AK, Cole DK. Unconventional modes of peptide-HLA-I presentation change the rules of TCR engagement. DISCOVERY IMMUNOLOGY 2022; 1:kyac001. [PMID: 38566908 PMCID: PMC10917088 DOI: 10.1093/discim/kyac001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/18/2022] [Accepted: 04/06/2022] [Indexed: 04/04/2024]
Abstract
The intracellular proteome of virtually every nucleated cell in the body is continuously presented at the cell surface via the human leukocyte antigen class I (HLA-I) antigen processing pathway. This pathway classically involves proteasomal degradation of intracellular proteins into short peptides that can be presented by HLA-I molecules for interrogation by T-cell receptors (TCRs) expressed on the surface of CD8+ T cells. During the initiation of a T-cell immune response, the TCR acts as the T cell's primary sensor, using flexible loops to mould around the surface of the pHLA-I molecule to identify foreign or dysregulated antigens. Recent findings demonstrate that pHLA-I molecules can also be highly flexible and dynamic, altering their shape according to minor polymorphisms between different HLA-I alleles, or interactions with different peptides. These flexible presentation modes have important biological consequences that can, for example, explain why some HLA-I alleles offer greater protection against HIV, or why some cancer vaccine approaches have been ineffective. This review explores how these recent findings redefine the rules for peptide presentation by HLA-I molecules and extend our understanding of the molecular mechanisms that govern TCR-mediated antigen discrimination.
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Affiliation(s)
- Jade R Hopkins
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - Bruce J MacLachlan
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | | | - Andrew K Sewell
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
| | - David K Cole
- Division of Infection and Immunity and Systems Immunity Research Institute, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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31
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Krovi SH, Kuchroo VK. Activation pathways that drive CD4 + T cells to break tolerance in autoimmune diseases . Immunol Rev 2022; 307:161-190. [PMID: 35142369 PMCID: PMC9255211 DOI: 10.1111/imr.13071] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases are characterized by dysfunctional immune systems that misrecognize self as non-self and cause tissue destruction. Several cell types have been implicated in triggering and sustaining disease. Due to a strong association of major histocompatibility complex II (MHC-II) proteins with various autoimmune diseases, CD4+ T lymphocytes have been thoroughly investigated for their roles in dictating disease course. CD4+ T cell activation is a coordinated process that requires three distinct signals: Signal 1, which is mediated by antigen recognition on MHC-II molecules; Signal 2, which boosts signal 1 in a costimulatory manner; and Signal 3, which helps to differentiate the activated cells into functionally relevant subsets. These signals are disrupted during autoimmunity and prompt CD4+ T cells to break tolerance. Herein, we review our current understanding of how each of the three signals plays a role in three different autoimmune diseases and highlight the genetic polymorphisms that predispose individuals to autoimmunity. We also discuss the drawbacks of existing therapies and how they can be addressed to achieve lasting tolerance in patients.
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Affiliation(s)
- Sai Harsha Krovi
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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32
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Barkhane Z, Elmadi J, Satish Kumar L, Pugalenthi LS, Ahmad M, Reddy S. Multiple Sclerosis and Autoimmunity: A Veiled Relationship. Cureus 2022; 14:e24294. [PMID: 35607574 PMCID: PMC9123335 DOI: 10.7759/cureus.24294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/02/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune inflammatory illness that affects the central nervous system (CNS) when the body's immune system attacks its tissue. It is characterized by demyelination and varying degrees of axonal loss. This article has compiled various studies elaborating MS and other autoimmune diseases (ADs) co-occurrence. Several conditions that fall into this category, including type 1 diabetes (T1D), rheumatoid arthritis (RA), Guillain-Barre syndrome (GBS), myasthenia gravis (MG), and many others, are found in MS patients and their relatives, suggesting one or more common etiologic mechanisms, including genetic, environmental, and immunological factors, supporting the concept of a possible influence of poly-autoimmunity on MS and the rest of ADs, as well as providing a significant feature for early detection of the disease and also a potential treatment option by clinical neurologists.
