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Yue T, Tan H, Wang C, Liu Z, Yang D, Ding Y, Xu W, Yan J, Zheng X, Weng J, Luo S. High-risk genotypes for type 1 diabetes are associated with the imbalance of gut microbiome and serum metabolites. Front Immunol 2022; 13:1033393. [PMID: 36582242 PMCID: PMC9794034 DOI: 10.3389/fimmu.2022.1033393] [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: 08/31/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Background The profile of gut microbiota, serum metabolites, and lipids of type 1 diabetes (T1D) patients with different human leukocyte antigen (HLA) genotypes remains unknown. We aimed to explore gut microbiota, serum metabolites, and lipids signatures in individuals with T1D typed by HLA genotypes. Methods We did a cross-sectional study that included 73 T1D adult patients. Patients were categorized into two groups according to the HLA haplotypes they carried: those with any two of three susceptibility haplotypes (DR3, DR4, DR9) and without any of the protective haplotypes (DR8, DR11, DR12, DR15, DR16) were defined as high-risk HLA genotypes group (HR, n=30); those with just one or without susceptibility haplotypes as the non-high-risk HLA genotypes group (NHR, n=43). We characterized the gut microbiome profile with 16S rRNA gene amplicon sequencing and analyzed serum metabolites with liquid chromatography-mass spectrometry. Results Study individuals were 32.5 (8.18) years old, and 60.3% were female. Compared to NHR, the gut microbiota of HR patients were characterized by elevated abundances of Prevotella copri and lowered abundances of Parabacteroides distasonis. Differential serum metabolites (hypoxanthine, inosine, and guanine) which increased in HR were involved in purine metabolism. Different lipids, phosphatidylcholines and phosphatidylethanolamines, decreased in HR group. Notably, Parabacteroides distasonis was negatively associated (p ≤ 0.01) with hypoxanthine involved in purine metabolic pathways. Conclusions The present findings enabled a better understanding of the changes in gut microbiome and serum metabolome in T1D patients with HLA risk genotypes. Alterations of the gut microbiota and serum metabolites may provide some information for distinguishing T1D patients with different HLA risk genotypes.
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Affiliation(s)
- Tong Yue
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Huiling Tan
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Chaofan Wang
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Ziyu Liu
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Daizhi Yang
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu Ding
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wen Xu
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jinhua Yan
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xueying Zheng
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jianping Weng
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China,*Correspondence: Jianping Weng, ; Sihui Luo,
| | - Sihui Luo
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China,*Correspondence: Jianping Weng, ; Sihui Luo,
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Pandi S, Chinniah R, Sevak V, Ravi PM, Raju M, Vellaiappan NA, Karuppiah B. Association of HLA-DRB1, DQA1 and DQB1 alleles and haplotype in Parkinson's disease from South India. Neurosci Lett 2021; 765:136296. [PMID: 34655711 DOI: 10.1016/j.neulet.2021.136296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 10/01/2021] [Accepted: 10/11/2021] [Indexed: 10/20/2022]
Abstract
Parkinson's disease (PD) is a chronic, neurodegenerative motor disease exhibiting familial and sporadic forms. The present study was aimed to elucidate the association of HLA-DRB1*, DQA1* and DQB1* alleles with PD. A total of 105 PD patients and 100 healthy controls were typed by PCR-SSP method. We further carried out high-resolution genotyping for DQB1 and DQA1. Results revealed the increased frequencies of alleles DRB1*04 (OR = 2.36), DRB1* 13 (OR = 4.04), DQA1* 01:04:01 (OR = 4.51), DQB1*02:01 (OR = 2.66) and DQB1*06:03 (OR = 2.65) in PD patients suggesting susceptible associations. Further, decreased frequencies observed for alleles DRB1*10 (OR = 0.34), DRB1*15 (OR = 0.44), DQA1*04:01 (OR = 0.28), DQA1*06:01 (OR = 0.11) and HLA-DQB1*05:01 (OR = 0.37) among patients have suggested protective associations. Significant disease associations were observed for two-locus haplotype such as DRB1*13-DQB1*06:03 (OR = 11.52), DQA1*01:041-DQB1*06:03 (OR = 16.50), DQA1*01:041-DQB1*05:02 (OR = 5.38) and DQA1*04:01-DQB1*06:03 (OR = 3.027). Protective associations were observed for haplotypes DRB1*10-DQB1*05:01 (OR = 0.21), DRB1*15-DQB1*06 (OR = 0.006), DQA1*04:01-DQB1*05:01 (OR = 0.400) and DQA1*04:01-DQB1*05:03 (OR = 0.196). The critical amino acid residue analyses have revealed strong susceptible association for the residues of DQB1 alleles such as: L26, S28, K71, T71 and A74, Y9, S30, D37, I37, A38, A57 and S57; and for the residues of DQA1 alleles such as: C11, F61, I74, and M76. Similarly, amino acid residues such as A13, G26, Y26, A71, S74, L9 and V38 of HLA-DQB1 alleles and residues such as Y11, G61, S74 and L76 of DQA1 alleles showed protective associations. Thus, our study documented the susceptible and protective associations of DRB1*, DQB1 and DQA1 alleles and haplotypes in developing the disease and their influence on longevity of PD patients in south India.
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Affiliation(s)
- Sasiharan Pandi
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Rathika Chinniah
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Vandit Sevak
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Padma Malini Ravi
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | - Muthuppandi Raju
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India
| | | | - Balakrishnan Karuppiah
- Department of Immunology, School of Biological Sciences, Madurai, Tamil Nadu 625021, India.
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Subramani S, Bellizzi AM, Borcherding N, Kao SC, Dillon J, Howe J, Norris AW, Tansey MJ, Pinnaro CT. Hypoglycemia secondary to insulinoma masking the onset of type 1 diabetes in an adolescent. Clin Case Rep 2021; 9:e04868. [PMID: 34594558 PMCID: PMC8462061 DOI: 10.1002/ccr3.4868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/16/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Type 1 diabetes and insulinoma can co-occur in pediatric patients and may present with episodes of hypo- and hyperglycemia, significant glycemic variability, and weight gain. Surgical resection leads to development of fulminant diabetes.
