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Douillard V, Dos Santos Brito Silva N, Bourguiba-Hachemi S, Naslavsky MS, Scliar MO, Duarte YAO, Zatz M, Passos-Bueno MR, Limou S, Gourraud PA, Launay É, Castelli EC, Vince N. Optimal population-specific HLA imputation with dimension reduction. HLA 2024; 103:e15282. [PMID: 37950640 DOI: 10.1111/tan.15282] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/29/2023] [Accepted: 10/14/2023] [Indexed: 11/13/2023]
Abstract
Human genomics has quickly evolved, powering genome-wide association studies (GWASs). SNP-based GWASs cannot capture the intense polymorphism of HLA genes, highly associated with disease susceptibility. There are methods to statistically impute HLA genotypes from SNP-genotypes data, but lack of diversity in reference panels hinders their performance. We evaluated the accuracy of the 1000 Genomes data as a reference panel for imputing HLA from admixed individuals of African and European ancestries, focusing on (a) the full dataset, (b) 10 replications from 6 populations, and (c) 19 conditions for the custom reference panels. The full dataset outperformed smaller models, with a good F1-score of 0.66 for HLA-B. However, custom models outperformed the multiethnic or population models of similar size (F1-scores up to 0.53, against up to 0.42). We demonstrated the importance of using genetically specific models for imputing populations, which are currently underrepresented in public datasets, opening the door to HLA imputation for every genetic population.
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Affiliation(s)
- Venceslas Douillard
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Nayane Dos Santos Brito Silva
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Sonia Bourguiba-Hachemi
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Michel S Naslavsky
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
- Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marilia O Scliar
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
| | - Yeda A O Duarte
- Medical-Surgical Nursing Department, School of Nursing, University of São Paulo, São Paulo, Brazil
- Epidemiology Department, Public Health School, University of São Paulo, São Paulo, Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Maria Rita Passos-Bueno
- Human Genome and Stem Cell Research Center, University of São Paulo, São Paulo, Brazil
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, São Paulo, Brazil
| | - Sophie Limou
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Pierre-Antoine Gourraud
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
| | - Élise Launay
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
- Department of Pediatrics and Pediatric Emergency, Hôpital Femme Enfant Adolescent, CHU de Nantes, Nantes, France
| | - Erick C Castelli
- São Paulo State University, Molecular Genetics and Bioinformatics Laboratory, School of Medicine, Botucatu, Brazil
| | - Nicolas Vince
- Nantes Université, INSERM, Ecole Centrale Nantes, Center for Research in Transplantation and Translational Immunology, Nantes, France
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Mohammadi F, Visagan S, Gross SM, Karginov L, Lagarde JC, Heiser LM, Meyer AS. A lineage tree-based hidden Markov model quantifies cellular heterogeneity and plasticity. Commun Biol 2022; 5:1258. [PMID: 36396800 PMCID: PMC9671968 DOI: 10.1038/s42003-022-04208-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/01/2022] [Indexed: 11/18/2022] Open
Abstract
Individual cells can assume a variety of molecular and phenotypic states and recent studies indicate that cells can rapidly adapt in response to therapeutic stress. Such phenotypic plasticity may confer resistance, but also presents opportunities to identify molecular programs that could be targeted for therapeutic benefit. Approaches to quantify tumor-drug responses typically focus on snapshot, population-level measurements. While informative, these methods lack lineage and temporal information, which are particularly critical for understanding dynamic processes such as cell state switching. As new technologies have become available to measure lineage relationships, modeling approaches will be needed to identify the forms of cell-to-cell heterogeneity present in these data. Here we apply a lineage tree-based adaptation of a hidden Markov model that employs single cell lineages as input to learn the characteristic patterns of phenotypic heterogeneity and state transitions. In benchmarking studies, we demonstrated that the model successfully classifies cells within experimentally-tractable dataset sizes. As an application, we analyzed experimental measurements in cancer and non-cancer cell populations under various treatments. We find evidence of multiple phenotypically distinct states, with considerable heterogeneity and unique drug responses. In total, this framework allows for the flexible modeling of single cell heterogeneity across lineages to quantify, understand, and control cell state switching.
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Affiliation(s)
- Farnaz Mohammadi
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Shakthi Visagan
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Sean M Gross
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Luka Karginov
- Department of Bioengineering, University of Illinois, Urbana Champaign, IL, USA
| | - J C Lagarde
- Department of Bioengineering, University of California, Los Angeles, CA, USA
| | - Laura M Heiser
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, USA
| | - Aaron S Meyer
- Department of Bioengineering, University of California, Los Angeles, CA, USA.
- Department of Bioinformatics, University of California, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, CA, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA.
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Brodnicki TC. A Role for lncRNAs in Regulating Inflammatory and Autoimmune Responses Underlying Type 1 Diabetes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:97-118. [DOI: 10.1007/978-3-030-92034-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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De novo germline mutation in the dual specificity phosphatase 10 gene accelerates autoimmune diabetes. Proc Natl Acad Sci U S A 2021; 118:2112032118. [PMID: 34782469 DOI: 10.1073/pnas.2112032118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2021] [Indexed: 01/22/2023] Open
Abstract
Insulin-dependent or type 1 diabetes (T1D) is a polygenic autoimmune disease. In humans, more than 60 loci carrying common variants that confer disease susceptibility have been identified by genome-wide association studies, with a low individual risk contribution for most variants excepting those of the major histocompatibility complex (MHC) region (40 to 50% of risk); hence the importance of missing heritability due in part to rare variants. Nonobese diabetic (NOD) mice recapitulate major features of the human disease including genetic aspects with a key role for the MHC haplotype and a series of Idd loci. Here we mapped in NOD mice rare variants arising from genetic drift and significantly impacting disease risk. To that aim we established by selective breeding two sublines of NOD mice from our inbred NOD/Nck colony exhibiting a significant difference in T1D incidence. Whole-genome sequencing of high (H)- and low (L)-incidence sublines (NOD/NckH and NOD/NckL) revealed a limited number of subline-specific variants. Treating age of diabetes onset as a quantitative trait in automated meiotic mapping (AMM), enhanced susceptibility in NOD/NckH mice was unambiguously attributed to a recessive missense mutation of Dusp10, which encodes a dual specificity phosphatase. The causative effect of the mutation was verified by targeting Dusp10 with CRISPR-Cas9 in NOD/NckL mice, a manipulation that significantly increased disease incidence. The Dusp10 mutation resulted in islet cell down-regulation of type I interferon signature genes, which may exert protective effects against autoimmune aggression. De novo mutations akin to rare human susceptibility variants can alter the T1D phenotype.
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Krischer JP, Liu X, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B. Characteristics of children diagnosed with type 1 diabetes before vs after 6 years of age in the TEDDY cohort study. Diabetologia 2021; 64:2247-2257. [PMID: 34291312 PMCID: PMC8429233 DOI: 10.1007/s00125-021-05514-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/29/2021] [Indexed: 10/20/2022]
Abstract
AIMS/HYPOTHESIS Prognostic factors and characteristics of children diagnosed with type 1 diabetes before 6 years of age were compared with those diagnosed at 6-13 years of age in the TEDDY study. METHODS Genetically high-risk children (n = 8502) were followed from birth for a median of 9.9 years; 328 (3.9%) were diagnosed with type 1 diabetes. Cox proportional hazard model was used to assess the association of prognostic factors with the risk of type 1 diabetes in the two age groups. RESULTS Children in the younger group tended to develop autoantibodies earlier than those in the older group did (mean age 1.5 vs 3.5 years), especially insulin autoantibodies (IAA), which developed earlier than GAD autoantibodies (GADA). Children in the younger group also progressed to diabetes more rapidly than the children in the older group did (mean duration 1.9 vs 5.4 years). Children with autoantibodies first appearing against insulinoma antigen-2 (IA-2A) were found only in the older group. The significant diabetes risk associated with the country of origin in the younger group was no longer significant in the older group. Conversely, the diabetes risk associated with HLA genotypes was statistically significant also in the older group. Initial seroconversion after and before 2 years of age was associated with decreased risk for diabetes diagnosis in children positive for multiple autoantibodies, but the diabetes risk did not decrease further with increasing age if initial seroconversion occurred after age 2. Diabetes risk associated with the minor alleles of rs1004446 (INS) was decreased in both the younger and older groups compared with other genotypes (HR 0.67). Diabetes risk was significantly increased with the minor alleles of rs2476601 (PTPN22) (HR 2.04 and 1.72), rs428595 (PPIL2) (HR 2.13 and 2.10), rs113306148 (PLEKHA1) (HR 2.34 and 2.21) and rs73043122 (RNASET2) (HR 2.31 and 2.54) (HR values represent the younger and older groups, respectively). CONCLUSIONS/INTERPRETATIONS Diabetes at an early age is likely to be preceded by IAA autoantibodies and is a more aggressive form of the disease. Among older children, once multiple autoantibodies have been observed there does not seem to be any association between progression to diabetes and the age of the child or family history. TRIAL REGISTRATION ClinicalTrials.gov identifier: NCT00279318.
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Affiliation(s)
- Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Xiang Liu
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital SUS, Malmo, Sweden
| | | | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA, USA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Institute of Biomedicine, Research Centre for Integrated Physiology and Pharmacology, and Population Research Centre, University of Turku, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München, and Klinikum rechts der Isar, Technische Universität München, and Forschergruppe Diabetes e.V, Neuherberg, Germany
| | - Beena Akolkar
- National Institute of Diabetes & Digestive & Kidney Diseases, Bethesda, MD, USA
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Marchand L, Li M, Leblicq C, Rafique I, Alarcon-Martinez T, Lange C, Rendon L, Tam E, Courville-Le Bouyonnec A, Polychronakos C. Monogenic Causes in the Type 1 Diabetes Genetics Consortium Cohort: Low Genetic Risk for Autoimmunity in Case Selection. J Clin Endocrinol Metab 2021; 106:1804-1810. [PMID: 33538814 PMCID: PMC8118360 DOI: 10.1210/clinem/dgab056] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/17/2022]
Abstract
HYPOTHESIS About 1% of patients clinically diagnosed as type 1 diabetes have non-autoimmune monogenic diabetes. The distinction has important therapeutic implications but, given the low prevalence and high cost of testing, selecting patients to test is important. We tested the hypothesis that low genetic risk for type 1 diabetes can substantially contribute to this selection. METHODS As proof of principle, we examined by exome sequencing families with 2 or more children, recruited by the Type 1 Diabetes Genetics Consortium (T1DGC) and selected for negativity for 2 autoantibodies and absence of risk human leukocyte antigen haplotypes. RESULTS We examined 46 families that met the criteria. Of the 17 with an affected parent, 7 (41.2%) had actionable monogenic variants. Of 29 families with no affected parent, 14 (48.3%) had such variants, including 5 with recessive pathogenic variants of WFS1 but no report of other features of Wolfram syndrome. Our approach diagnosed 55.8% of the estimated number of monogenic families in the entire T1DGC cohort, by sequencing only 11.1% of the autoantibody-negative ones. CONCLUSIONS Our findings justify proceeding to large-scale prospective screening studies using markers of autoimmunity, even in the absence of an affected parent. We also confirm that nonsyndromic WFS1 variants are common among cases of monogenic diabetes misdiagnosed as type 1 diabetes.