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33
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Kissler S. Genetic Modifiers of Thymic Selection and Central Tolerance in Type 1 Diabetes. Front Immunol 2022; 13:889856. [PMID: 35464420 PMCID: PMC9021641 DOI: 10.3389/fimmu.2022.889856] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/21/2022] [Indexed: 02/02/2023] Open
Abstract
Type 1 diabetes (T1D) is caused by the T cell-driven autoimmune destruction of insulin-producing cells in the pancreas. T1D served as the prototypical autoimmune disease for genome wide association studies (GWAS) after having already been the subject of many linkage and association studies prior to the development of GWAS technology. Of the many T1D-associated gene variants, a minority appear disease-specific, while most are shared with one or more other autoimmune condition. Shared disease variants suggest defects in fundamental aspects of immune tolerance. The first layer of protective tolerance induction is known as central tolerance and takes place during the thymic selection of T cells. In this article, we will review candidate genes for type 1 diabetes whose function implicates them in central tolerance. We will describe examples of gene variants that modify the function of T cells intrinsically and others that indirectly affect thymic selection. Overall, these insights will show that a significant component of the genetic risk for T1D - and autoimmunity in general - pertains to the earliest stages of tolerance induction, at a time when protective intervention may not be feasible.
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Affiliation(s)
- Stephan Kissler
- Section for Immunobiology, Joslin Diabetes Center, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States,*Correspondence: Stephan Kissler,
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34
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Fasolino M, Schwartz GW, Patil AR, Mongia A, Golson ML, Wang YJ, Morgan A, Liu C, Schug J, Liu J, Wu M, Traum D, Kondo A, May CL, Goldman N, Wang W, Feldman M, Moore JH, Japp AS, Betts MR, Faryabi RB, Naji A, Kaestner KH, Vahedi G. Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. Nat Metab 2022; 4:284-299. [PMID: 35228745 PMCID: PMC8938904 DOI: 10.1038/s42255-022-00531-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease in which immune cells destroy insulin-producing beta cells. The aetiology of this complex disease is dependent on the interplay of multiple heterogeneous cell types in the pancreatic environment. Here, we provide a single-cell atlas of pancreatic islets of 24 T1D, autoantibody-positive and nondiabetic organ donors across multiple quantitative modalities including ~80,000 cells using single-cell transcriptomics, ~7,000,000 cells using cytometry by time of flight and ~1,000,000 cells using in situ imaging mass cytometry. We develop an advanced integrative analytical strategy to assess pancreatic islets and identify canonical cell types. We show that a subset of exocrine ductal cells acquires a signature of tolerogenic dendritic cells in an apparent attempt at immune suppression in T1D donors. Our multimodal analyses delineate cell types and processes that may contribute to T1D immunopathogenesis and provide an integrative procedure for exploration and discovery of human pancreatic function.
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Affiliation(s)
- Maria Fasolino
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Gregory W Schwartz
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Abhijeet R Patil
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aanchal Mongia
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Maria L Golson
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yue J Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ashleigh Morgan
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Chengyang Liu
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jonathan Schug
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jinping Liu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Minghui Wu
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Daniel Traum
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Ayano Kondo
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Catherine L May
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Naomi Goldman
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Wenliang Wang
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael Feldman
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alberto S Japp
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R Betts
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Robert B Faryabi
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Ali Naji
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Klaus H Kaestner
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
| | - Golnaz Vahedi
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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35
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Deakin CT, Bowes J, Rider LG, Miller FW, Pachman LM, Sanner H, Rouster-Stevens K, Mamyrova G, Curiel R, Feldman BM, Huber AM, Reed AM, Schmeling H, Cook CG, Marshall LR, Wilkinson MGL, Eyre S, Raychaudhuri S, Wedderburn LR. Association with HLA-DRβ1 position 37 distinguishes juvenile Dermatomyositis from adult-onset myositis. Hum Mol Genet 2022; 31:2471-2481. [PMID: 35094092 PMCID: PMC9307311 DOI: 10.1093/hmg/ddac019] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
Objectives
Juvenile dermatomyositis (JDM) is a rare, severe autoimmune disease and the most common idiopathic inflammatory myopathy (IIM) of children. JDM and adult-onset dermatomyositis (DM) have similar clinical, biological and serological features, although these features differ in prevalence between childhood-onset and adult-onset disease, suggesting age of disease onset may influence pathogenesis. Therefore, a JDM-focused genetic analysis was performed using the largest collection of JDM samples to date.
Methods
Caucasian JDM samples (n = 952) obtained via international collaboration were genotyped using the Illumina HumanCoreExome chip. Additional non-assayed HLA loci and genome-wide SNPs were imputed.
Results
HLA-DRB1*03:01 was confirmed as the classical HLA allele most strongly associated with JDM (OR 1.66; 95% CI 1.46, 1.89; P = 1.4 × 10−14), with an independent association at HLA-C*02:02 (OR = 1.74; 95% CI 1.42, 2.13, P = 7.13 × 10−8). Analyses of amino acid positions within HLA-DRB1 indicated the strongest association was at position 37 (omnibus P = 3.3 × 10−19), with suggestive evidence this association was independent of position 74 (omnibus P = 5.1 × 10−5), the position most strongly associated with adult-onset DM. Conditional analyses also suggested the association at position 37 of HLA-DRB1 was independent of some alleles of the Caucasian HLA 8.1 ancestral haplotype (AH8.1) such as HLA-DQB1*02:01 (OR = 1.62; 95% CI 1.36, 1.93; P = 8.70 × 10−8), but not HLA-DRB1*03:01 (OR = 1.49; 95% CR 1.24, 1.80; P = 2.24 × 10−5). No associations outside the HLA region were identified.