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Affiliation(s)
- Sriya Subramani
- Stead Family Department of PediatricsUniversity of IowaIowa CityIAUSA
| | | | - Nicholas Borcherding
- Department of Pathology & ImmunologyWashington University School of Medicine in St. LouisSt. LouisMOUSA
| | - Simon C. Kao
- Department of RadiologyDivision of Pediatric RadiologyUniversity of IowaIowa CityIAUSA
| | - Joseph Dillon
- Department of Internal MedicineDivision of EndocrinologyUniversity of IowaIowa CityIAUSA
| | - James Howe
- Department of SurgeryDivision of Surgical Oncology and Endocrine SurgeryUniversity of IowaIowa CityIAUSA
| | - Andrew W. Norris
- Stead Family Department of PediatricsUniversity of IowaIowa CityIAUSA
- Fraternal Order of Eagles Diabetes Research CenterUniversity of IowaIowa CityIAUSA
| | - Michael J. Tansey
- Stead Family Department of PediatricsUniversity of IowaIowa CityIAUSA
- Fraternal Order of Eagles Diabetes Research CenterUniversity of IowaIowa CityIAUSA
| | - Catherina T. Pinnaro
- Stead Family Department of PediatricsUniversity of IowaIowa CityIAUSA
- Fraternal Order of Eagles Diabetes Research CenterUniversity of IowaIowa CityIAUSA
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Mobini Kesheh M, Shavandi S, Hosseini P, Kakavand-Ghalehnoei R, Keyvani H. Bioinformatic HLA Studies in the Context of SARS-CoV-2 Pandemic and Review on Association of HLA Alleles with Preexisting Medical Conditions. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6693909. [PMID: 34136572 PMCID: PMC8162251 DOI: 10.1155/2021/6693909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 02/10/2021] [Accepted: 05/06/2021] [Indexed: 12/15/2022]
Abstract
After the announcement of a new coronavirus in China in December 2019, which was then called SARS-CoV-2, this virus changed to a global concern and it was then declared as a pandemic by WHO. Human leukocyte antigen (HLA) alleles, which are one of the most polymorphic genes, play a pivotal role in both resistance and vulnerability of the body against viruses and other infections as well as chronic diseases. The association between HLA alleles and preexisting medical conditions such as cardiovascular diseases and diabetes mellitus is reported in various studies. In this review, we focused on the bioinformatic HLA studies to summarize the HLA alleles which responded to SARS-CoV-2 peptides and have been used to design vaccines. We also reviewed HLA alleles that are associated with comorbidities and might be related to the high mortality rate among COVID-19 patients. Since both genes and patients' medical conditions play a key role in both severity of the disease and the mortality rate in COVID-19 patients, a better understanding of the connection between HLA alleles and SARS-CoV-2 can provide a wider perspective on the behavior of the virus. Such understanding can help scientists, especially in terms of protecting healthcare workers and designing effective vaccines.
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Affiliation(s)
- Mina Mobini Kesheh
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sara Shavandi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Parastoo Hosseini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Hossein Keyvani
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Abstract
Neonatal diabetes (ND) appears during the first months of life and is caused by a single gene mutation. It is heterogenous and very different compared to other forms of multi-factorial or polygenic diabetes. Clinically, this form is extremely severe, however, early genetic diagnosis is pivotal for successful therapy. A large palette of genes is demonstrated to be a cause of ND, however, the mechanisms of permanent hyperglycemia are different. This review will give an overview of more frequent genetic mutations causing ND, including the function of the mutated genes and the specific therapy for certain sub-forms.
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Jacobi T, Massier L, Klöting N, Horn K, Schuch A, Ahnert P, Engel C, Löffler M, Burkhardt R, Thiery J, Tönjes A, Stumvoll M, Blüher M, Doxiadis I, Scholz M, Kovacs P. HLA Class II Allele Analyses Implicate Common Genetic Components in Type 1 and Non-Insulin-Treated Type 2 Diabetes. J Clin Endocrinol Metab 2020; 105:5715056. [PMID: 31974565 DOI: 10.1210/clinem/dgaa027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/15/2020] [Indexed: 12/20/2022]
Abstract
CONTEXT Common genetic susceptibility may underlie the frequently observed co-occurrence of type 1 and type 2 diabetes in families. Given the role of HLA class II genes in the pathophysiology of type 1 diabetes, the aim of the present study was to test the association of high density imputed human leukocyte antigen (HLA) genotypes with type 2 diabetes. OBJECTIVES AND DESIGN Three cohorts (Ntotal = 10 413) from Leipzig, Germany were included in this study: LIFE-Adult (N = 4649), LIFE-Heart (N = 4815) and the Sorbs (N = 949) cohort. Detailed metabolic phenotyping and genome-wide single nucleotide polymorphism (SNP) data were available for all subjects. Using 1000 Genome imputation data, HLA genotypes were imputed on 4-digit level and association tests for type 2 diabetes, and related metabolic traits were conducted. RESULTS In a meta-analysis including all 3 cohorts, the absence of HLA-DRB5 was associated with increased risk of type 2 diabetes (P = 0.001). In contrast, HLA-DQB*06:02 and HLA-DQA*01:02 had a protective effect on type 2 diabetes (P = 0.005 and 0.003, respectively). Both alleles are part of the well-established type 1 diabetes protective haplotype DRB1*15:01~DQA1*01:02~DQB1*06:02, which was also associated with reduced risk of type 2 diabetes (OR 0.84; P = 0.005). On the contrary, the DRB1*07:01~DQA1*02:01~DQB1*03:03 was identified as a risk haplotype in non-insulin-treated diabetes (OR 1.37; P = 0.002). CONCLUSIONS Genetic variation in the HLA class II locus exerts risk and protective effects on non-insulin-treated type 2 diabetes. Our data suggest that the genetic architecture of type 1 diabetes and type 2 diabetes might share common components on the HLA class II locus.