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Affiliation(s)
- Luc Marchand
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Meihang Li
- Clinical Research Center, Maoming People’s Hospital, Guangdong, China
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
- The Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
- MaiDa Gene Technology, Zhoushan, China
- Meihang Li, PhD, Maoming People’s Hospital, 101 Weimin Road, Maoming 525000, Guangdong, China.
| | - Coralie Leblicq
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Ibrar Rafique
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Tugba Alarcon-Martinez
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Claire Lange
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Laura Rendon
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Emily Tam
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Ariane Courville-Le Bouyonnec
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Constantin Polychronakos
- Montreal Children’s Hospital and the Endocrine Genetics Laboratory, Child Health and Human Development Program, the Research Institute of the McGill University Health Centre, Montreal, Canada
- MaiDa Gene Technology, Zhoushan, China
- Correspondence: Constantin Polychronakos, MD, 1001 Décarie Boulevard, Montreal, QC H4A 3J1, Canada.
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7
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Arneth B. Insulin gene mutations and posttranslational and translocation defects: associations with diabetes. Endocrine 2020; 70:488-497. [PMID: 32656694 DOI: 10.1007/s12020-020-02413-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 07/01/2020] [Indexed: 02/06/2023]
Abstract
The mechanism underlying the pathogenesis of diabetes is complex and poorly understood. Recent investigations have revealed that insulin gene mutations can lead to the development of specific subtypes of diabetes. This systematic review aimed to explore the associations of insulin gene mutations and insulin translocation defects with diabetes. This review was generated using articles from PsycINFO, PubMed, Web of Science, and CINAHL. Search terms and phrases such as "diabetes," "mutations," "insulin," "preproinsulin," "INS gene," "role," "VNTR polymorphisms," and "INS promotor" were used to identify articles relevant to the research topic. The gathered data showed the significant role of insulin gene mutations and insulin translocation defects during diabetes development and progression. Genetic changes can adversely affect the development of various types of diabetes, such as neonatal diabetes mellitus and MIDY. Genetic alterations can affect insulin production, thus compromising the regulation of glucose utilization by tissues. Targeting insulin gene mutations is a potential new avenue for diagnosing and managing diabetes. There are specific subcategories of diabetes, such as MIDY and neonatal diabetes mellitus, caused by insulin gene mutations and defects in posttranslational modification. Further investigations are needed to examine the diagnostic and therapeutic potential of mutation-based biomarkers.
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Affiliation(s)
- Borros Arneth
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics, University Hospital of Giessen and Marburg (UKGM), Justus Liebig University Giessen, Feulgenstr 12, 35332, Giessen, Germany.
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Zhang X, Seman NA, Falhammar H, Brismar K, Gu HF. Genetic and Biological Effects of ICAM-1 E469K Polymorphism in Diabetic Kidney Disease. J Diabetes Res 2020; 2020:8305460. [PMID: 32626783 PMCID: PMC7313107 DOI: 10.1155/2020/8305460] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/22/2020] [Indexed: 12/19/2022] Open
Abstract
Diabetic kidney disease (DKD) is a complex disease, in which local inflammatory stress results from both metabolic and hemodynamic derangements. Intercellular adhesion molecule 1 (ICAM-1) is an acute-phase protein marker of inflammation. In the recent years, clinical observations have reported that increased serum/plasma ICAM-1 levels are positively correlated with albuminuria in the patients with type 1 (T1D) and type 2 diabetes (T2D). Genetic association studies have demonstrated that genetic polymorphisms, including SNP rs5498 (E469K, G/A), in the ICAM1 gene is associated with DKD. rs5498 is a nonsynonymous SNP and caused by substitution between E (Glu) and K (Lys) for ICAM-1 protein. In this review, we first summarized the genetic effects of ICAM1 E469K polymorphism in DKD and then demonstrated the possible changes of ICAM-1 protein crystal structures according to the genotypes of this polymorphism. Finally, we discussed the genetic effects of the ICAM1 E469K polymorphism and the biological role of increased circulating ICAM-1 protein and its formation changes in DKD.
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Affiliation(s)
- Xiuli Zhang
- Department of Nephrology, The second People's Hospital, Shenzhen, The first Affiliated Hospital of Shenzhen University, Guangdong 518000, China
| | - Norhashimah Abu Seman
- Cardiovascular, Diabetes and Nutrition Research Center, Institute for Medical Research, Kuala Lumpur 50588, Malaysia
| | - Henrik Falhammar
- Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17176, Sweden
- Department of Endocrinology, Metabolism and Diabetes, Karolinska University Hospital, Stockholm 17176, Sweden
| | - Kerstin Brismar
- Rolf Luft Research Center for Diabetes and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm 17176, Sweden
| | - Harvest F. Gu
- Center for Pathophysiology, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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9
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Alper CA, Larsen CE, Trautwein MR, Alford DR. A stochastic epigenetic Mendelian oligogenic disease model for type 1 diabetes. J Autoimmun 2018; 96:123-133. [PMID: 30309752 DOI: 10.1016/j.jaut.2018.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/12/2018] [Indexed: 01/14/2023]
Abstract
The incidence of type 1 diabetes (T1D) and some other complex diseases is increasing. The cause has been attributed to an undefined changing environment. We examine the role of the environment (or any changing non-genetic mechanism) in causing the rising incidence, and find much evidence against it: 1) Dizygotic twin T1D concordance is the same as siblings of patients in general; 2) If the environment is responsible for both the discordance among identical twins of patients with T1D and its rising incidence, the twin concordance rate should be rising, but it is not; 3) Migrants from high-to low-incidence countries continue to have high-incidence children; 4) TID incidence among the offspring of two T1D parents is identical to the monozygotic twin rate. On the other hand, genetic association studies of T1D have revealed strong susceptibility in the major histocompatibility complex and many optional additive genes of small effect throughout the human genome increasing T1D risk. We have, from an analysis of previously published family studies, developed a stochastic epigenetic Mendelian oligogenic (SEMO) model consistent with published observations. The model posits a few required recessive causal genes with incomplete penetrance explaining virtually all of the puzzling features of T1D, including its rising incidence and the specific low T1D incidence rates among first-degree relatives of patients. Since historic selection against any causal gene could prevent T1D, we postulate that the rising incidence is because of increasing population mixing of parents from some previously isolated populations that had selected against different causal genes.
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Affiliation(s)
- Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Charles E Larsen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA; Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
| | - Michael R Trautwein
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Dennis R Alford
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
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10
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Frohnert BI, Laimighofer M, Krumsiek J, Theis FJ, Winkler C, Norris JM, Ziegler AG, Rewers MJ, Steck AK. Prediction of type 1 diabetes using a genetic risk model in the Diabetes Autoimmunity Study in the Young. Pediatr Diabetes 2018; 19:277-283. [PMID: 28695611 PMCID: PMC5764829 DOI: 10.1111/pedi.12543] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Genetic predisposition for type 1 diabetes (T1D) is largely determined by human leukocyte antigen (HLA) genes; however, over 50 other genetic regions confer susceptibility. We evaluated a previously reported 10-factor weighted model derived from the Type 1 Diabetes Genetics Consortium to predict the development of diabetes in the Diabetes Autoimmunity Study in the Young (DAISY) prospective cohort. Performance of the model, derived from individuals with first-degree relatives (FDR) with T1D, was evaluated in DAISY general population (GP) participants as well as FDR subjects. METHODS The 10-factor weighted risk model (HLA, PTPN22 , INS , IL2RA , ERBB3 , ORMDL3 , BACH2 , IL27 , GLIS3 , RNLS ), 3-factor model (HLA, PTPN22, INS ), and HLA alone were compared for the prediction of diabetes in children with complete SNP data (n = 1941). RESULTS Stratification by risk score significantly predicted progression to diabetes by Kaplan-Meier analysis (GP: P = .00006; FDR: P = .0022). The 10-factor model performed better in discriminating diabetes outcome than HLA alone (GP, P = .03; FDR, P = .01). In GP, the restricted 3-factor model was superior to HLA (P = .03), but not different from the 10-factor model (P = .22). In contrast, for FDR the 3-factor model did not show improvement over HLA (P = .12) and performed worse than the 10-factor model (P = .02) CONCLUSIONS: We have shown a 10-factor risk model predicts development of diabetes in both GP and FDR children. While this model was superior to a minimal model in FDR, it did not confer improvement in GP. Differences in model performance in FDR vs GP children may lead to important insights into screening strategies specific to these groups.
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Affiliation(s)
- Brigitte I. Frohnert
- Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado, Aurora, CO 80045 USA
| | - Michael Laimighofer
- Institute of Computational Biology, Helmholtz Zentrum München, München-Neuherberg 85764 Germany
| | - Jan Krumsiek
- Institute of Computational Biology, Helmholtz Zentrum München, München-Neuherberg 85764 Germany,German Center for Diabetes Research (DZD), München-Neuherberg 85764 Germany
| | - Fabian J. Theis
- Institute of Computational Biology, Helmholtz Zentrum München, München-Neuherberg 85764 Germany
| | - Christiane Winkler
- Institute of Diabetes Research, Helmholtz Zentrum München and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Neuherberg 85764 Germany
| | - Jill M. Norris
- Department of Epidemiology, Colorado School of Public Health, University of Colorado, Aurora, CO, 80045 USA
| | - Anette-Gabriele Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München and Forschergruppe Diabetes, Klinikum rechts der Isar, Technische Universität München, Neuherberg 85764 Germany
| | - Marian J. Rewers
- Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado, Aurora, CO 80045 USA
| | - Andrea K. Steck
- Barbara Davis Center for Childhood Diabetes, School of Medicine, University of Colorado, Aurora, CO 80045 USA
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11
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Pociot F. Type 1 diabetes genome-wide association studies: not to be lost in translation. Clin Transl Immunology 2017; 6:e162. [PMID: 29333267 PMCID: PMC5750451 DOI: 10.1038/cti.2017.51] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/15/2017] [Accepted: 10/16/2017] [Indexed: 12/13/2022] Open
Abstract
Genetic studies have identified >60 loci associated with the risk of developing type 1 diabetes (T1D). The vast majority of these are identified by genome-wide association studies (GWAS) using large case-control cohorts of European ancestry. More than 80% of the heritability of T1D can be explained by GWAS data in this population group. However, with few exceptions, their individual contribution to T1D risk is low and understanding their function in disease biology remains a huge challenge. GWAS on its own does not inform us in detail on disease mechanisms, but the combination of GWAS data with other omics-data is beginning to advance our understanding of T1D etiology and pathogenesis. Current knowledge supports the notion that genetic variation in both pancreatic β cells and in immune cells is central in mediating T1D risk. Advances, perspectives and limitations of GWAS are discussed in this review.