Conclusions
Our findings confirm previous associations with AH8.1 and HLA-DRB1*03:01, HLA-C*02:02 and identify a novel association with amino acid position 37 within HLA-DRB1 which may distinguish JDM from adult DM.
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Affiliation(s)
- Claire T Deakin
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCL Hospital and Great Ormond Street Hospital, London, UK
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
- National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Lisa G Rider
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Frederick W Miller
- Environmental Autoimmunity Group, Clinical Research Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland, USA
| | - Lauren M Pachman
- Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Helga Sanner
- Department of Rheumatology, University of Oslo, Oslo, Norway
- Oslo New University College, Oslo, Norway
| | | | - Gulnara Mamyrova
- Division of Rheumatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Rodolfo Curiel
- Division of Rheumatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Brian M Feldman
- Division of Rheumatology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Adam M Huber
- IWK Health Centre and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Ann M Reed
- Pediatrics, Duke University, Durham, North Carolina, USA
| | - Heinrike Schmeling
- Alberta Children's Hospital and Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Charlotte G Cook
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Lucy R Marshall
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCL Hospital and Great Ormond Street Hospital, London, UK
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
| | - Meredyth G Ll Wilkinson
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCL Hospital and Great Ormond Street Hospital, London, UK
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
- National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Soumya Raychaudhuri
- Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
- National Institute of Health Research Manchester Biomedical Research Centre, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Lucy R Wedderburn
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL, UCL Hospital and Great Ormond Street Hospital, London, UK
- NIHR Biomedical Research Centre at Great Ormond Street Hospital, London, UK
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Alpha-Lipoic Acid Inhibits Spontaneous Diabetes and Autoimmune Recurrence in Non-Obese Diabetic Mice by Enhancing Differentiation of Regulatory T Cells and Showed Potential for Use in Cell Therapies for the Treatment of Type 1 Diabetes. Int J Mol Sci 2022; 23:ijms23031169. [PMID: 35163121 PMCID: PMC8835933 DOI: 10.3390/ijms23031169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/10/2022] Open
Abstract
Type 1 diabetes (T1D) is caused by the destruction of β cells in pancreatic islets by autoimmune T cells. Islet transplantation has been established as an effective treatment for T1D. However, the survival of islet grafts is often disrupted by recurrent autoimmunity. Alpha-lipoic acid (ALA) has been reported to have immunomodulatory effects and, therefore, may have therapeutic potential in the treatment of T1D. In this study, we investigated the therapeutic potential of ALA in autoimmunity inhibition. We treated non-obese diabetic (NOD) mice with spontaneous diabetes and islet-transplantation mice with ALA. The onset of diabetes was decreased and survival of the islet grafts was extended. The populations of Th1 cells decreased, and regulatory T cells (Tregs) increased in ALA-treated mice. The in vitro Treg differentiation was significantly increased by treatment with ALA. The adoptive transfer of ALA-differentiated Tregs into NOD recipients improved the outcome of the islet grafts. Our results showed that in vivo ALA treatment suppressed spontaneous diabetes and autoimmune recurrence in NOD mice by inhibiting the Th1 immune response and inducing the differentiation of Tregs. Our study also demonstrated the therapeutic potential of ALA in Treg-based cell therapies and islet transplantation used in the treatment of T1D.