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Affiliation(s)
- Thomas Jacobi
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Lucas Massier
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Nora Klöting
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Alexander Schuch
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Peter Ahnert
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Markus Löffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Ralph Burkhardt
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine and Clinical Chemistry, University of Leipzig, Leipzig, Germany
| | - Anke Tönjes
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Michael Stumvoll
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Matthias Blüher
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Ilias Doxiadis
- Institute for Transfusion Medicine, University Hospital of Leipzig, Leipzig, Germany
| | - Markus Scholz
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- University of Leipzig Medical Center, IFB Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
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Zhao LP, Papadopoulos GK, Kwok WW, Xu B, Kong M, Moustakas AK, Bondinas GP, Carlsson A, Elding-Larsson H, Ludvigsson J, Marcus C, Persson M, Samuelsson U, Wang R, Pyo CW, Nelson WC, Geraghty DE, Lernmark Å. Eleven Amino Acids of HLA-DRB1 and Fifteen Amino Acids of HLA-DRB3, 4, and 5 Include Potentially Causal Residues Responsible for the Risk of Childhood Type 1 Diabetes. Diabetes 2019; 68:1692-1704. [PMID: 31127057 PMCID: PMC6692811 DOI: 10.2337/db19-0273] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/21/2019] [Indexed: 12/25/2022]
Abstract
Next-generation targeted sequencing of HLA-DRB1 and HLA-DRB3, -DRB4, and -DRB5 (abbreviated as DRB345) provides high resolution of functional variant positions to investigate their associations with type 1 diabetes risk and with autoantibodies against insulin (IAA), GAD65 (GADA), IA-2 (IA-2A), and ZnT8 (ZnT8A). To overcome exceptional DR sequence complexity as a result of high polymorphisms and extended linkage disequilibrium among the DR loci, we applied a novel recursive organizer (ROR) to discover disease-associated amino acid residues. ROR distills disease-associated DR sequences and identifies 11 residues of DRB1, sequences of which retain all significant associations observed by DR genes. Furthermore, all 11 residues locate under/adjoining the peptide-binding groove of DRB1, suggesting a plausible functional mechanism through peptide binding. The 15 residues of DRB345, located respectively in the β49-55 homodimerization patch and on the face of the molecule shown to interact with and bind to the accessory molecule CD4, retain their significant disease associations. Further ROR analysis of DR associations with autoantibodies finds that DRB1 residues significantly associated with ZnT8A and DRB345 residues with GADA. The strongest association is between four residues (β14, β25, β71, and β73) and IA-2A, in which the sequence ERKA confers a risk association (odds ratio 2.15, P = 10-18), and another sequence, ERKG, confers a protective association (odds ratio 0.59, P = 10-11), despite a difference of only one amino acid. Because motifs of identified residues capture potentially causal DR associations with type 1 diabetes, this list of residuals is expected to include corresponding causal residues in this study population.
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Affiliation(s)
- Lue Ping Zhao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Corresponding authors: Lue Ping Zhao, ; George K. Papadopoulos, ; and Åke Lernmark,
| | - George K. Papadopoulos
- Laboratory of Biophysics, Biochemistry, Biomaterials and Bioprocessing, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece, presently known as Department of Agriculture, University of Ioannina, Ioannina, Greece
| | | | - Bryan Xu
- College of Letters and Sciences, University of California, Berkeley, CA
| | - Matthew Kong
- Department of Computer Sciences, Carnegie Mellon University, Pittsburgh, PA
| | - Antonis K. Moustakas
- Department of Food Science and Technology, Ionian University, Argostoli, Cephalonia, Greece
| | - George P. Bondinas
- Laboratory of Biophysics, Biochemistry, Biomaterials and Bioprocessing, Faculty of Agricultural Technology, Technological Educational Institute of Epirus, Arta, Greece, presently known as Department of Agriculture, University of Ioannina, Ioannina, Greece
| | - Annelie Carlsson
- Department of Clinical Sciences, Lund University/Clinical Research Centre, Skåne University Hospital, Malmö, Sweden
| | | | - Johnny Ludvigsson
- Crown Princess Victoria Children’s Hospital, Region Östergötland, and Division of Pediatrics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Claude Marcus
- Department of Clinical Science and Education and Institution of Medicine, Clinical Epidemiology, Karolinska Institutet, Solna, Sweden
| | - Martina Persson
- Department of Clinical Science and Education and Institution of Medicine, Clinical Epidemiology, Karolinska Institutet, Solna, Sweden
| | - Ulf Samuelsson
- Crown Princess Victoria Children’s Hospital, Region Östergötland, and Division of Pediatrics, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Ruihan Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Chul-Woo Pyo
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Wyatt C. Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Daniel E. Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/Clinical Research Centre, Skåne University Hospital, Malmö, Sweden
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Abstract
PURPOSE OF REVIEW Theories about the pathogenesis of type 1 diabetes (T1D) refer to the potential of primary islet inflammatory signaling as a trigger for the loss of self-tolerance leading to disease onset. Emerging evidence suggests that extracellular vesicles (EV) may represent the missing link between inflammation and autoimmunity. Here, we review the evidence for a role of EV in the pathogenesis of T1D, as well as discuss their potential value in the clinical sphere, as biomarkers and therapeutic agents. RECENT FINDINGS EV derived from β cells are enriched in diabetogenic autoantigens and miRNAs that are selectively sorted and packaged. These EV play a pivotal role in antigen presentation and cell to cell communication leading to activation of autoimmune responses. Furthermore, recent evidence suggests the potential of EV as novel tools in clinical diagnostics and therapeutic interventions. In-depth analysis of EV cargo using modern multi-parametric technologies may be useful in enhancing our understanding of EV-mediated immune mechanisms and in identifying robust biomarkers and therapeutic strategies for T1D.