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Affiliation(s)
- Flemming Pociot
- Department of Pediatrics, Herlev and Gentofte Hospital, Herlev, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Steno Diabetes Center Copenhagen, Gentofte, Denmark
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12
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Krischer JP, Liu X, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B. The Influence of Type 1 Diabetes Genetic Susceptibility Regions, Age, Sex, and Family History on the Progression From Multiple Autoantibodies to Type 1 Diabetes: A TEDDY Study Report. Diabetes 2017; 66:3122-3129. [PMID: 28903990 PMCID: PMC5697938 DOI: 10.2337/db17-0261] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 09/07/2017] [Indexed: 01/01/2023]
Abstract
This article seeks to determine whether factors related to autoimmunity risk remain significant after the initiation of two or more diabetes-related autoantibodies and continue to contribute to type 1 diabetes (T1D) risk among autoantibody-positive children in The Environmental Determinants of Diabetes in the Young (TEDDY) study. Characteristics included are age at multiple autoantibody positivity, sex, selected high-risk HLA-DR-DQ genotypes, relationship to a family member with T1D, autoantibody at seroconversion, INS gene (rs1004446_A), and non-HLA gene polymorphisms identified by the Type 1 Diabetes Genetics Consortium (T1DGC). The risk of progression to T1D was not different among those with or without a family history of T1D (P = 0.39) or HLA-DR-DQ genotypes (P = 0.74). Age at developing multiple autoantibodies (hazard ratio = 0.96 per 1-month increase in age; 95% CI 0.95, 0.97; P < 0.001) and the type of first autoantibody (when more than a single autoantibody was the first-appearing indication of seroconversion [P = 0.006]) were statistically significant. Female sex was also a significant risk factor (P = 0.03). Three single nucleotide polymorphisms were associated with increased diabetes risk (rs10517086_A [P = 0.03], rs1534422_G [P = 0.006], and rs2327832_G [P = 0.03] in TNFAIP3) and one with decreased risk (rs1004446_A in INS [P = 0.006]). The TEDDY data suggest that non-HLA gene polymorphisms may play a different role in the initiation of autoimmunity than they do in progression to T1D once autoimmunity has appeared. The strength of these associations may be related to the age of the population and the high-risk HLA-DR-DQ subtypes studied.
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Affiliation(s)
- Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Xiang Liu
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University Clinical Research Center, Skåne University Hospital, Malmö, Sweden
| | | | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Augusta University, Augusta, GA
| | - Jorma Toppari
- Department of Pediatrics, Turku University Hospital, Turku, Finland
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anette-G Ziegler
- Institute of Diabetes Research, Helmholtz Zentrum München; Klinikum rechts der Isar, Technische Universität München; and Forschergruppe Diabetes e.V., Neuherberg, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
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13
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Newman JRB, Conesa A, Mika M, New FN, Onengut-Gumuscu S, Atkinson MA, Rich SS, McIntyre LM, Concannon P. Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes. Genome Res 2017; 27:1807-1815. [PMID: 29025893 PMCID: PMC5668939 DOI: 10.1101/gr.217984.116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
Abstract
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4+, CD8+, and CD19+ lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D). We characterize and compare the expression patterns across these cell types for three gene sets: all genes, the set of genes implicated in autoimmune disease risk by GWAS, and the subset of these genes specifically implicated in T1D. We performed RNA sequencing and aligned the reads to both the human reference genome and a catalog of all possible splicing events developed from the genome, thereby providing a comprehensive evaluation of the roles of gene expression and alternative splicing (AS) in autoimmunity. Autoimmune candidate genes displayed greater expression specificity in the three lymphocyte populations relative to other genes, with significantly increased levels of splicing events, particularly those predicted to have substantial effects on protein isoform structure and function (e.g., intron retention, exon skipping). The majority of single-nucleotide polymorphisms within T1D-associated loci were also associated with one or more cis-expression quantitative trait loci (cis-eQTLs) and/or splicing eQTLs. Our findings highlight a substantial, and previously underrecognized, role for AS in the pathogenesis of autoimmune disorders and particularly for T1D.
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Affiliation(s)
- Jeremy R B Newman
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32610, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Matthew Mika
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Felicia N New
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
| | - Suna Onengut-Gumuscu
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Mark A Atkinson
- Diabetes Institute, University of Florida, Gainesville, Florida 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
| | - Stephen S Rich
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32610, USA
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
| | - Patrick Concannon
- Genetics Institute, University of Florida, Gainesville, Florida 32610, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida 32610, USA
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14
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The A946T variant of the RNA sensor IFIH1 mediates an interferon program that limits viral infection but increases the risk for autoimmunity. Nat Immunol 2017; 18:744-752. [PMID: 28553952 PMCID: PMC5697900 DOI: 10.1038/ni.3766] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/05/2017] [Indexed: 12/20/2022]
Abstract
The single-nucleotide polymorphism rs1990760 in the gene encoding the cytosolic viral sensor IFIH1 results in an amino-acid change (A946T; IFIH1T946) that is associated with multiple autoimmune diseases. The effect of this polymorphism on both viral sensing and autoimmune pathogenesis remains poorly understood. Here we found that human peripheral blood mononuclear cells (PBMCs) and cell lines expressing the risk variant IFIH1T946 exhibited heightened basal and ligand-triggered production of type I interferons. Consistent with those findings, mice with a knock-in mutation encoding IFIH1T946 displayed enhanced basal expression of type I interferons, survived a lethal viral challenge and exhibited increased penetrance in autoimmune models, including a combinatorial effect with other risk variants. Furthermore, IFIH1T946 mice manifested an embryonic survival defect consistent with enhanced responsiveness to RNA self ligands. Together our data support a model wherein the production of type I interferons driven by an autoimmune risk variant and triggered by ligand functions to protect against viral challenge, which probably accounts for its selection within human populations but provides this advantage at the cost of modestly promoting the risk of autoimmunity.
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15
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Apportioning Blame: Autoreactive CD4 + and CD8 + T Cells in Type 1 Diabetes. Arch Immunol Ther Exp (Warsz) 2017; 65:275-284. [PMID: 28083620 DOI: 10.1007/s00005-016-0452-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/18/2016] [Indexed: 01/14/2023]
Abstract
Type 1 diabetes (T1D) is one of the most studied archetypal organ-specific autoimmune diseases. Although many clinical, epidemiological, and pathological characteristics have been described, there are still important issues which need to be resolved as these will have a major impact on the development of future antigen-specific immunotherapies. An important question relates to T lymphocytes in the development of the disease, in particular their role in the destruction of insulin-producing beta cells. Since the discovery that certain class II histocompatibility complex molecules (HLA) are linked to the development of T1D, much research has focused on CD4+ helper T lymphocytes; however, recent studies highlight class I HLA molecules as an independent risk factor; hence, research into the role played by CD8+ cytotoxic T lymphocytes has gained momentum. In this review, we summarize recent studies clarifying the role played by both sets of autoreactive T lymphocytes in T1D, discuss the targets recognized by these cells and their phenotype in T1D patients. Finally, we will examine the possible generation of regulatory CD8+ T lymphocytes upon different immuno-intervention strategies.
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16
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Abstract
A haplotype is a string of nucleotides or alleles at nearby loci on one chromosome, usually inherited as a unit. Within the major histocompatibility complex (MHC) region on human chromosome 6p, independent population studies of multiple families have identified conserved extended haplotypes (CEHs) that segregate as long stretches (≥1 megabase) of essentially identical DNA sequence at relatively high (≥0.5 %) population frequency ("genetic fixity"). CEHs were first identified through segregation analysis in the early 1980s. In European Caucasian populations, the most frequent 30 CEHs account for at least one-third of all MHC haplotypes. These CEHs provide all of the known individual MHC susceptibility and protective genetic markers within those populations for several complex genetic diseases. Haplotypes are rigorously determined directly by sequencing single chromosomes or by Mendelian segregation analysis using families with informative genotypes. Four parental haplotypes are assigned unambiguously using genotypes from the two parents and from two of their haploidentical (to each other) children. However, the most common current technique to phase haplotypes is probabilistic statistical imputation, using unrelated subjects. Such probabilistic techniques have failed to detect CEHs and are thus of questionable value in identifying long-range haplotype structure and, consequently, genetic structure-function relationships. Finally, with haplotypes rigorously defined, association studies can determine frequencies of alleles among unrelated patient haplotypes vs. those among only unaffected family members (i.e., control alleles/haplotypes). Such studies reduce, as much as possible, the confounding effects of population stratification common to all genetic studies.
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Affiliation(s)
- Chester A Alper
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, CLS_03, 3 Blackfan Circle, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA.
| | - Charles E Larsen
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, CLS_03, 3 Blackfan Circle, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, 25 Shattuck Street, Boston, MA, 02115, USA
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17
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Newby BN, Mathews CE. Type I Interferon Is a Catastrophic Feature of the Diabetic Islet Microenvironment. Front Endocrinol (Lausanne) 2017; 8:232. [PMID: 28959234 PMCID: PMC5604085 DOI: 10.3389/fendo.2017.00232] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/25/2017] [Indexed: 01/01/2023] Open
Abstract
A detailed understanding of the molecular pathways and cellular interactions that result in islet beta cell (β cell) destruction is essential for the development and implementation of effective therapies for prevention or reversal of type 1 diabetes (T1D). However, events that define the pathogenesis of human T1D have remained elusive. This gap in our knowledge results from the complex interaction between genetics, the immune system, and environmental factors that precipitate T1D in humans. A link between genetics, the immune system, and environmental factors are type 1 interferons (T1-IFNs). These cytokines are well known for inducing antiviral factors that limit infection by regulating innate and adaptive immune responses. Further, several T1D genetic risk loci are within genes that link innate and adaptive immune cell responses to T1-IFN. An additional clue that links T1-IFN to T1D is that these cytokines are a known constituent of the autoinflammatory milieu within the pancreas of patients with T1D. The presence of IFNα/β is correlated with characteristic MHC class I (MHC-I) hyperexpression found in the islets of patients with T1D, suggesting that T1-IFNs modulate the cross-talk between autoreactive cytotoxic CD8+ T lymphocytes and insulin-producing pancreatic β cells. Here, we review the evidence supporting the diabetogenic potential of T1-IFN in the islet microenvironment.