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37
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The analysis of a subset of HLA region associations in type 1 diabetes and multiple sclerosis suggests the involvement mechanisms other than antigen presentation in the pathogenesis. INFORMATICS IN MEDICINE UNLOCKED 2022. [DOI: 10.1016/j.imu.2021.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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38
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Nakayama M, Michels AW. Using the T Cell Receptor as a Biomarker in Type 1 Diabetes. Front Immunol 2021; 12:777788. [PMID: 34868047 PMCID: PMC8635517 DOI: 10.3389/fimmu.2021.777788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/26/2021] [Indexed: 12/20/2022] Open
Abstract
T cell receptors (TCRs) are unique markers that define antigen specificity for a given T cell. With the evolution of sequencing and computational analysis technologies, TCRs are now prime candidates for the development of next-generation non-cell based T cell biomarkers, which provide a surrogate measure to assess the presence of antigen-specific T cells. Type 1 diabetes (T1D), the immune-mediated form of diabetes, is a prototypical organ specific autoimmune disease in which T cells play a pivotal role in targeting pancreatic insulin-producing beta cells. While the disease is now predictable by measuring autoantibodies in the peripheral blood directed to beta cell proteins, there is an urgent need to develop T cell markers that recapitulate T cell activity in the pancreas and can be a measure of disease activity. This review focuses on the potential and challenges of developing TCR biomarkers for T1D. We summarize current knowledge about TCR repertoires and clonotypes specific for T1D and discuss challenges that are unique for autoimmune diabetes. Ultimately, the integration of large TCR datasets produced from individuals with and without T1D along with computational 'big data' analysis will facilitate the development of TCRs as potentially powerful biomarkers in the development of T1D.
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Affiliation(s)
- Maki Nakayama
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States
| | - Aaron W Michels
- Barbara Davis Center for Childhood Diabetes, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, United States.,Department of Medicine, University of Colorado School of Medicine, Aurora, CO, United States
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39
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Farahani RH, Esmaeilzadeh E, Asl AN, Heidari MF, Hazrati E. Frequency of HLA Alleles in a Group of Severe COVID-19 Iranian Patients. IRANIAN JOURNAL OF PUBLIC HEALTH 2021; 50:1882-1886. [PMID: 34722384 PMCID: PMC8542815 DOI: 10.18502/ijph.v50i9.7061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/12/2020] [Indexed: 11/24/2022]
Abstract
Background: Human Leukocyte Antigen (HLA) system composed of a group of related proteins with important functions in the immune system. Several studies have reported that there is a significant association between specific HLA alleles and the susceptibility to different infectious diseases. This study aimed to detect the specific HLA alleles that cause higher susceptibility to COVID-19, we analyzed the HLA allele frequency distribution in Iranian patients with a severe form of COVID-19. Methods: Overall, 48 severe cases of COVID-19 that were hospitalized and required intensive care unit (ICU) admission between Oct and Dec 2020 were included in this study. Genomic DNA was extracted from the peripheral blood samples and HLA typing (Locus A, B, and DR) was performed for the patients. Results: After analyzing and comparing the results with a reference group of 500 Iranian individuals, a significant association was found for HLA-B*38, HLA-A*68, HLA-A*24, and HLA-DRB1*01. Conclusion: These results may be valuable for studying the potential association of specific HLA alleles with susceptibility to COVID-19 and mortality due to the disease.
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Affiliation(s)
- Ramin Hamidi Farahani
- Department of Infectious Diseases, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Emran Esmaeilzadeh
- Department of Basic Medical Sciences, School of Medicine, AJA University of Medical Sciences, Tehran, Iran.,Fetal Health Research Center, Hope Generation Foundation, Tehran, Iran
| | - Amir Nezami Asl
- Department of Aerospace Medicine, School of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Mohammad Foad Heidari
- Department of Laboratory Sciences, School of Aerospace and Subaquatic Medicine, AJA University of Medical Sciences, Tehran, Iran
| | - Ebrahim Hazrati
- Department of Critical Care Medicine, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran, Iran
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40
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Badal D, Sachdeva N, Maheshwari D, Basak P. Role of nucleic acid sensing in the pathogenesis of type 1 diabetes. World J Diabetes 2021; 12:1655-1673. [PMID: 34754369 PMCID: PMC8554372 DOI: 10.4239/wjd.v12.i10.1655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/22/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023] Open
Abstract
During infections, nucleic acids of pathogens are also engaged in recognition via several exogenous and cytosolic pattern recognition receptors, such as the toll-like receptors, retinoic acid inducible gene-I-like receptors, and nucleotide-binding and oligomerization domain-like receptors. The binding of the pathogen-derived nucleic acids to their corresponding sensors initiates certain downstream signaling cascades culminating in the release of type-I interferons (IFNs), especially IFN-α and other cytokines to induce proinflammatory responses towards invading pathogens leading to their clearance from the host. Although these sensors are hardwired to recognize pathogen associated molecular patterns, like viral and bacterial nucleic acids, under unusual physiological conditions, such as excessive cellular stress and increased apoptosis, endogenous self-nucleic acids like DNA, RNA, and mitochondrial DNA are also released. The presence of these self-nucleic acids in extranuclear compartments or extracellular spaces or their association with certain proteins sometimes leads to the failure of discriminating mechanisms of nucleic acid sensors leading to proinflammatory responses as seen in autoimmune disorders, like systemic lupus erythematosus, psoriasis and to some extent in type 1 diabetes (T1D). This review discusses the involvement of various nucleic acid sensors in autoimmunity and discusses how aberrant recognition of self-nucleic acids by their sensors activates the innate immune responses during the pathogenesis of T1D.