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Affiliation(s)
- Sarita Negi
- Human Islet Transplant Laboratory, Department of Surgery, D5.5736, Royal Victoria Hospital, McGill University Health Centre, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, Alberta, T6G 2E1, Canada
| | - Alissa K Rutman
- Human Islet Transplant Laboratory, Department of Surgery, D5.5736, Royal Victoria Hospital, McGill University Health Centre, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, Alberta, T6G 2E1, Canada
| | - Steven Paraskevas
- Human Islet Transplant Laboratory, Department of Surgery, D5.5736, Royal Victoria Hospital, McGill University Health Centre, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada.
- Canadian Donation and Transplantation Research Program, Edmonton, Alberta, T6G 2E1, Canada.
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9
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Anderson K, Carey B, Martin A, Roark C, Chalk C, Nowell-Bostic M, Freed B, Aubrey M, Trapnell B, Fontenot A. Pulmonary alveolar proteinosis: An autoimmune disease lacking an HLA association. PLoS One 2019; 14:e0213179. [PMID: 30845238 PMCID: PMC6405167 DOI: 10.1371/journal.pone.0213179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 02/15/2019] [Indexed: 11/29/2022] Open
Abstract
Pulmonary alveolar proteinosis (PAP) is a rare lung disease characterized by the accumulation of pulmonary surfactant in alveolar macrophages and alveoli, resulting in respiratory impairment and an increased risk of opportunistic infections. Autoimmune PAP is an autoimmune lung disease that is caused by autoantibodies directed against granulocyte-macrophage colony-stimulating factor (GM-CSF). A shared feature among many autoimmune diseases is a distinct genetic association to HLA alleles. In the present study, we HLA-typed patients with autoimmune PAP to determine if this disease had any HLA association. We analyzed amino acid and allele associations for HLA-A, B, C, DRB1, DQB1, DPB1, DRB3, DRB4 and DRB5 in 41 autoimmune PAP patients compared to 1000 ethnic-matched controls and did not find any HLA association with autoimmune PAP. Collectively, these data may suggest the absence of a genetic association to the HLA in the development of autoimmune PAP.
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Affiliation(s)
- Kirsten Anderson
- University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, United States of America
- ClinImmune Labs Aurora, CO, United States of America
- * E-mail: (KA); (AF)
| | - Brenna Carey
- Cincinatti Children’s Hospital Medical Center (CCHMC) Cincinnati, OH, United States of America
| | - Allison Martin
- University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, United States of America
| | | | - Claudia Chalk
- Cincinatti Children’s Hospital Medical Center (CCHMC) Cincinnati, OH, United States of America
| | - Marchele Nowell-Bostic
- Cincinatti Children’s Hospital Medical Center (CCHMC) Cincinnati, OH, United States of America
| | - Brian Freed
- University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, United States of America
- ClinImmune Labs Aurora, CO, United States of America
| | - Michael Aubrey
- University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, United States of America
- ClinImmune Labs Aurora, CO, United States of America
| | - Bruce Trapnell
- Cincinatti Children’s Hospital Medical Center (CCHMC) Cincinnati, OH, United States of America
| | - Andrew Fontenot
- University of Colorado Anschutz Medical Campus, Department of Medicine, Aurora, CO, United States of America
- * E-mail: (KA); (AF)
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10
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Cavalli M, Baltzer N, Umer HM, Grau J, Lemnian I, Pan G, Wallerman O, Spalinskas R, Sahlén P, Grosse I, Komorowski J, Wadelius C. Allele specific chromatin signals, 3D interactions, and motif predictions for immune and B cell related diseases. Sci Rep 2019; 9:2695. [PMID: 30804403 PMCID: PMC6389883 DOI: 10.1038/s41598-019-39633-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 01/24/2019] [Indexed: 12/20/2022] Open
Abstract
Several Genome Wide Association Studies (GWAS) have reported variants associated to immune diseases. However, the identified variants are rarely the drivers of the associations and the molecular mechanisms behind the genetic contributions remain poorly understood. ChIP-seq data for TFs and histone modifications provide snapshots of protein-DNA interactions allowing the identification of heterozygous SNPs showing significant allele specific signals (AS-SNPs). AS-SNPs can change a TF binding site resulting in altered gene regulation and are primary candidates to explain associations observed in GWAS and expression studies. We identified 17,293 unique AS-SNPs across 7 lymphoblastoid cell lines. In this set of cell lines we interrogated 85% of common genetic variants in the population for potential regulatory effect and we identified 237 AS-SNPs associated to immune GWAS traits and 714 to gene expression in B cells. To elucidate possible regulatory mechanisms we integrated long-range 3D interactions data to identify putative target genes and motif predictions to identify TFs whose binding may be affected by AS-SNPs yielding a collection of 173 AS-SNPs associated to gene expression and 60 to B cell related traits. We present a systems strategy to find functional gene regulatory variants, the TFs that bind differentially between alleles and novel strategies to detect the regulated genes.