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Affiliation(s)
- Brittney N. Newby
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, United States
- *Correspondence: Clayton E. Mathews,
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18
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Hu Y, Jin P, Peng J, Zhang X, Wong FS, Wen L. Different immunological responses to early-life antibiotic exposure affecting autoimmune diabetes development in NOD mice. J Autoimmun 2016; 72:47-56. [PMID: 27178773 DOI: 10.1016/j.jaut.2016.05.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 12/29/2022]
Abstract
Environmental factors clearly influence the pathogenesis of Type 1 diabetes, an autoimmune disease. We have studied gut microbiota as important environmental agents that could affect the initiation or progression of type 1 diabetes especially in the prenatal period. We used neomycin, targeting mainly Gram negative or vancomycin, targeting mainly Gram positive bacteria, to treat pregnant NOD mothers and to study autoimmune diabetes development in their offspring. Neomycin-treated offspring were protected from diabetes, while vancomycin-treated offspring had accelerated diabetes development, and both antibiotics caused distinctly different shifts in gut microbiota composition compared with the offspring from untreated control mice. Our study demonstrated that neomycin treatment of pregnant mothers leads to generation of immune-tolerogenic antigen-presenting cells (APCs) in the offspring and these APCs had reduced specific autoantigen-presenting function both in vitro and in vivo. Moreover, the protection from diabetes mediated by tolerogenic APCs was vertically transmissible to the second generation. In contrast, more diabetogenic inflammatory T cells were found in the lymphoid organs of the offspring from the vancomycin-treated pregnant mothers. This change however was not transmitted to the second generation. Our results suggested that prenatal exposure to antibiotic influenced gut bacterial composition at the earliest time point in life and is critical for consequent education of the immune system. As different bacteria can induce different immune responses, understanding these differences and how to generate self-tolerogenic APCs could be important for developing new therapy for type 1 diabetes.
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Affiliation(s)
- Youjia Hu
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Ping Jin
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Endocrinology, The Third Xiangya Hospital of Central South University, Changsha, Hunan 410013, China
| | - Jian Peng
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Xiaojun Zhang
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - F Susan Wong
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, CF14 4XN, UK
| | - Li Wen
- Section of Endocrinology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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19
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Evans PD, Mueller KL, Gamazon ER, Cox NJ, Tomblin JB. A genome-wide sib-pair scan for quantitative language traits reveals linkage to chromosomes 10 and 13. GENES BRAIN AND BEHAVIOR 2016; 14:387-97. [PMID: 25997078 DOI: 10.1111/gbb.12223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 02/03/2023]
Abstract
Although there is considerable evidence that individual differences in language development are highly heritable, there have been few genome-wide scans to locate genes associated with the trait. Previous analyses of language impairment have yielded replicable evidence for linkage to regions on chromosomes 16q, 19q, 13q (within lab) and at 13q (between labs). Here we report the first linkage study to screen the continuum of language ability, from normal to disordered, as found in the general population. 383 children from 147 sib-ships (214 sib-pairs) were genotyped on the Illumina(®) Linkage IVb Marker Panel using three composite language-related phenotypes and a measure of phonological memory (PM). Two regions (10q23.33; 13q33.3) yielded genome-wide significant peaks for linkage with PM. A peak suggestive of linkage was also found at 17q12 for the overall language composite. This study presents two novel genetic loci for the study of language development and disorders, but fails to replicate findings by previous groups. Possible reasons for this are discussed.
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Affiliation(s)
- P D Evans
- Department of Medicine, The University of Chicago, IL, USA
| | - K L Mueller
- Murdoch Childrens Research Institute, Melbourne, Australia.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
| | - E R Gamazon
- Department of Medicine, The University of Chicago, IL, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - N J Cox
- Department of Medicine, The University of Chicago, IL, USA.,Department of Communication Sciences and Disorders, The University of Iowa, IA, USA.,Present address: Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - J B Tomblin
- Department of Communication Sciences and Disorders, The University of Iowa, IA, USA
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20
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Pérol L, Piaggio E. New Molecular and Cellular Mechanisms of Tolerance: Tolerogenic Actions of IL-2. Methods Mol Biol 2016; 1371:11-28. [PMID: 26530792 DOI: 10.1007/978-1-4939-3139-2_2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Interleukin-2 (IL-2) is an old molecule with brand new functions. Indeed, IL-2 has been first described as a T-cell growth factor but recent data pointed out that its main function in vivo is the maintenance of immune tolerance. Mechanistically, IL-2 is essential for the development and function of CD4(+) Foxp3(+) regulatory T cells (Treg cells) that are essential players in the control of immune responded to self, tumors, microbes and grafts. Treg cells are exquisitely sensitive to IL-2 due to their constitutive expression of the high affinity IL-2 receptor (IL-2R) and the new paradigm suggests that low-doses of IL-2 could selectively boost Treg cells in vivo. Consequently, a growing body of clinical research is aiming at using IL-2 at low doses as a tolerogenic drug to boost endogenous Treg cells in patients suffering from autoimmune or inflammatory conditions. In this manuscript, we briefly review IL-2/IL-2R biology and the role of IL-2 in the development, maintenance, and function of Treg cells; and also its effects on other immune cell populations such as CD4(+) T helper cells and CD8(+) memory T cells. Then, focusing on type 1 diabetes, we review the preclinical studies and clinical trials supporting the use of low-doses IL-2 as a tolerogenic immunotherapy. Finally, we discuss the limitations and future directions for IL-2 based immunotherapy.
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Affiliation(s)
- Louis Pérol
- INSERM U932, 26 rue d'Ulm, 75005, Paris, France.
- Institut Curie, Section Recherche, 26 rue d'Ulm, 75005, Paris, France.
| | - Eliane Piaggio
- INSERM U932, 26 rue d'Ulm, 75005, Paris, France
- Institut Curie, Section Recherche, 26 rue d'Ulm, 75005, Paris, France
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21
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Rich SS, Concannon P. Role of Type 1 Diabetes-Associated SNPs on Autoantibody Positivity in the Type 1 Diabetes Genetics Consortium: Overview. Diabetes Care 2015; 38 Suppl 2:S1-3. [PMID: 26405066 PMCID: PMC4582912 DOI: 10.2337/dcs15-2001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Type 1 diabetes (T1D) arises from the autoimmune destruction of the β-cells of the pancreas, resulting in dependence on exogenously administered insulin for survival. Key biomarkers of the autoimmune process in T1D are the occurrence of autoantibodies directed against β-cells and other antigens. The Type 1 Diabetes Genetics Consortium (T1DGC) assembled collections to 1) discover genes that modify the risk of T1D, 2) conduct phenotyping related to risk, and 3) make available biologic and genetic resources for research. The goal of the T1DGC Autoantibody Workshop was to use T1DGC phenotypic, genotypic, and autoantibody data on affected sibling pair (ASP) families to discover genes accounting for variation in presence of autoantibodies. RESEARCH DESIGN AND METHODS The T1DGC provided the working groups with autoantibody and genetic data on 9,976 subjects from 2,321 ASP families. Data were distributed to numerous working groups for analyses of specific autoantibody subsets and targets. RESULTS Seven groups analyzed the joint autoantibody and genetic data within the ASP families. Six reports are provided in this collection, ranging from candidate gene analyses of selected autoantibodies to evaluation of regions of genetic variants associated with autoimmunity on the collection of autoantibodies. CONCLUSIONS Although selected variants in the available genes remain important genetic predictors for prevalence of T1D, other genes and nongenetic factors are expected to contribute to the initiation of islet autoimmunity, the first step in the pathogenesis of T1D.
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Affiliation(s)
- Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Patrick Concannon
- Genetics Institute and Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
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22
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Akolkar B, Hilner J, Nierras CR. Design and Measurement of Nonislet-Specific Autoantibodies for the Type 1 Diabetes Genetics Consortium Autoantibody Workshop. Diabetes Care 2015; 38 Suppl 2:S4-7. [PMID: 26405071 PMCID: PMC4582913 DOI: 10.2337/dcs15-2002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The Type 1 Diabetes Genetics Consortium (T1DGC) comprised groups of investigators from many countries throughout the world, with a common goal of identifying genes predisposing to type 1 diabetes. The T1DGC ascertained and collected samples from families with two or more affected siblings with type 1 diabetes and generated a broad array of clinical, genetic, and immunologic data. The T1DGC Autoantibody Workshop was designed to distribute data for analyses to discover genes associated with autoantibodies in those with type 1 diabetes. In the T1DGC-affected sibling pair families, three T1DGC Network laboratories measured antibodies to the islet autoantigens GAD65 and the intracellular portion of protein tyrosine phosphatase (IA-2A). The availability of extensive genetic data provided an opportunity to investigate the associations between type 1 diabetes and other autoimmune diseases for which autoantibodies could be measured. Measurements of additional nonislet autoantibodies, including thyroid peroxidase, tissue transglutaminase, 21-hydroxylase, and the potassium/hydrogen ion transporter H+/K+-ATPase, were performed by the T1DGC laboratory at the Barbara Davis Center for Childhood Diabetes, Aurora, CO. Measurements of all autoantibodies were transmitted to the T1DGC Coordinating Center, and the data were made available to members of the T1DGC Autoantibody Working Groups for analysis in conjunction with existing T1DGC genetic data. This article describes the design of the T1DGC Autoantibody Workshop and the quality-control procedures to maintain and monitor the performance of each laboratory and provides the quality-control results for the nonislet autoantibody measurements.