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Affiliation(s)
- Darshan Badal
- Department of Pediatrics, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Naresh Sachdeva
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Deep Maheshwari
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
| | - Preetam Basak
- Department of Endocrinology, Post Graduate Institute of Medical Education and Research, Chandigarh 160012, India
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41
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Kahn SE, Chen YC, Esser N, Taylor AJ, van Raalte DH, Zraika S, Verchere CB. The β Cell in Diabetes: Integrating Biomarkers With Functional Measures. Endocr Rev 2021; 42:528-583. [PMID: 34180979 PMCID: PMC9115372 DOI: 10.1210/endrev/bnab021] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Indexed: 02/08/2023]
Abstract
The pathogenesis of hyperglycemia observed in most forms of diabetes is intimately tied to the islet β cell. Impairments in propeptide processing and secretory function, along with the loss of these vital cells, is demonstrable not only in those in whom the diagnosis is established but typically also in individuals who are at increased risk of developing the disease. Biomarkers are used to inform on the state of a biological process, pathological condition, or response to an intervention and are increasingly being used for predicting, diagnosing, and prognosticating disease. They are also proving to be of use in the different forms of diabetes in both research and clinical settings. This review focuses on the β cell, addressing the potential utility of genetic markers, circulating molecules, immune cell phenotyping, and imaging approaches as biomarkers of cellular function and loss of this critical cell. Further, we consider how these biomarkers complement the more long-established, dynamic, and often complex measurements of β-cell secretory function that themselves could be considered biomarkers.
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Affiliation(s)
- Steven E Kahn
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and University of Washington, Seattle, 98108 WA, USA
| | - Yi-Chun Chen
- BC Children's Hospital Research Institute and Centre for Molecular Medicine and Therapeutics, Vancouver, BC, V5Z 4H4, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Nathalie Esser
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and University of Washington, Seattle, 98108 WA, USA
| | - Austin J Taylor
- BC Children's Hospital Research Institute and Centre for Molecular Medicine and Therapeutics, Vancouver, BC, V5Z 4H4, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
| | - Daniël H van Raalte
- Department of Internal Medicine, Amsterdam University Medical Center (UMC), Vrije Universiteit (VU) University Medical Center, 1007 MB Amsterdam, The Netherlands.,Department of Experimental Vascular Medicine, Amsterdam University Medical Center (UMC), Academic Medical Center, 1007 MB Amsterdam, The Netherlands
| | - Sakeneh Zraika
- Division of Metabolism, Endocrinology and Nutrition, Department of Medicine, VA Puget Sound Health Care System and University of Washington, Seattle, 98108 WA, USA
| | - C Bruce Verchere
- BC Children's Hospital Research Institute and Centre for Molecular Medicine and Therapeutics, Vancouver, BC, V5Z 4H4, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada.,Department of Surgery, University of British Columbia, Vancouver, BC, V5Z 4H4, Canada
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42
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Clinical features, epidemiology, autoantibody status, HLA haplotypes and genetic mechanisms of type 1 diabetes mellitus among children in Qatar. Sci Rep 2021; 11:18887. [PMID: 34556755 PMCID: PMC8460652 DOI: 10.1038/s41598-021-98460-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 09/03/2021] [Indexed: 11/08/2022] Open
Abstract
To describe the clinical features, epidemiology, autoantibody status, HLA haplotypes and genetic mechanisms of type 1 diabetes mellitus (T1DM). Patients (0-18 years) with diabetes were recruited. Clinical data was collected, autoantibodies and c-peptide were measured. Whole Genome Sequencing was performed. Genomic data analysis was compared with the known genes linked with T1DM and HLA alleles were studied. 1096 patients had one or more antibody positivity. The incidence of T1DM in 2020 was 38.05 per 100,000 children and prevalence was 249.73. GADA was the most common autoantibody followed by IAA. Variants in GSTCD, SKAP2, SLC9B1, BANK1 were most prevalent. An association of HLA haplotypes DQA1*03:01:01G (OR = 2.46, p value = 0.011) and DQB1*03:02:01G (OR = 2.43, p value = 0.022) was identified. The incidence of T1DM in Qatar is the fourth highest in the world, IA2 autoantibody was the most specific with some patients only having ZnT8 or IA2 autoantibodies thus underlining the necessity of profiling all 4 autoantibodies. The genes associated with T1DM in the Arab population were different from those that are common in the Caucasian population. HLA-DQ was enriched in the Qatari patients suggesting that it can be considered a major risk factor at an early age.