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Affiliation(s)
- Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Nicholas Baltzer
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Uppsala University, Uppsala, Sweden
| | - Husen M Umer
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Uppsala University, Uppsala, Sweden
| | - Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Ioana Lemnian
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rapolas Spalinskas
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Pelin Sahlén
- Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ivo Grosse
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Computational Biology and Bioinformatics, Uppsala University, Uppsala, Sweden.,Institute of Computer Science, Polish Academy of Sciences, Warszawa, Poland
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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11
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Tung YC, Fann CSJ, Chang CC, Chu CC, Yang WS, Hwu WL, Chen PL, Tsai WY. Comprehensive human leukocyte antigen genotyping of patients with type 1 diabetes mellitus in Taiwan. Pediatr Diabetes 2018; 19:699-706. [PMID: 29383806 DOI: 10.1111/pedi.12645] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 12/11/2017] [Accepted: 12/27/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Type 1 diabetes (T1D) mellitus is an autoimmune disorder involving both complex genetic and environmental factors. The incidence rates are low in Asian countries, and the specific, explanatory genetic factors underlying this have been investigated. The aim of this study was to elucidate the association of human leukocyte antigen (HLA) alleles/haplotypes with T1D in Taiwan. METHODS We performed direct comprehensive genotyping of 6 classical HLA loci (HLA-A, -B, -C, -DPB1, -DQB1, and -DRB1) to 4-digit resolution in 104 unrelated T1D patients and 504 controls. Twenty-four of the 104 patients also exhibited thyroid autoimmunity. RESULTS Three major susceptibility haplotypes were identified: DRB1*03:01-DQB1*02:01 (odds ratio [OR] = 5.39 under the dominant model, P = 2.3 × 10-13 ), DRB1*04:05-DQB1*04:01 (OR = 2.44, P = 5.0 × 10-4 ), and DRB1*09:01-DQB1*03:03 (OR = 2.02, P = 1.4 × 10-3 ); one protective haplotype was identified: DRB1*08:03-DQB1*06:01 (OR = 0.10, P = 1.6 × 10-3 ). DRB1*03:01-DQB1*02:01, the major T1D susceptibility haplotype, was found at a lower frequency in T1D patients with thyroid autoimmunity. The T1D protective allele DRB1*12:02 was shown to be protective against Graves' disease in our previous report. CONCLUSION In addition to clarifying the roles of several known T1D HLA alleles and haplotypes, we discovered that the DRB1*08:03-DQB1*06:01 haplotype is protective against T1D. The DRB1*12:02 allele protected against both T1D and Graves' disease.
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Affiliation(s)
- Yi-Ching Tung
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Cathy S-J Fann
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | | | - Chen-Chung Chu
- Department of Medical Research, Mackay Memorial Hospital, Taipei, Taiwan
| | - Wei-Shiung Yang
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wuh-Liang Hwu
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan.,Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Yu Tsai
- Department of Pediatrics, National Taiwan University Hospital and College of Medicine, National Taiwan University, Taipei, Taiwan
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12
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Racine JJ, Stewart I, Ratiu J, Christianson G, Lowell E, Helm K, Allocco J, Maser RS, Chen YG, Lutz CM, Roopenian D, Schloss J, DiLorenzo TP, Serreze DV. Improved Murine MHC-Deficient HLA Transgenic NOD Mouse Models for Type 1 Diabetes Therapy Development. Diabetes 2018; 67:923-935. [PMID: 29472249 PMCID: PMC5909999 DOI: 10.2337/db17-1467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 02/12/2018] [Indexed: 02/04/2023]
Abstract
Improved mouse models for type 1 diabetes (T1D) therapy development are needed. T1D susceptibility is restored to normally resistant NOD.β2m-/- mice transgenically expressing human disease-associated HLA-A*02:01 or HLA-B*39:06 class I molecules in place of their murine counterparts. T1D is dependent on pathogenic CD8+ T-cell responses mediated by these human class I variants. NOD.β2m-/--A2.1 mice were previously used to identify β-cell autoantigens presented by this human class I variant to pathogenic CD8+ T cells and for testing therapies to attenuate such effectors. However, NOD.β2m-/- mice also lack nonclassical MHC I family members, including FcRn, required for antigen presentation, and maintenance of serum IgG and albumin, precluding therapies dependent on these molecules. Hence, we used CRISPR/Cas9 to directly ablate the NOD H2-Kd and H2-Db classical class I variants either individually or in tandem (cMHCI-/-). Ablation of the H2-Ag7 class II variant in the latter stock created NOD mice totally lacking in classical murine MHC expression (cMHCI/II-/-). NOD-cMHCI-/- mice retained nonclassical MHC I molecule expression and FcRn activity. Transgenic expression of HLA-A2 or -B39 restored pathogenic CD8+ T-cell development and T1D susceptibility to NOD-cMHCI-/- mice. These next-generation HLA-humanized NOD models may provide improved platforms for T1D therapy development.
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13
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Skog O, Korsgren O. Aetiology of type 1 diabetes: Physiological growth in children affects disease progression. Diabetes Obes Metab 2018; 20:775-785. [PMID: 29083510 DOI: 10.1111/dom.13144] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/06/2017] [Accepted: 10/25/2017] [Indexed: 12/16/2022]
Abstract
The prevailing view is that type 1 diabetes (T1D) develops as a consequence of a severe decline in β-cell mass resulting from T-cell-mediated autoimmunity; however, progression from islet autoantibody seroconversion to overt diabetes and finally to total loss of C-peptide production occurs in most affected individuals only slowly over many years or even decades. This slow disease progression should be viewed in relation to the total β-cell mass of only 0.2 to 1.5 g in adults without diabetes. Focal lesions of acute pancreatitis with accumulation of leukocytes, often located around the ducts, are frequently observed in people with recent-onset T1D, and most patients display extensive periductal fibrosis, the end stage of inflammation. An injurious inflammatory adverse event, occurring within the periductal area, may have negative implications for islet neogenesis, dependent on stem cells residing within or adjacent to the ductal epithelium. This could in part prevent the 30-fold increase in β-cell mass that would normally occur during the first 20 years of life. This increase occurs in order to maintain glucose metabolism during the physiological increases in insulin production that are required to balance the 20-fold increase in body weight during childhood and increased insulin resistance during puberty. Failure to expand β-cell mass during childhood would lead to clinically overt T1D and could help to explain the apparently more aggressive form of T1D occurring in growing children when compared with that observed in affected adults.