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Affiliation(s)
- Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | - Joan Hilner
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL
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23
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Miller FW, Chen W, O’Hanlon TP, Cooper RG, Vencovsky J, Rider LG, Danko K, Wedderburn LR, Lundberg IE, Pachman LM, Reed AM, Ytterberg SR, Padyukov L, Selva-O’Callaghan A, Radstake TR, Isenberg DA, Chinoy H, Ollier WE, Scheet P, Peng B, Lee A, Byun J, Lamb JA, Gregersen PK, Amos CI. Genome-wide association study identifies HLA 8.1 ancestral haplotype alleles as major genetic risk factors for myositis phenotypes. Genes Immun 2015; 16:470-80. [PMID: 26291516 PMCID: PMC4840953 DOI: 10.1038/gene.2015.28] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 06/15/2015] [Accepted: 06/18/2015] [Indexed: 02/06/2023]
Abstract
Autoimmune muscle diseases (myositis) comprise a group of complex phenotypes influenced by genetic and environmental factors. To identify genetic risk factors in patients of European ancestry, we conducted a genome-wide association study (GWAS) of the major myositis phenotypes in a total of 1710 cases, which included 705 adult dermatomyositis, 473 juvenile dermatomyositis, 532 polymyositis and 202 adult dermatomyositis, juvenile dermatomyositis or polymyositis patients with anti-histidyl-tRNA synthetase (anti-Jo-1) autoantibodies, and compared them with 4724 controls. Single-nucleotide polymorphisms showing strong associations (P<5×10(-8)) in GWAS were identified in the major histocompatibility complex (MHC) region for all myositis phenotypes together, as well as for the four clinical and autoantibody phenotypes studied separately. Imputation and regression analyses found that alleles comprising the human leukocyte antigen (HLA) 8.1 ancestral haplotype (AH8.1) defined essentially all the genetic risk in the phenotypes studied. Although the HLA DRB1*03:01 allele showed slightly stronger associations with adult and juvenile dermatomyositis, and HLA B*08:01 with polymyositis and anti-Jo-1 autoantibody-positive myositis, multiple alleles of AH8.1 were required for the full risk effects. Our findings establish that alleles of the AH8.1 comprise the primary genetic risk factors associated with the major myositis phenotypes in geographically diverse Caucasian populations.
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Affiliation(s)
- Frederick W. Miller
- National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Wei Chen
- M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Terrance P. O’Hanlon
- National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Robert G. Cooper
- MRC/ARUK Institute for Ageing and Chronic Disease, University of Liverpool, United Kingdom, L69 3GA
| | - Jiri Vencovsky
- Institute of Rheumatology, Charles University, Prague, Czech Republic; Na Slupi, 12850 Prague
| | - Lisa G. Rider
- National Institute of Environmental Health Sciences, National Institutes of Health, Bethesda, Maryland 20892
| | - Katalin Danko
- 3 Department of Internal Medicine, Division of Immunology University of Debrecen, Debrecen, Hungary H-4032
| | - Lucy R. Wedderburn
- Institute of Child Health, University College London, London, United Kingdom, WC1N 1EH
| | - Ingrid E. Lundberg
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Solna, Karolinska Institutet, Stockholm, Sweden SE-171 77
| | - Lauren M. Pachman
- Department of Pediatric Rheumatology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
| | | | | | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska University Hospital, Solna, Karolinska Institutet, Stockholm, Sweden SE-171 77
| | | | - Timothy R. Radstake
- Department of Rheumatology and Clinical Immunology, Laboratory for Translational Immunology, Utrecht University Medical Center; and Nijmegen Center for Molecular Life Sciences, Nijmegen, The Netherlands 6500.HB
| | - David A. Isenberg
- Division of Medicine, University College London, London, United Kingdom WC1E63T
| | - Hector Chinoy
- The National Institute for Health Research Manchester Musculoskeletal Biomedical Research Unit, Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom M139PT
| | - William E.R. Ollier
- Centre for Integrated Genomic Medical Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom M13 9PT
| | - Paul Scheet
- M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Bo Peng
- M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Annette Lee
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York 11030
| | - Jinyoung Byun
- Department of Community and Family Medicine, Dartmouth College, Hanover, New Hampshire 03755
| | - Janine A. Lamb
- Centre for Integrated Genomic Medical Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom M13 9PT
| | - Peter K. Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, Manhasset, New York 11030
| | - Christopher I. Amos
- Department of Community and Family Medicine, Dartmouth College, Hanover, New Hampshire 03755
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Abstract
Within the past 20 years the spectrum of complications of coeliac disease (CD) has been considerably extended. Besides the classic complications, autoimmune diseases and osteopenia, numerous forms of CD non-responsive to a gluten-free diet have been recently identified. Among the non-responsive CD, the majority of patients presents as long term responders. However a small subset of CD patients becomes refractory to a gluten-free diet with persistent malabsorption and intestinal villous atrophy. Whereas refractory coeliac disease type I (RCDI) is hardly distinguishable from active CD, the type II (RCDII) has a severe clinical presentation and a very poor prognosis. Enteropathy Associated T cell Lymphoma (EATL) is even more aggressive with a five year survival of 20%. Classic adriamycin-based chemotherapy is poorly efficient in the lymphomatous complications of CD and current therapeutic strategies focus on more intensive regimen with autologous or allogenic stem cell transplantation. Notable pathogenic advances let us to test targeted therapy both in low (RCDII) and high grade lymphomatous (EATL) complications associated with CD.
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Törn C, Hadley D, Lee HS, Hagopian W, Lernmark Å, Simell O, Rewers M, Ziegler A, Schatz D, Akolkar B, Onengut-Gumuscu S, Chen WM, Toppari J, Mykkänen J, Ilonen J, Rich SS, She JX, Steck AK, Krischer J. Role of Type 1 Diabetes-Associated SNPs on Risk of Autoantibody Positivity in the TEDDY Study. Diabetes 2015; 64:1818-29. [PMID: 25422107 PMCID: PMC4407865 DOI: 10.2337/db14-1497] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
Abstract
The Environmental Determinants of Diabetes in the Young (TEDDY) study prospectively follows 8,677 children enrolled from birth who carry HLA-susceptibility genotypes for development of islet autoantibodies (IA) and type 1 diabetes (T1D). During the median follow-up time of 57 months, 350 children developed at least one persistent IA (GAD antibody, IA-2A, or micro insulin autoantibodies) and 84 of them progressed to T1D. We genotyped 5,164 Caucasian children for 41 non-HLA single nucleotide polymorphisms (SNPs) that achieved genome-wide significance for association with T1D in the genome-wide association scan meta-analysis conducted by the Type 1 Diabetes Genetics Consortium. In TEDDY participants carrying high-risk HLA genotypes, eight SNPs achieved significant association to development of IA using time-to-event analysis (P < 0.05), whereof four were significant after adjustment for multiple testing (P < 0.0012): rs2476601 in PTPN22 (hazard ratio [HR] 1.54 [95% CI 1.27-1.88]), rs2292239 in ERBB3 (HR 1.33 [95% CI 1.14-1.55]), rs3184504 in SH2B3 (HR 1.38 [95% CI 1.19-1.61]), and rs1004446 in INS (HR 0.77 [0.66-0.90]). These SNPs were also significantly associated with T1D in particular: rs2476601 (HR 2.42 [95% CI 1.70-3.44]). Although genes in the HLA region remain the most important genetic risk factors for T1D, other non-HLA genetic factors contribute to IA, a first step in the pathogenesis of T1D, and the progression of the disease.
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Affiliation(s)
- Carina Törn
- Department of Clinical Sciences, Lund University/CRC, Malmö, Sweden
| | - David Hadley
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL Division of Population Health Sciences and Education, St George's University of London, London, U.K
| | - Hye-Seung Lee
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL
| | | | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Malmö, Sweden
| | - Olli Simell
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO
| | - Anette Ziegler
- Department of Pediatrics, Diabetes Research Institute, Munich, Germany
| | - Desmond Schatz
- Department of Pediatrics, University of Florida, Gainesville, FL
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD
| | | | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jorma Toppari
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Juha Mykkänen
- Department of Pediatrics, University of Turku, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Turku, Finland Department of Clinical Microbiology, University of Eastern Finland, Kuopio, Finland
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA
| | - Jin-Xiong She
- Center for Biotechnology and Genomic Medicine, Georgia Regents University, Augusta, GA
| | - Andrea K Steck
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Denver, Aurora, CO
| | - Jeffrey Krischer
- Pediatric Epidemiology Center, Department of Pediatrics, University of South Florida, Tampa, FL
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Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P, Todd JA, Wallace C, Concannon P, Rich SS. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat Genet 2015; 47:381-6. [PMID: 25751624 PMCID: PMC4380767 DOI: 10.1038/ng.3245] [Citation(s) in RCA: 486] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 02/13/2015] [Indexed: 02/06/2023]
Abstract
Genetic studies of type 1 diabetes (T1D) have identified 50 susceptibility regions, finding major pathways contributing to risk, with some loci shared across immune disorders. To make genetic comparisons across autoimmune disorders as informative as possible, a dense genotyping array, the Immunochip, was developed, from which we identified four new T1D-associated regions (P < 5 × 10(-8)). A comparative analysis with 15 immune diseases showed that T1D is more similar genetically to other autoantibody-positive diseases, significantly most similar to juvenile idiopathic arthritis and significantly least similar to ulcerative colitis, and provided support for three additional new T1D risk loci. Using a Bayesian approach, we defined credible sets for the T1D-associated SNPs. The associated SNPs localized to enhancer sequences active in thymus, T and B cells, and CD34(+) stem cells. Enhancer-promoter interactions can now be analyzed in these cell types to identify which particular genes and regulatory sequences are causal.
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Affiliation(s)
- Suna Onengut-Gumuscu
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, Division of Endocrinology, University of Virginia, Charlottesville, VA, USA
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA
| | - Oliver Burren
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Nick J. Cooper
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Aaron R. Quinlan
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA
| | - Emily Farber
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jessica K. Bonnie
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Michal Szpak
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ellen Schofield
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Premanand Achuthan
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Hui Guo
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Mary D. Fortune
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Helen Stevens
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Neil M. Walker
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Luke D. Ward
- Department of Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anshul Kundaje
- Department of Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA. Department of Genetics, Stanford University, Stanford, CA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Manolis Kellis
- Department of Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mark J. Daly
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA
| | | | - Jason D. Cooper
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | | | | | - John A. Todd
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
| | - Chris Wallace
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, NIHR Biomedical Research Centre, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0XY, UK
- MRC Biostatistics Unit, Institute of Public Health, University Forvie Site, Robinson Way, CB2 0SR, Cambridge, United Kingdom
| | - Patrick Concannon
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, VA, USA
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Rosenzwajg M, Churlaud G, Hartemann A, Klatzmann D. Interleukin 2 in the pathogenesis and therapy of type 1 diabetes. Curr Diab Rep 2014; 14:553. [PMID: 25344788 DOI: 10.1007/s11892-014-0553-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Regulatory T cells (Tregs) play a major role in controlling effector T cells (Teffs) responding to self-antigens, which cause autoimmune diseases. An improper Treg/Teff balance contributes to most autoimmune diseases, including type 1 diabetes (T1D). To restore a proper balance, blocking Teffs with immunosuppressants has been the only option, which was partly effective and too toxic. It now appears that expanding/activating Tregs with low-dose interleukin-2 (IL-2) could provide immunoregulation without immunosuppression. This is particularly interesting in T1D as Tregs from T1D patients are reported as dysfunctional and a relative deficiency in IL-2 production and/or IL-2-mediated signaling could contribute to this phenotype. A clinical study of low-dose IL-2 showed a very good safety profile and good Treg expansion/activation in T1D patients. This opens the way for efficacy trials to test low-dose IL-2 in prevention and treatment of T1D and to establish in which condition restoration of a proper Treg/Teff balance would be beneficial in the field of autoimmune and inflammatory diseases.