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43
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Functional interrogation of autoimmune disease genetics using CRISPR/Cas9 technologies and massively parallel reporter assays. Semin Immunopathol 2021; 44:137-147. [PMID: 34508276 PMCID: PMC8837574 DOI: 10.1007/s00281-021-00887-4] [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: 06/30/2021] [Accepted: 08/13/2021] [Indexed: 02/07/2023]
Abstract
Genetic studies, including genome-wide association studies, have identified many common variants that are associated with autoimmune diseases. Strikingly, in addition to being frequently observed in healthy individuals, a number of these variants are shared across diseases with diverse clinical presentations. This highlights the potential for improved autoimmune disease understanding which could be achieved by characterising the mechanism by which variants lead to increased risk of disease. Of particular interest is the potential for identifying novel drug targets or of repositioning drugs currently used in other diseases. The majority of autoimmune disease variants do not alter coding regions and it is often difficult to generate a plausible hypothetical mechanism by which variants affect disease-relevant genes and pathways. Given the interest in this area, considerable effort has been invested in developing and applying appropriate methodologies. Two of the most important technologies in this space include both low- and high-throughput genomic perturbation using the CRISPR/Cas9 system and massively parallel reporter assays. In this review, we introduce the field of autoimmune disease functional genomics and use numerous examples to demonstrate the recent and potential future impact of these technologies.
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44
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Jiang Z, Ren W, Liang H, Yan J, Yang D, Luo S, Zheng X, Lin GW, Xian Y, Xu W, Yao B, Noble JA, Bei JX, Groop L, Weng J. HLA class I genes modulate disease risk and age at onset together with DR-DQ in Chinese patients with insulin-requiring type 1 diabetes. Diabetologia 2021; 64:2026-2036. [PMID: 34023962 PMCID: PMC8382651 DOI: 10.1007/s00125-021-05476-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 04/01/2021] [Indexed: 02/08/2023]
Abstract
AIMS/HYPOTHESIS The study aimed to investigate the effects of HLA class I genes on susceptibility to type 1 diabetes with different onset ages, in addition to the well-established effects of HLA class II genes. METHODS A total of 361 patients with type 1 diabetes (192 patients with onset <18 years and 169 patients with onset ≥18 years) and 500 healthy control participants from China were enrolled and genotyped for the HLA-A, -B, -C, -DQA1, -DQB1 and -DRB1 genes using next-generation sequencing. RESULTS The susceptible DR3 (β = -0.09, p = 0.0009) and DR4-DQ8 (β = -0.13, p = 0.0059) haplotypes were negatively associated with onset age, while the protective DR11 (β = 0.21, p = 0.0314) and DR12 (β = 0.27, p < 0.0001) haplotypes were positively associated with onset age. After adjustment for linkage disequilibrium with DR-DQ haplotypes, A*11:01:01 was positively associated with onset age (β = 0.06, p = 0.0370), while the susceptible C*15:02:01 was negatively associated with onset age (β = -0.21, p = 0.0050). The unit for β was double square-root (fourth root) transformed years of change in onset age associated with per copy of the HLA haplotype/allele. In addition, B*46:01:01 was protective (OR 0.41, 0.46; pc [corrected for multiple comparisons] = 0.0044, 0.0040), whereas A*24:02:01 (OR 2.71, 2.25; pc = 0.0003, 0.0002) and B*54:01:01 (OR 3.96, 3.79; pc = 0.0018, 0.0004) were predisposing in both the <18 group and the ≥18 group compared with healthy control participants. In the context of DR4-DQ4, A*11:01:01 (61.29% vs 28.26%, pc = 0.0144) was increased while the predisposing A*24:02:01 (19.35% vs 47.83%, pc = 0.0403) was decreased in patients with onset ≥18 years when compared with patients with onset <18 years. CONCLUSIONS/INTERPRETATION In addition to DR-DQ haplotypes, novel HLA class I alleles were detected to play a role in susceptibility to type 1 diabetes with different onset ages, which could improve the understanding of disease heterogeneity and has implications for the design of future studies.