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Affiliation(s)
- Oskar Skog
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Olle Korsgren
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
- Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
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14
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Bahendeka S, Wesonga R, Were TP, Nyangabyaki C. Autoantibodies and HLA class II DR-DQ genotypes in Ugandan children and adolescents with type 1 diabetes mellitus. Int J Diabetes Dev Ctries 2018. [DOI: 10.1007/s13410-018-0622-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
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15
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Gerasimou P, Nicolaidou V, Skordis N, Picolos M, Monos D, Costeas PA. Combined effect of glutamine at position 70 of HLA-DRB1 and alanine at position 57 of HLA-DQB1 in type 1 diabetes: An epitope analysis. PLoS One 2018; 13:e0193684. [PMID: 29494662 PMCID: PMC5832312 DOI: 10.1371/journal.pone.0193684] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/15/2018] [Indexed: 02/06/2023] Open
Abstract
The contribution of specific HLA Class II alleles in type 1 diabetes is determined by polymorphic amino acid epitopes that direct antigen binding therefore, along with conventional allele frequency analysis, epitope analysis can provide important insights into disease susceptibility. We analyzed the highly heterogeneous Cypriot population for the HLA class II loci of T1DM patients and controls and we report for the first time their allele frequencies. Within our patient cohort we identified a subgroup that did not carry the DRB1*03:01-DQA1*05:01-DQB1*02:01 and DRB1*04:xx-DQA1*03:01-DQB1*03:02 risk haplotypes but a novel recombinant one, DRB1*04:XX-DQA1*03:01-DQB1*02:01 designated DR4-DQ2.3. Through epitope analysis we identified established susceptibility (DQB1 A57, DRB1 H13) and resistance (DQB1 D57) residues as well as other novel susceptibility residues DRB1 Q70, DQB1 L26 and resistance residues DRB1 D70, R70 and DQB1 Y47. Prevalence of susceptibility epitopes was higher in patients and was not exclusively a result of linkage disequilibrium. Residues DRB1 Q70, DQB1 L26 and A57 and a 10 amino acid epitope of DQA1 were the most significant in discriminating risk alleles. An extended haplotype containing these epitopes was carried by 92% of our patient cohort. Sharing of susceptibility epitopes could also explain the absence of risk haplotypes in patients. Finally, many significantly associated epitopes were non-pocket residues suggesting that critical immune functions may exist spanning further from the binding pockets.
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Affiliation(s)
- Petroula Gerasimou
- Karaiskakio Foundation, Nicosia, Cyprus
- University of Cyprus, Department of Biological Sciences, Nicosia, Cyprus
| | - Vicky Nicolaidou
- Department of Life and Health Sciences, School of Sciences and Engineering, University of Nicosia, Nicosia Cyprus
| | - Nicos Skordis
- Division of Paediatric Endocrinology, Paedi Centre for Specialized Paediatrics, Nicosia, Cyprus
| | | | - Demetrios Monos
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
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16
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Hamed CT, Meiloud G, Veten F, Hadrami M, Ghaber SM, Boussaty EC, Habti N, Houmeida A. HLA class I (-A, -B, -C) and class II (-DR, -DQ) polymorphism in the Mauritanian population. BMC MEDICAL GENETICS 2018; 19:2. [PMID: 29298671 PMCID: PMC5751816 DOI: 10.1186/s12881-017-0514-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 12/19/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND HLA antigens have been widely studied for their role in transplantation biology, human diseases and population diversity. The aim of this study was to provide the first profile of HLA class I and class II alleles in the Mauritanian population. METHODS HLA typing was carried in 93 healthy Mauritanian blood donors, using single specific primer amplification (PCR-SSP). RESULTS Occurrences of the main HLA class I (-A, -B, -C) and class II (-DR, -DQ) antigens in the general population showed that out of the 17 HLA-A allele groups detected, five main HLA-A allele groups: A*02 (18.42%), A*01 (14.04%), A*23 (14.04%), A*30 (13.16%) and A*29 (12.28%) were the most common identified along other 12 relatively minor allele groups. Twenty three allele groups were observed in the locus B of which B*07 (13.46%) was the most prevalent followed by B*15, B*35, B*08 and B*27 all, with a frequency between 7 to 8%. Three prevalent HLA-C allele groups (C*02: 35.09%, C*07: 20.19% and C*06: 13.6%) were detected. The main HLA class II observed allele groups were: DRB1*13 (27.42%), DRB1*03 (24.73%), DRB1*11 (13.98%), DQB1*03 (36.03%), DQB1*02 (22.06%) and DQB1*05 (18.8%). Except for few haplotype in class I (A*02-B*07: 4.45%, A*02-C02: 10%, A*23-C*02: 8.8%, B*07-C*02: 8.8%, B*15-C*02: 8.8%) and in class II (DRB1*13-DQB1*06: 11.94%, DRB1*03-DQB1*02:11.19% and DRB1*03-DQB1*03: 10.45%), the majority of locus combination were in the range of 2-3%. A single predominant haplotype C*02-DRB1*03 (16.67%) was found. CONCLUSIONS These results, in agreement with previous data using different tissues markers, underlined the ethnic heterogeneity of the Mauritanian population.
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Affiliation(s)
- Cheikh Tijani Hamed
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie.,Centre National de Transfusion Sanguine, Nouakchott, Mauritanie
| | - Ghlana Meiloud
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie
| | - Fatimetou Veten
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie
| | - Mouna Hadrami
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie
| | - Sidi M Ghaber
- Laboratoire d'hématologie Faculté de Médecine, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie
| | - Ely C Boussaty
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie
| | - Norddine Habti
- Laboratoire d'hématologie et de génie génétique et cellulaire, Faculté de Médecine et de Pharmacie de Casablanca, Université HASSAN II-Ain Chock, Casablanca, Maroc
| | - Ahmed Houmeida
- Unité de Recherche sur les Biomarqueurs dans la Population Mauritanienne, Université des Sciences de Technologies et de médecine (USTM), Nouakchott, Mauritanie.