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Affiliation(s)
- Michelle Rosenzwajg
- Biotherapy (CIC-BTi) and Inflammation-Immunopathology-Biotherapy Department (i2B), AP-HP, Hôpital Pitié-Salpêtrière, 83 Boulevard de l'Hôpital, 75651, Paris, France,
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Delvin E, Souberbielle JC, Viard JP, Salle B. Role of vitamin D in acquired immune and autoimmune diseases. Crit Rev Clin Lab Sci 2014; 51:232-47. [DOI: 10.3109/10408363.2014.901291] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Elevated levels of extracellular heat-shock protein 72 (eHSP72) are positively correlated with insulin resistance in vivo and cause pancreatic β-cell dysfunction and death in vitro. Clin Sci (Lond) 2014; 126:739-52. [PMID: 24325467 DOI: 10.1042/cs20130678] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
eHSP72 (extracellular heat-shock protein 72) is increased in the plasma of both types of diabetes and is positively correlated with inflammatory markers. Since aging is associated with a low-grade inflammation and IR (insulin resistance), we aimed to: (i) analyse the concentration of eHSP72 in elderly people and determine correlation with insulin resistance, and (ii) determine the effects of eHSP72 on β-cell function and viability in human and rodent pancreatic β-cells. Fasting blood samples were collected from 50 older people [27 females and 23 males; 63.4±4.4 years of age; BMI (body mass index)=25.5±2.7 kg/m2]. Plasma samples were analysed for eHSP72, insulin, TNF (tumour necrosis factor)-α, leptin, adiponectin and cortisol, and glycaemic and lipid profile. In vitro studies were conducted using rodent islets and clonal rat and human pancreatic β-cell lines (BRIN-BD11 and 1.1B4 respectively). Cells/islets were incubated for 24 h with eHSP72 (0, 0.2, 4, 8 and 40 ng/ml). Cell viability was measured using three different methods. The impact of HSP72 on β-cell metabolic status was determined using Seahorse Bioscience XFe96 technology. To assess whether the effects of eHSP72 were mediated by Toll-like receptors (TLR2/TLR4), we co-incubated rodent islets with eHSP72 and the TLR2/TLR4 inhibitor OxPAPC (oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine; 30 μg/ml). We found a positive correlation between plasma eHSP72 and HOMA-IR (homoeostasis model assessment of IR) (r=0.528, P<0.001), TNF-α (r=0.389, P<0.014), cortisol (r=0.348, P<0.03) and leptin/adiponectin (r=0.334, P<0.03). In the in vitro studies, insulin secretion was decreased in an eHSP72 dose-dependent manner in BRIN-BD11 cells (from 257.7±33 to 84.1±10.2 μg/mg of protein per 24 h with 40 ng/ml eHSP72), and in islets in the presence of 40 ng/ml eHSP72 (from 0.48±0.07 to 0.33±0.009 μg/20 islets per 24 h). Similarly, eHSP72 reduced β-cell viability (at least 30% for BRIN-BD11 and 10% for 1.1B4 cells). Bioenergetic studies revealed that eHSP72 altered pancreatic β-cell metabolism. OxPAPC restored insulin secretion in islets incubated with 40 ng/ml eHSP72. In conclusion, we have demonstrated a positive correlation between eHSP72 and IR. In addition, we suggest that chronic eHSP72 exposure may mediate β-cell failure.
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Song L. Genetic counseling in post-genomic era: Don’t pretend to know the meaning of a gene mutation if you don’t know. World J Med Genet 2014; 4:1-5. [DOI: 10.5496/wjmg.v4.i1.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 12/13/2013] [Indexed: 02/06/2023] Open
Abstract
In this post-genomic era, more and more susceptibility loci of many possible genetic diseases are published. As our knowledge about these susceptibility loci is limited and partial, we should be very careful and responsible when patients seek genetic counseling about these possible genetic diseases. We should apply Confucius’s principle about knowledge and information to genetic conseling, and tell the truth to our patients about what we know and what we do not know. Like many other cancers, breast cancer is a very complicated, multifactorial disease; genetic factors, lifestyles and eating habits, environmental factors, and viral infections might be involved in breast cancer; hence, it is difficult to figure out the real etiology of breast cancer. It is not crystal clear that a person who carries mutations of the breast cancer 1, early onset and/or breast cancer 2, early onset genes would eventually get breast cancer in her/his lifetime. No person should undergo a preventive double mastectomy, unless we know the etiology of breast cancer someday.
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Groop L, Pociot F. Genetics of diabetes--are we missing the genes or the disease? Mol Cell Endocrinol 2014; 382:726-739. [PMID: 23587769 DOI: 10.1016/j.mce.2013.04.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 01/25/2013] [Accepted: 04/02/2013] [Indexed: 12/20/2022]
Abstract
Diabetes is a group of metabolic diseases characterized by hyperglycemia resulting from defects in insulin secretion, insulin action, or both. The chronic hyperglycemia of diabetes is associated with long-term damage, dysfunction, and failure of different organs, especially the eyes, kidneys, nerves, heart, and blood vessels. Several pathogenic processes are involved in the development of diabetes. These range from autoimmune destruction of the beta-cells of the pancreas with consequent insulin deficiency to abnormalities that result in resistance to insulin action (American Diabetes Association, 2011). The vast majority of cases of diabetes fall into two broad categories. In type 1 diabetes (T1D), the cause is an absolute deficiency of insulin secretion, whereas in type 2 diabetes (T2D), the cause is a combination of resistance to insulin action and an inadequate compensatory insulin secretory response. However, the subdivision into two main categories represents a simplification of the real situation, and research during the recent years has shown that the disease is much more heterogeneous than a simple subdivision into two major subtypes assumes. Worldwide prevalence figures estimate that there are 280 million diabetic patients in 2011 and more than 500 million in 2030 (http://www.diabetesatlas.org/). In Europe, about 6-8% of the population suffer from diabetes, of them about 90% has T2D and 10% T1D, thereby making T2D to the fastest increasing disease in Europe and worldwide. This epidemic has been ascribed to a collision between the genes and the environment. While our knowledge about the genes is clearly better for T1D than for T2D given the strong contribution of variation in the HLA region to the risk of T1D, the opposite is the case for T2D, where our knowledge about the environmental triggers (obesity, lack of exercise) is much better than the understanding of the underlying genetic causes. This lack of knowledge about the underlying genetic causes of diabetes is often referred to as missing heritability (Manolio et al., 2009) which exceeds 80% for T2D but less than 25% for T1D. In the following review, we will discuss potential sources of this missing heritability which also includes the possibility that our definition of diabetes and its subgroups is imprecise and thereby making the identification of genetic causes difficult.
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Affiliation(s)
- Leif Groop
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Skåne, Malmö, Sweden; Glostrup Research Institute, Glostrup University Hospital, Glostrup, Denmark.
| | - Flemming Pociot
- Department of Clinical Sciences, Diabetes and Endocrinology, Lund University, University Hospital Skåne, Malmö, Sweden; Glostrup Research Institute, Glostrup University Hospital, Glostrup, Denmark
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Kamel AM, Mira MF, Mossallam GI, Ebid GT, Radwan ER, Aly Eldin NH, Mamdouh M, Amin M, Badawy N, Bazaraa H, Ibrahim A, Salah N, Hansen J. Lack of association of CTLA-4 +49 A/G polymorphism with predisposition to type 1 diabetes in a cohort of Egyptian families. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2014. [DOI: 10.1016/j.ejmhg.2013.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Price JD, Beauchamp NM, Rahir G, Zhao Y, Rieger CC, Lau-Kilby AW, Tarbell KV. CD8+ dendritic cell-mediated tolerance of autoreactive CD4+ T cells is deficient in NOD mice and can be corrected by blocking CD40L. J Leukoc Biol 2013; 95:325-36. [PMID: 24082013 DOI: 10.1189/jlb.0113013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DCs are important mediators of peripheral tolerance for the prevention of autoimmunity. Chimeric αDEC-205 antibodies with attached antigens allow in vivo antigen-specific stimulation of T cells by CD8(+) DCs, resulting in tolerance in nonautoimmune mice. However, it is not clear whether DC-mediated tolerance induction occurs in the context of ongoing autoimmunity. We assessed the role of CD8(+) DCs in stimulation of autoreactive CD4(+) T cells in the NOD mouse model of type 1 diabetes. Targeting of antigen to CD8(+) DCs via αDEC-205 led to proliferation and expansion of β-cell specific BDC2.5 T cells. These T cells also produced IL-2 and IFN-γ and did not up-regulate FoxP3, consistent with an activated rather than tolerant phenotype. Similarly, endogenous BDC peptide-reactive T cells, identified with I-A(g7) tetramers, did not become tolerant after antigen delivery via αDEC-205: no deletion or Treg induction was observed. We observed that CD8(+) DCs from NOD mice expressed higher surface levels of CD40 than CD8(+) DCs from C57BL/6 mice. Blockade of CD40-CD40L interactions reduced the number of BDC2.5 T cells remaining in mice, 10 days after antigen targeting to CD8 DCs, and blocked IFN-γ production by BDC2.5 T cells. These data indicate that the ability of autoreactive CD4(+) T cells to undergo tolerance mediated by CD8(+) DCs is defective in NOD mice and that blocking CD40-CD40L interactions can restore tolerance induction.
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Affiliation(s)
- Jeffrey D Price
- 1.Diabetes, Endocrinology, and Obesity Branch, NIDDK, NIH, Bldg. 10, CRC, West Labs, 5-5940, Bethesda, MD 20892, USA.