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Affiliation(s)
- Ziyu Jiang
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wenqian Ren
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Hua Liang
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jinhua Yan
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Daizhi Yang
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sihui Luo
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Endocrinology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xueying Zheng
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Department of Endocrinology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Guo-Wang Lin
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yingxin Xian
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wen Xu
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Bin Yao
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Leif Groop
- Department of Clinical Sciences, Lund University Diabetes Centre, Lund University, Skåne University Hospital, Malmö, Sweden
| | - Jianping Weng
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
- Department of Endocrinology of the First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
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45
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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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The Multifactorial Progression from the Islet Autoimmunity to Type 1 Diabetes in Children. Int J Mol Sci 2021; 22:ijms22147493. [PMID: 34299114 PMCID: PMC8305179 DOI: 10.3390/ijms22147493] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/04/2021] [Accepted: 07/09/2021] [Indexed: 12/12/2022] Open
Abstract
Type 1 Diabetes (T1D) results from autoimmune destruction of insulin producing pancreatic ß-cells. This disease, with a peak incidence in childhood, causes the lifelong need for insulin injections and necessitates careful monitoring of blood glucose levels. However, despite the current insulin therapies, it still shortens life expectancy due to complications affecting multiple organs. Recently, the incidence of T1D in childhood has increased by 3-5% per year in most developed Western countries. The heterogeneity of the disease process is supported by the findings of follow-up studies started early in infancy. The development of T1D is usually preceded by the appearance of autoantibodies targeted against antigens expressed in the pancreatic islets. The risk of T1D increases significantly with an increasing number of positive autoantibodies. The order of autoantibody appearance affects the disease risk. Genetic susceptibility, mainly defined by the human leukocyte antigen (HLA) class II gene region and environmental factors, is important in the development of islet autoimmunity and T1D. Environmental factors, mainly those linked to the changes in the gut microbiome as well as several pathogens, especially viruses, and diet are key modulators of T1D. The aim of this paper is to expand the understanding of the aetiology and pathogenesis of T1D in childhood by detailed description and comparison of factors affecting the progression from the islet autoimmunity to T1D in children.
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Amdare N, Purcell AW, DiLorenzo TP. Noncontiguous T cell epitopes in autoimmune diabetes: From mice to men and back again. J Biol Chem 2021; 297:100827. [PMID: 34044020 PMCID: PMC8233151 DOI: 10.1016/j.jbc.2021.100827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/18/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
Type 1 diabetes (T1D) is a T cell-mediated autoimmune disease that affects the insulin-producing beta cells of the pancreatic islets. The nonobese diabetic mouse is a widely studied spontaneous model of the disease that has contributed greatly to our understanding of T1D pathogenesis. This is especially true in the case of antigen discovery. Upon review of existing knowledge concerning the antigens and peptide epitopes that are recognized by T cells in this model, good concordance is observed between mouse and human antigens. A fascinating recent illustration of the contribution of the nonobese diabetic mouse in the area of epitope identification is the discovery of noncontiguous CD4+ T cell epitopes. This novel epitope class is characterized by the linkage of an insulin-derived peptide to, most commonly, a fragment of a natural cleavage product of another beta cell secretory granule constituent. These so-called hybrid insulin peptides are also recognized by T cells in patients with T1D, although the precise mechanism for their generation has yet to be defined and is the subject of active investigation. Although evidence from the tumor immunology arena documented the existence of noncontiguous CD8+ T cell epitopes, generated by proteasome-mediated peptide splicing involving transpeptidation, such CD8+ T cell epitopes were thought to be a rare immunological curiosity. However, recent advances in bioinformatics and mass spectrometry have challenged this view. These developments, coupled with the discovery of hybrid insulin peptides, have spurred a search for noncontiguous CD8+ T cell epitopes in T1D, an exciting frontier area still in its infancy.
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Affiliation(s)
- Nitin Amdare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Teresa P DiLorenzo
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA; Division of Endocrinology, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA; Einstein-Mount Sinai Diabetes Research Center, Albert Einstein College of Medicine, Bronx, New York, USA; The Fleischer Institute for Diabetes and Metabolism, Albert Einstein College of Medicine, Bronx, New York, USA.
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Satin LS, Soleimanpour SA, Walker EM. New Aspects of Diabetes Research and Therapeutic Development. Pharmacol Rev 2021; 73:1001-1015. [PMID: 34193595 DOI: 10.1124/pharmrev.120.000160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Both type 1 and type 2 diabetes mellitus are advancing at exponential rates, placing significant burdens on health care networks worldwide. Although traditional pharmacologic therapies such as insulin and oral antidiabetic stalwarts like metformin and the sulfonylureas continue to be used, newer drugs are now on the market targeting novel blood glucose-lowering pathways. Furthermore, exciting new developments in the understanding of beta cell and islet biology are driving the potential for treatments targeting incretin action, islet transplantation with new methods for immunologic protection, and the generation of functional beta cells from stem cells. Here we discuss the mechanistic details underlying past, present, and future diabetes therapies and evaluate their potential to treat and possibly reverse type 1 and 2 diabetes in humans. SIGNIFICANCE STATEMENT: Diabetes mellitus has reached epidemic proportions in the developed and developing world alike. As the last several years have seen many new developments in the field, a new and up to date review of these advances and their careful evaluation will help both clinical and research diabetologists to better understand where the field is currently heading.