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17
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Spínola H, Lemos A, Couto AR, Parreira B, Soares M, Dutra I, Bruges-Armas J, Brehm A, Abreu S. Human leucocyte antigens class II allele and haplotype association with Type 1 Diabetes in Madeira Island (Portugal). Int J Immunogenet 2017; 44:305-313. [DOI: 10.1111/iji.12335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/12/2017] [Accepted: 07/20/2017] [Indexed: 12/30/2022]
Affiliation(s)
- H. Spínola
- Human Genetics Laboratory; University of Madeira; Funchal Portugal
| | - A. Lemos
- Human Genetics Laboratory; University of Madeira; Funchal Portugal
| | - A. R. Couto
- SEEBMO; Hospital Santo Espírito de Angra do Heroísmo; Azores Portugal
- Institute for Molecular and Cell Biology (IBMC); Porto Portugal
| | - B. Parreira
- SEEBMO; Hospital Santo Espírito de Angra do Heroísmo; Azores Portugal
- Institute for Molecular and Cell Biology (IBMC); Porto Portugal
| | - M. Soares
- SEEBMO; Hospital Santo Espírito de Angra do Heroísmo; Azores Portugal
- Institute for Molecular and Cell Biology (IBMC); Porto Portugal
| | - I. Dutra
- SEEBMO; Hospital Santo Espírito de Angra do Heroísmo; Azores Portugal
- Institute for Molecular and Cell Biology (IBMC); Porto Portugal
| | - J. Bruges-Armas
- SEEBMO; Hospital Santo Espírito de Angra do Heroísmo; Azores Portugal
- Institute for Molecular and Cell Biology (IBMC); Porto Portugal
| | - A. Brehm
- Human Genetics Laboratory; University of Madeira; Funchal Portugal
| | - S. Abreu
- Endocrinology Service; Hospital Central do Funchal; Funchal Portugal
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18
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The Clinical Course of Patients with Preschool Manifestation of Type 1 Diabetes Is Independent of the HLA DR-DQ Genotype. Genes (Basel) 2017; 8:genes8050146. [PMID: 28534863 PMCID: PMC5448020 DOI: 10.3390/genes8050146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/03/2017] [Accepted: 05/16/2017] [Indexed: 12/16/2022] Open
Abstract
Introduction: Major histocompatibility complex class II genes are considered major genetic risk factors for autoimmune diabetes. We analysed Human Leukocyte Antigen (HLA) DR and DQ haplotypes in a cohort with early-onset (age < 5 years), long term type 1 diabetes (T1D) and explored their influence on clinical and laboratory parameters. Methods: Intermediate resolution HLA-DRB1, DQA1 and DQB1 typing was performed in 233 samples from the German Paediatric Diabetes Biobank and compared with a local control cohort of 19,544 cases. Clinical follow-up data of 195 patients (diabetes duration 14.2 ± 2.9 years) and residual C-peptide levels were compared between three HLA risk groups using multiple linear regression analysis. Results: Genetic variability was low, 44.6% (104/233) of early-onset T1D patients carried the highest-risk genotype HLA-DRB1*03:01-DQA1*05:01-DQB1*02:01/DRB1*04-DQA1*03:01-DQB1*03:02 (HLA-DRB1*04 denoting 04:01/02/04/05), and 231 of 233 individuals carried at least one of six risk haplotypes. Comparing clinical data between the highest (n = 83), moderate (n = 106) and low risk (n = 6) genotypes, we found no difference in age at diagnosis (mean age 2.8 ± 1.1 vs. 2.8 ± 1.2 vs. 3.2 ± 1.5 years), metabolic control, or frequency of associated autoimmune diseases between HLA risk groups (each p > 0.05). Residual C-peptide was detectable in 23.5% and C-peptide levels in the highest-risk group were comparable to levels in moderate to high risk genotypes. Conclusion: In this study, we saw no evidence for a different clinical course of early-onset T1D based on the HLA genotype within the first ten years after manifestation.
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19
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Pociot F, Kaur S, Nielsen LB. Effects of the genome on immune regulation in type 1 diabetes. Pediatr Diabetes 2016; 17 Suppl 22:37-42. [PMID: 27411435 DOI: 10.1111/pedi.12336] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 10/12/2015] [Indexed: 12/26/2022] Open
Abstract
Type 1 diabetes (T1DM) is a complex disease, arising through the interaction of an incompletely defined combination of genetic susceptibility and environmental factors. It is well accepted that T1DM results from selective immune-mediated destruction of the insulin-producing β cells in the islets of langerhans. Genetic studies of T1DM have identified several regions of susceptibility and identified major networks and pathways contributing to risk. In this study, we have taken advantages of the Immunochip fine-mapping genotyping data to address different aspects of immune regulation in relation to T1DM. First, we confirm that dense single nucleotide polymorphism (SNP) genotyping of the major histocompatibility complex/human leukocyte antigen (MHC/HLA) region capture the complex genetic contribution of this region to disease risk. Furthermore, it is shown that Immunochip genotyping can translate into a limited number of DRB1 and DQB1 amino acid residues that account for most of the HLA-risk. Second, we use the Immunochip data to look for functional significance by correlation to circulating levels of chemokines and demonstrate that genetic variation at chromosome 2, 3, and 6 correlates with circulating CCL2 and CCL4 in recent onset T1DM patients. Finally, we report that genetic variants predict autoantibody positivity in T1DM cases.