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Howell WM. HLA and disease: guilt by association. Int J Immunogenet 2013; 41:1-12. [DOI: 10.1111/iji.12088] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/10/2013] [Indexed: 02/06/2023]
Affiliation(s)
- W. M. Howell
- Department of Histocompatibility and Immunogenetics; NHS Blood and Transplant; Newcastle upon Tyne UK
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A novel ALMS1 splice mutation in a non-obese juvenile-onset insulin-dependent syndromic diabetic patient. Eur J Hum Genet 2013; 22:140-3. [PMID: 23652376 DOI: 10.1038/ejhg.2013.87] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 02/11/2013] [Accepted: 04/04/2013] [Indexed: 12/13/2022] Open
Abstract
Insulin-dependent juvenile-onset diabetes may occur in the context of rare syndromic presentations suggesting monogenic inheritance rather than common multifactorial autoimmune type 1 diabetes. Here, we report the case of a Lebanese patient diagnosed with juvenile-onset insulin-dependent diabetes presenting ketoacidosis, early-onset retinopathy with optic atrophy, hearing loss, diabetes insipidus, epilepsy, and normal weight and stature, who later developed insulin resistance. Despite similarities with Wolfram syndrome, we excluded the WFS1 gene as responsible for this disease. Using combined linkage and candidate gene study, we selected ALMS1, responsible for Alström syndrome, as a candidate gene. We identified a novel splice mutation in intron 18 located 3 bp before the intron-exon junction (IVS18-3T>G), resulting in exon 19 skipping and consequent frameshift generating a truncated protein (V3958fs3964X). The clinical presentation of the patient significantly differed from typical Alström syndrome by the absence of truncal obesity and short stature, and by the presence of ketoacidotic insulin-dependent diabetes, optic atrophy and diabetes insipidus. Our observation broadens the clinical spectrum of Alström syndrome and suggests that ALMS1 mutations may be considered in patients who initially present with an acute onset of insulin-dependent diabetes.
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Skog O, Korsgren S, Melhus A, Korsgren O. Revisiting the notion of type 1 diabetes being a T-cell-mediated autoimmune disease. Curr Opin Endocrinol Diabetes Obes 2013; 20:118-23. [PMID: 23422243 DOI: 10.1097/med.0b013e32835edb89] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
PURPOSE OF REVIEW Type 1 diabetes (T1D) research is at present in a critical period of development and during the past few years several large phase III studies targeting T-cell autoimmunity in recent-onset patients with T1D failed to reach the primary endpoint. RECENT FINDINGS Cause and pathogenesis of T1D remain largely unknown. In humans, insulitis is discrete, affects few islets and is present only in about one-third of patients with recent-onset T1D. The rapid increase in incidence of T1D argues against a decisive role for genetic factors and instead for the hypothesis that infectious agents, possibly entering the pancreas via the ductal compartment, are involved in disease pathogenesis. Repeated episodes of bacteria or virus-induced innate inflammations affecting only certain lobes of the pancreas fit well with the reported heterogeneity of the disease within the pancreas as well as with the slow progression over many years. SUMMARY In humans there is limited support for T1D being primarily an autoimmune disease; instead available findings support the view that T1D can be regarded as an innate inflammatory disease affecting the entire pancreas, but with its main clinical manifestations emanating from the loss of the insulin-producing cells.
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Affiliation(s)
- Oskar Skog
- Department of Immunology, Uppsala University, Uppsala, Sweden
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Baxter AG, Jordan MA. From markers to molecular mechanisms: type 1 diabetes in the post-GWAS era. Rev Diabet Stud 2012; 9:201-23. [PMID: 23804261 DOI: 10.1900/rds.2012.9.201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data.
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Affiliation(s)
- Alan G Baxter
- Comparative Genomics Centre, Molecular Sciences Building 21, James Cook University, Townsville QLD 4811, Australia.
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Jahromi MM. Haplotype specific alteration of diabetes MHC risk by olfactory receptor gene polymorphism. Autoimmun Rev 2012; 12:270-4. [DOI: 10.1016/j.autrev.2012.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 04/23/2012] [Indexed: 12/12/2022]
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Abstract
Type 1 diabetes (T1D) is a chronic autoimmune disease affecting millions of people worldwide. The disease is characterized by the loss of self-tolerance to the insulin-producing β-cells in the pancreas, the destruction of β-cells, and finally the development of chronic hyperglycemia at diagnosis of T1D. Its incidence and prevalence are rising dramatically, highlighting the need for immunotherapeutic strategies able to prevent or treat the disease in a safe and specific manner. Immunotherapeutic strategies are being developed, and aim to restore immunological self-tolerance, thereby limiting unwanted immunity and β-cell destruction. Foxp3+ regulatory T (Treg) cells exert essential functions to maintain and restore immunological self-tolerance. The identification of the transcription factor Foxp3 as the specification factor for the Treg cell lineage facilitated our understanding in the biology of Treg generation and function. This review highlights the current understanding of immunotherapeutic approaches as preventative and curative measures for autoimmune T1D. It includes an overview on early immunointervention studies, which made use of general immunosuppressive agents such as cyclosporin A, followed by a discussion on newly emerging clinical trials. Besides non-antigen-specific therapies, particular attention is given to antigen-specific generation of Foxp3+ Treg cells and their potential use to limit autoimmunity such as T1D.
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Affiliation(s)
- Benno Weigmann
- Research Campus of the Friedrich-Alexander University Erlangen-Nuernberg, Medical Clinic I, 91052 Erlangen, Germany
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Gu HF, Ma J, Gu KT, Brismar K. Association of intercellular adhesion molecule 1 (ICAM1) with diabetes and diabetic nephropathy. Front Endocrinol (Lausanne) 2012; 3:179. [PMID: 23346076 PMCID: PMC3551242 DOI: 10.3389/fendo.2012.00179] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 12/17/2012] [Indexed: 12/26/2022] Open
Abstract
Diabetes and diabetic nephropathy are complex diseases affected by genetic and environmental factors. Identification of the susceptibility genes and investigation of their roles may provide useful information for better understanding of the pathogenesis and for developing novel therapeutic approaches. Intercellular adhesion molecule 1 (ICAM1) is a cell surface glycoprotein expressed on endothelial cells and leukocytes in the immune system. The ICAM1 gene is located on chromosome 19p13 within the linkage region of diabetes. In the recent years, accumulating reports have implicated that genetic polymorphisms in the ICAM1 gene are associated with diabetes and diabetic nephropathy. Serum ICAM1 levels in diabetes patients and the icam1 gene expression in kidney tissues of diabetic animals are increased compared to the controls. Therefore, ICAM1 may play a role in the development of diabetes and diabetic nephropathy. In this review, we present genomic structure, variation, and regulation of the ICAM1 gene, summarized genetic and biological studies of this gene in diabetes and diabetic nephropathy and discussed about the potential application using ICAM1 as a biomarker and target for prediction and treatment of diabetes and diabetic nephropathy.
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Affiliation(s)
- Harvest F. Gu
- M1:03 Rolf Luft Center for Diabetes and Endocrinology Research, Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University HospitalStockholm, Sweden
- *Correspondence: Harvest F. Gu, M1:03 Rolf Luft Center for Diabetes and Endocrinology Research, Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Stockholm SE-17176, Sweden. e-mail:
| | - Jun Ma
- Department of Anesthesiology, Anzhen Hospital, Capital Medical UniversityBeijing, People’s Republic of China
| | - Karolin T. Gu
- Viktor Rydberg Gymnasium Odenplan SchoolStockholm, Sweden
| | - Kerstin Brismar
- M1:03 Rolf Luft Center for Diabetes and Endocrinology Research, Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University HospitalStockholm, Sweden
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McKillop AM, Flatt PR. Emerging applications of metabolomic and genomic profiling in diabetic clinical medicine. Diabetes Care 2011; 34:2624-30. [PMID: 22110171 PMCID: PMC3220869 DOI: 10.2337/dc11-0837] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Clinical and epidemiological metabolomics provides a unique opportunity to look at genotype-phenotype relationships as well as the body\x{2019}s responses to environmental and lifestyle factors. Fundamentally, it provides information on the universal outcome of influencing factors on disease states and has great potential in the early diagnosis, therapy monitoring, and understanding of the pathogenesis of disease. Diseases, such as diabetes, with a complex set of interactions between genetic and environmental factors, produce changes in the body\x{2019}s biochemical profile, thereby providing potential markers for diagnosis and initiation of therapies. There is clearly a need to discover new ways to aid diagnosis and assessment of glycemic status to help reduce diabetes complications and improve the quality of life. Many factors, including peptides, proteins, metabolites, nucleic acids, and polymorphisms, have been proposed as putative biomarkers for diabetes. Metabolomics is an approach used to identify and assess metabolic characteristics, changes, and phenotypes in response to influencing factors, such as environment, diet, lifestyle, and pathophysiological states. The specificity and sensitivity using metabolomics to identify biomarkers of disease have become increasingly feasible because of advances in analytical and information technologies. Likewise, the emergence of high-throughput genotyping technologies and genome-wide association studies has prompted the search for genetic markers of diabetes predisposition or susceptibility. In this review, we consider the application of key metabolomic and genomic methodologies in diabetes and summarize the established, new, and emerging metabolomic and genomic biomarkers for the disease. We conclude by summarizing future insights into the search for improved biomarkers for diabetes research and human diagnostics.
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Affiliation(s)
- Aine M McKillop
- AAD Centre for Pharmacy and Diabetes, School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK.
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Abstract
Diabetes mellitus diagnosed during the first 2 years of life differs from the disease in older children regarding its causes, clinical characteristics, treatment options and needs in terms of education and psychosocial support. Over the past decade, new genetic causes of neonatal diabetes mellitus have been elucidated, including monogenic β-cell defects and chromosome 6q24 abnormalities. In patients with KCNJ11 or ABCC8 mutations and diabetes mellitus, oral sulfonylurea offers an easy and effective treatment option. Type 1 diabetes mellitus in infants is characterized by a more rapid disease onset, poorer residual β-cell function and lower rate of partial remission than in older children. Insulin therapy in infants with type 1 diabetes mellitus or other monogenic causes of diabetes mellitus is a challenge, and novel data highlight the value of continuous subcutaneous insulin infusion in this very young patient population. Infants are entirely dependent on caregivers for insulin therapy, nutrition and glucose monitoring, which emphasizes the need for appropriate education and psychosocial support of parents. To achieve optimal long-term metabolic control with low rates of acute and chronic complications, continuous and structured diabetes care should be provided by a multidisciplinary health-care team.