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Affiliation(s)
- Leslie S Satin
- Department of Pharmacology (L.S.S.), Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine (L.S.S., S.A.S., E.M.W.), and Brehm Diabetes Center (L.S.S., S.A.S., E.M.W.), University of Michigan Medical School, Ann Arbor, Michigan; and VA Ann Arbor Healthcare System, Ann Arbor, Michigan (S.A.S.) ; ;
| | - Scott A Soleimanpour
- Department of Pharmacology (L.S.S.), Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine (L.S.S., S.A.S., E.M.W.), and Brehm Diabetes Center (L.S.S., S.A.S., E.M.W.), University of Michigan Medical School, Ann Arbor, Michigan; and VA Ann Arbor Healthcare System, Ann Arbor, Michigan (S.A.S.)
| | - Emily M Walker
- Department of Pharmacology (L.S.S.), Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine (L.S.S., S.A.S., E.M.W.), and Brehm Diabetes Center (L.S.S., S.A.S., E.M.W.), University of Michigan Medical School, Ann Arbor, Michigan; and VA Ann Arbor Healthcare System, Ann Arbor, Michigan (S.A.S.) ; ;
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Epigenetic Changes Induced by Maternal Factors during Fetal Life: Implication for Type 1 Diabetes. Genes (Basel) 2021; 12:genes12060887. [PMID: 34201206 PMCID: PMC8227197 DOI: 10.3390/genes12060887] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
Organ-specific autoimmune diseases, such as type 1 diabetes, are believed to result from T-cell-mediated damage of the target tissue. The immune-mediated tissue injury, in turn, is known to depend on complex interactions between genetic and environmental factors. Nevertheless, the mechanisms whereby environmental factors contribute to the pathogenesis of autoimmune diseases remain elusive and represent a major untapped target to develop novel strategies for disease prevention. Given the impact of the early environment on the developing immune system, epigenetic changes induced by maternal factors during fetal life have been linked to a likelihood of developing an autoimmune disease later in life. In humans, DNA methylation is the epigenetic mechanism most extensively investigated. This review provides an overview of the critical role of DNA methylation changes induced by prenatal maternal conditions contributing to the increased risk of immune-mediated diseases on the offspring, with a particular focus on T1D. A deeper understanding of epigenetic alterations induced by environmental stressors during fetal life may be pivotal for developing targeted prevention strategies of type 1 diabetes by modifying the maternal environment.
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50
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Alshiekh S, Geraghty DE, Agardh D. High-resolution genotyping of HLA class I loci in children with type 1 diabetes and celiac disease. HLA 2021; 97:505-511. [PMID: 33885207 DOI: 10.1111/tan.14280] [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: 12/15/2020] [Accepted: 04/19/2021] [Indexed: 01/12/2023]
Abstract
OBJECTIVES HLA-DQ2 and DQ8 contribute to the strongest risk haplotypes for type 1 diabetes (T1D) and celiac disease (CD). The variation in genetic risk association is likely linked to different HLA class II loci susceptibility, but association studies of HLA class I alleles are scarce. The aim was to investigate HLA class I A, B, and C alleles polymorphisms in children with only T1D, CD, and a subgroup with both T1D and CD (T1D w/CD). MATERIALS AND METHODS HLA class I A, B, and C genes were genotyped using next-generation targeted sequencing. A conditional analysis was performed on 68 children with T1D, 219 children with CD and seven children with T1D w/CD enrolled from a birth cohort study at high genetic risk children from the South of Sweden. RESULTS Among 1764 HLA class I allele variants, A*29:02:01 in T1D w/CD was associated with both T1D (OR = 21.42 [1.05, 1322.4], p = 0.0231) and CD (OR = 35 [2.36, 529.12], p = 0.0051) along with C*05:01:01 with both T1D (OR = 5.54 [1.06, 24.8], p = 0.02) and CD (OR = 6.84 [1.46, 26.01], p = 0.0077). No independent effects of HLA-B allele associations were observed in T1D w/CD. CONCLUSION Although the distribution of HLA class I alleles differs between children with T1D and CD, the A*29:02:01 and C*05:01:01 alleles showed shared risk association of both diseases.
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Affiliation(s)
- Shehab Alshiekh
- Department of Clinical Sciences, Lund University, Malmö, Sweden.,Department of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Daniel Agardh
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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