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Affiliation(s)
- Flemming Pociot
- Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev and Gentofte Hospital, Herlev, Denmark.,Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | - Simranjeet Kaur
- Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Lotte B Nielsen
- Copenhagen Diabetes Research Center, Department of Pediatrics, Herlev and Gentofte Hospital, Herlev, Denmark
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20
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Abstract
Type 1 diabetes (T1D) is a complex autoimmune disorder that results from the T cell-mediated destruction of the pancreatic β cells and is due to interactions between environmental and genetic factors. Although Arabs have one of the highest global incidence and prevalence rates of T1D, unfortunately, there is a dearth of information regarding the genetic epidemiology of T1D in the Arab world. Arabs share several HLA haplotypes with other ethnic groups, which confer either susceptibility or protection to T1D, but they have specific haplotypes that are distinctive from other ethnicities. Among different Arab countries, several non-HLA genes were reported to be associated with susceptibility to T1D, including CTLA4, CD28, PTPN22, TCRβ, CD3z, IL15, BANK1, and ZAP70. In Arab countries, consanguinity, endogamy, and first-cousin marriage rates are some of the highest reported worldwide and are responsible for the creation of several inbreeding communities within the Arab world that have led to an increase in homozygosity of both the HLA haplotypes and non-HLA genes associated with either protection or susceptibility to T1D among Arabs. Homozygosity reduces the HLA complexity and is expected to facilitate our understanding of the mode of inheritance of HLA haplotypes and provide valuable insight into the intricate genotype-phenotype correlations in T1D patients. In this review, based on literature studies, I will discuss the current epidemiological profile and molecular genetic risks of Arabs with T1D.
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Affiliation(s)
- Hatem Zayed
- College of Health Sciences, Biomedical Program, Qatar University, Doha, Qatar.
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21
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Noble JA. Immunogenetics of type 1 diabetes: A comprehensive review. J Autoimmun 2015; 64:101-12. [PMID: 26272854 DOI: 10.1016/j.jaut.2015.07.014] [Citation(s) in RCA: 151] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/13/2022]
Abstract
Type 1 diabetes (T1D) results from the autoimmune destruction of insulin-producing beta cells in the pancreas. Prevention of T1D will require the ability to detect and modulate the autoimmune process before the clinical onset of disease. Genetic screening is a logical first step in identification of future patients to test prevention strategies. Susceptibility to T1D includes a strong genetic component, with the strongest risk attributable to genes that encode the classical Human Leukocyte Antigens (HLA). Other genetic loci, both immune and non-immune genes, contribute to T1D risk; however, the results of decades of small and large genetic linkage and association studies show clearly that the HLA genes confer the most disease risk and protection and can be used as part of a prediction strategy for T1D. Current predictive genetic models, based on HLA and other susceptibility loci, are effective in identifying the highest-risk individuals in populations of European descent. These models generally include screening for the HLA haplotypes "DR3" and "DR4." However, genetic variation among racial and ethnic groups reduces the predictive value of current models that are based on low resolution HLA genotyping. Not all DR3 and DR4 haplotypes are high T1D risk; some versions, rare in Europeans but high frequency in other populations, are even T1D protective. More information is needed to create predictive models for non-European populations. Comparative studies among different populations are needed to complete the knowledge base for the genetics of T1D risk to enable the eventual development of screening and intervention strategies applicable to all individuals, tailored to their individual genetic background. This review summarizes the current understanding of the genetic basis of T1D susceptibility, focusing on genes of the immune system, with particular emphasis on the HLA genes.
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Affiliation(s)
- Janelle A Noble
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA.
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22
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Woittiez NJC, Roep BO. Impact of disease heterogeneity on treatment efficacy of immunotherapy in Type 1 diabetes: different shades of gray. Immunotherapy 2015; 7:163-74. [DOI: 10.2217/imt.14.104] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Type 1 diabetes results from selective destruction of insulin-producing pancreatic β-cells by a progressive autoimmune process. Type 1 diabetes proves very heterogeneous in pathology, disease progression and efficacy of therapeutic intervention. Indeed, several immunotherapies that appear ineffective for the entire treated patient population in fact look promising in subgroups of patients. It therefore seems inconceivable that one standard therapy will provide the golden bullet of disease intervention. Instead, personalized medicine may improve immune intervention efficacy rates. We discuss the effect of disease heterogeneity on treatment outcome of immunotherapies, identifying apparent gaps in our understanding of treatment efficacy in subgroups of Type 1 diabetic patients as well as identifying future opportunities for immunotherapy.
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Affiliation(s)
- Nicky JC Woittiez
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, E3-Q, LUMC, PO Box 9600, NL-2300RC Leiden, The Netherlands
| | - Bart O Roep
- Department of Immunohematology & Blood Transfusion, Leiden University Medical Center, E3-Q, LUMC, PO Box 9600, NL-2300RC Leiden, The Netherlands
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23
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Hartmann N, Luesink E, Khokhlovich E, Szustakowski JD, Baeriswyl L, Peterson J, Scherer A, Nanguneri NR, Staedtler F. The use of haplotype-specific transcripts improves sample annotation consistency. Biomark Res 2014; 2:17. [PMID: 25285214 PMCID: PMC4184161 DOI: 10.1186/2050-7771-2-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 08/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background Exact sample annotation in expression microarray datasets is essential for any type of pharmacogenomics research. Results Candidate markers were explored through the application of Hartigans’ dip test statistics to a publically available human whole genome microarray dataset. The marker performance was tested on 188 serial samples from 53 donors and of variable tissue origin from five public microarray datasets. A qualified transcript marker panel consisting of three probe sets for human leukocyte antigens HLA-DQA1 (2 probe sets) and HLA-DRB4 identified sample donor identifier inconsistencies in six of the 188 test samples. About 3% of the test samples require root-cause analysis due to unresolvable inaccuracies. Conclusions The transcript marker panel consisting of HLA-DQA1 and HLA-DRB4 represents a robust, tissue-independent composite marker to assist control donor annotation concordance at the transcript level. Allele-selectivity of HLA genes renders them good candidates for “fingerprinting” with donor specific expression pattern.
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Affiliation(s)
- Nicole Hartmann
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Evert Luesink
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Edward Khokhlovich
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Joseph D Szustakowski
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Lukas Baeriswyl
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Joshua Peterson
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | | | - Nirmala R Nanguneri
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
| | - Frank Staedtler
- Novartis Institutes for BioMedical Research (NIBR), Biomarker Development, Fabrikstrasse 10.13, CH-4002 Basel, Switzerland
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