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Affiliation(s)
- Beate Karges
- Division of Endocrinology and Diabetes, RWTH Aachen University, Pauwelsstraße 30, D-52074 Aachen, Germany.
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Polychronakos C, Li Q. Understanding type 1 diabetes through genetics: advances and prospects. Nat Rev Genet 2011; 12:781-92. [PMID: 22005987 DOI: 10.1038/nrg3069] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Starting with early crucial discoveries of the role of the major histocompatibility complex, genetic studies have long had a role in understanding the biology of type 1 diabetes (T1D), which is one of the most heritable common diseases. Recent genome-wide association studies (GWASs) have given us a clearer picture of the allelic architecture of genetic susceptibility to T1D. Fine mapping and functional studies are gradually revealing the complex mechanisms whereby immune self-tolerance is lost, involving multiple aspects of adaptive immunity. The triggering of these events by dysregulation of the innate immune system has also been implicated by genetic evidence. Finally, genetic prediction of T1D risk is showing promise of use for preventive strategies.
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Affiliation(s)
- Constantin Polychronakos
- Departments of Pediatrics and Human Genetics, McGill University, Montreal, Québec, Canada H3H 1P3. Constantin.
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Huntingtin-interacting protein 14 is a type 1 diabetes candidate protein regulating insulin secretion and beta-cell apoptosis. Proc Natl Acad Sci U S A 2011; 108:E681-8. [PMID: 21705657 DOI: 10.1073/pnas.1104384108] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Type 1 diabetes (T1D) is a complex disease characterized by the loss of insulin-secreting β-cells. Although the disease has a strong genetic component, and several loci are known to increase T1D susceptibility risk, only few causal genes have currently been identified. To identify disease-causing genes in T1D, we performed an in silico "phenome-interactome analysis" on a genome-wide linkage scan dataset. This method prioritizes candidates according to their physical interactions at the protein level with other proteins involved in diabetes. A total of 11 genes were predicted to be likely disease genes in T1D, including the INS gene. An unexpected top-scoring candidate gene was huntingtin-interacting protein (HIP)-14/ZDHHC17. Immunohistochemical analysis of pancreatic sections demonstrated that HIP14 is almost exclusively expressed in insulin-positive cells in islets of Langerhans. RNAi knockdown experiments established that HIP14 is an antiapoptotic protein required for β-cell survival and glucose-stimulated insulin secretion. Proinflammatory cytokines (IL-1β and IFN-γ) that mediate β-cell dysfunction in T1D down-regulated HIP14 expression in insulin-secreting INS-1 cells and in isolated rat and human islets. Overexpression of HIP14 was associated with a decrease in IL-1β-induced NF-κB activity and protection against IL-1β-mediated apoptosis. Our study demonstrates that the current network biology approach is a valid method to identify genes of importance for T1D and may therefore embody the basis for more rational and targeted therapeutic approaches.
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Gurzov EN, Eizirik DL. Bcl-2 proteins in diabetes: mitochondrial pathways of β-cell death and dysfunction. Trends Cell Biol 2011; 21:424-31. [PMID: 21481590 DOI: 10.1016/j.tcb.2011.03.001] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/03/2011] [Accepted: 03/09/2011] [Indexed: 01/08/2023]
Abstract
Diabetes is a metabolic disease affecting nearly 300 million individuals worldwide. Both types of diabetes (1 and 2) are characterized by loss of functional pancreatic β-cell mass causing different degrees of insulin deficiency. The Bcl-2 family has a double-edged effect in diabetes. These proteins are crucial controllers of the mitochondrial pathway of β-cell apoptosis induced by pro-inflammatory cytokines or lipotoxicity. In parallel, some Bcl-2 members also regulate glucose metabolism and β-cell function. In this review, we describe the role of Bcl-2 proteins in β-cell homeostasis and death. We focus on how these proteins interact, their contribution to the crosstalk between endoplasmic reticulum stress and mitochondrial permeabilization, their context-dependent usage following different pro-apoptotic stimuli, and their role in β-cell physiology.
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Affiliation(s)
- Esteban N Gurzov
- Laboratory of Experimental Medicine, Université Libre de Bruxelles, Route de Lennik, 808, 1070, Brussels, Belgium.
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Wolters VM, Xu W, Zhao X, Walters TD, Griffiths AM, Silverberg MS, Muise AM. Replication of genetic variation in the MYO9B gene in Crohn's disease. Hum Immunol 2011; 72:592-7. [PMID: 21515326 DOI: 10.1016/j.humimm.2011.03.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 03/14/2011] [Accepted: 03/31/2011] [Indexed: 11/16/2022]
Abstract
Various genes that may influence the intestinal barrier have been identified, including MAGI2, PARD3, and MYO9B. These genes are associated with inflammatory bowel disease (IBD) in several European studies. A total of 2,049 individuals (656 Crohn's disease [CD], 544 ulcerative colitis [UC], and 849 controls) were genotyped and association studies were performed for 1 single nucleotide polymorphism (SNP) in MAGI2, 1 SNP in PARD3, and 6 SNPs in MYO9B. We reported an association between 3 SNPs in MYO9B and ileal involvement with rs1457092 as the most significant SNP (p = 0.0073, odds ratio [OR] 0.69 [95% confidence interval (95% CI) 0.52-0.90]). The nonsynonymous SNP rs1545620 exhibited a p value of 0.014, OR 0.72 (95% CI 0.55-0.93). MYO9B was not associated with UC. MAGI2 or PARD3 was not associated with IBD. A 6-SNP haplotype block in MYO9B demonstrated association with CD and ileal CD (p = 0.0030 and 0.0065, respectively). These data demonstrate an association of MYO9B with ileal CD; however, there was no association of MAGI2 and PARD3 with IBD. Because the direction of association of MYO9B in this Canadian study was not consistent with European studies, further studies are needed to elucidate the role of MYO9B in IBD.
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Affiliation(s)
- Victorien M Wolters
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, The Hospital for Sick Children, Toronto, Canada
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Morahan G, Mehta M, James I, Chen WM, Akolkar B, Erlich HA, Hilner JE, Julier C, Nerup J, Nierras C, Pociot F, Todd JA, Rich SS. Tests for genetic interactions in type 1 diabetes: linkage and stratification analyses of 4,422 affected sib-pairs. Diabetes 2011; 60:1030-40. [PMID: 21266329 PMCID: PMC3046821 DOI: 10.2337/db10-1195] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVE Interactions between genetic and environmental factors lead to immune dysregulation causing type 1 diabetes and other autoimmune disorders. Recently, many common genetic variants have been associated with type 1 diabetes risk, but each has modest individual effects. Familial clustering of type 1 diabetes has not been explained fully and could arise from many factors, including undetected genetic variation and gene interactions. RESEARCH DESIGN AND METHODS To address this issue, the Type 1 Diabetes Genetics Consortium recruited 3,892 families, including 4,422 affected sib-pairs. After genotyping 6,090 markers, linkage analyses of these families were performed, using a novel method and taking into account factors such as genotype at known susceptibility loci. RESULTS Evidence for linkage was robust at the HLA and INS loci, with logarithm of odds (LOD) scores of 398.6 and 5.5, respectively. There was suggestive support for five other loci. Stratification by other risk factors (including HLA and age at diagnosis) identified one convincing region on chromosome 6q14 showing linkage in male subjects (corrected LOD = 4.49; replication P = 0.0002), a locus on chromosome 19q in HLA identical siblings (replication P = 0.006), and four other suggestive loci. CONCLUSIONS This is the largest linkage study reported for any disease. Our data indicate there are no major type 1 diabetes subtypes definable by linkage analyses; susceptibility is caused by actions of HLA and an apparently random selection from a large number of modest-effect loci; and apart from HLA and INS, there is no important susceptibility factor discoverable by linkage methods.
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Affiliation(s)
- Grant Morahan
- Centre for Diabetes Research, Western Australian Institute for Medical Research, University of Western Australia, Crawley, Australia.
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Swafford ADE, Howson JM, Davison LJ, Wallace C, Smyth DJ, Schuilenburg H, Maisuria-Armer M, Mistry T, Lenardo MJ, Todd JA. An allele of IKZF1 (Ikaros) conferring susceptibility to childhood acute lymphoblastic leukemia protects against type 1 diabetes. Diabetes 2011; 60:1041-4. [PMID: 21270240 PMCID: PMC3046822 DOI: 10.2337/db10-0446] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Accepted: 11/30/2010] [Indexed: 12/29/2022]
Abstract
OBJECTIVE IKZF1 encoding Ikaros, an essential regulator of lymphopoiesis and immune homeostasis, has been implicated in the development of childhood acute lymphoblastic leukemia (C-ALL). Because recent genome-wide association (GWA) studies have linked a region of the 3'-UTR of IKZF1 with C-ALL susceptibility, we tested whether IKZF1 is associated with the autoimmune disease type 1 diabetes. RESEARCH DESIGN AND METHODS rs10272724 (T>C) near IKZF1 at 7p12 was genotyped in 8,333 individuals with type 1 diabetes, 9,947 control subjects, and 3,997 families of European ancestry. Association was tested using logistic regression in the case-control data and by the transmission disequilibrium test in the families. Expression data for IKZF1 by rs10272724 genotype were obtained using quantitative PCR of mRNA/cDNA generated from peripheral blood mononuclear cells from 88 individuals, whereas expression data for five other neighboring genes were obtained from the online Genevar dataset. RESULTS The minor allele of rs10272724 (C) was found to be protective from type 1 diabetes (odds ratio 0.87 [95% CI 0.83-0.91]; P = 1.1 × 10(-11)). rs10272724 was not correlated with levels of two transcripts of IKZF1 in peripheral blood mononuclear cells. CONCLUSIONS The major susceptibility genotype for C-ALL confers protection from type 1 diabetes. Our finding strengthens the link between autoimmunity and lymphoid cancers. Further investigation is warranted for the genetic effect marked by rs10272724, its impact on IKZF1, and the role of Ikaros and other family members, Ailios (IKZF3) and Eos (IKZF4), in autoimmunity.
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Affiliation(s)
- Austin D.-E. Swafford
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
- Laboratory of Immunology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - Joanna M.M. Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Lucy J. Davison
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Chris Wallace
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Helen Schuilenburg
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Meeta Maisuria-Armer
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Trupti Mistry
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
| | - Michael J. Lenardo
- Laboratory of Immunology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, Maryland
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke’s Hospital, Cambridge, U.K
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