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Kulski JK, Suzuki S, Shiina T, Pfaff AL, Kõks S. Regulatory SVA retrotransposons and classical HLA genotyped-transcripts associated with Parkinson's disease. Front Immunol 2024; 15:1349030. [PMID: 38590523 PMCID: PMC10999589 DOI: 10.3389/fimmu.2024.1349030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/06/2024] [Indexed: 04/10/2024] Open
Abstract
Introduction Parkinson's disease (PD) is a neurodegenerative and polygenic disorder characterised by the progressive loss of neural dopamine and onset of movement disorders. We previously described eight SINE-VNTR-Alu (SVA) retrotransposon-insertion-polymorphisms (RIPs) located and expressed within the Human Leucocyte Antigen (HLA) genomic region of chromosome 6 that modulate the differential co-expression of 71 different genes including the HLA classical class I and class II genes in a Parkinson's Progression Markers Initiative (PPMI) cohort. Aims and methods In the present study, we (1) reanalysed the PPMI genomic and transcriptomic sequencing data obtained from whole blood of 1521 individuals (867 cases and 654 controls) to infer the genotypes of the transcripts expressed by eight classical HLA class I and class II genes as well as DRA and the DRB3/4/5 haplotypes, and (2) examined the statistical differences between three different PD subgroups (cases) and healthy controls (HC) for the HLA and SVA transcribed genotypes and inferred haplotypes. Results Significant differences for 57 expressed HLA alleles (21 HLA class I and 36 HLA class II alleles) up to the three-field resolution and four of eight expressed SVA were detected at p<0.05 by the Fisher's exact test within one or other of three different PD subgroups (750 individuals with PD, 57 prodromes, 60 individuals who had scans without evidence of dopamine deficits [SWEDD]), when compared against a group of 654 HCs within the PPMI cohort and when not corrected by the Bonferroni test for multiple comparisons. Fourteen of 20 significant alleles were unique to the PD-HC comparison, whereas 31 of the 57 alleles overlapped between two or more different subgroup comparisons. Only the expressed HLA-DRA*01:01:01 and -DQA1*03:01:01 protective alleles (PD v HC), the -DQA1*03:03:01 risk (HC v Prodrome) or protective allele (PD v Prodrome), the -DRA*01:01:02 and -DRB4*01:03:02 risk alleles (SWEDD v HC), and the NR_SVA_381 present genotype (PD v HC) at a 5% homozygous insertion frequency near HLA-DPA1, were significant (Pc<0.1) after Bonferroni corrections. The homologous NR_SVA_381 insertion significantly decreased the transcription levels of HLA-DPA1 and HLA-DPB1 in the PPMI cohort and its presence as a homozygous genotype is a risk factor (Pc=0.012) for PD. The most frequent NR_SVA_381 insertion haplotype in the PPMI cohort was NR_SVA_381/DPA1*02/DPB1*01 (3.7%). Although HLA C*07/B*07/DRB5*01/DRB1*15/DQB1*06 was the most frequent HLA 5-loci phased-haplotype (n, 76) in the PPMI cohort, the NR_SVA_381 insertion was present in only six of them (8%). Conclusions These data suggest that expressed SVA and HLA gene alleles in circulating white blood cells are coordinated differentially in the regulation of immune responses and the long-term onset and progression of PD, the mechanisms of which have yet to be elucidated.
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Affiliation(s)
- Jerzy K. Kulski
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Health and Medical Science, Division of Immunology and Microbiology, School of Biomedical Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Shingo Suzuki
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
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2
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van den Bosch AMR, van der Poel M, Fransen NL, Vincenten MCJ, Bobeldijk AM, Jongejan A, Engelenburg HJ, Moerland PD, Smolders J, Huitinga I, Hamann J. Profiling of microglia nodules in multiple sclerosis reveals propensity for lesion formation. Nat Commun 2024; 15:1667. [PMID: 38396116 PMCID: PMC10891081 DOI: 10.1038/s41467-024-46068-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Microglia nodules (HLA-DR+ cell clusters) are associated with brain pathology. In this post-mortem study, we investigated whether they represent the first stage of multiple sclerosis (MS) lesion formation. We show that microglia nodules are associated with more severe MS pathology. Compared to microglia nodules in stroke, those in MS show enhanced expression of genes previously found upregulated in MS lesions. Furthermore, genes associated with lipid metabolism, presence of T and B cells, production of immunoglobulins and cytokines, activation of the complement cascade, and metabolic stress are upregulated in microglia nodules in MS. Compared to stroke, they more frequently phagocytose oxidized phospholipids and possess a more tubular mitochondrial network. Strikingly, in MS, some microglia nodules encapsulate partially demyelinated axons. Taken together, we propose that activation of microglia nodules in MS by cytokines and immunoglobulins, together with phagocytosis of oxidized phospholipids, may lead to a microglia phenotype prone to MS lesion formation.
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Affiliation(s)
- Aletta M R van den Bosch
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
| | - Marlijn van der Poel
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Nina L Fransen
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Maria C J Vincenten
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Anneleen M Bobeldijk
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Aldo Jongejan
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Hendrik J Engelenburg
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
| | - Perry D Moerland
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Institute, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Joost Smolders
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands
- MS Center ErasMS, Department of Neurology and Immunology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Inge Huitinga
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands.
| | - Jörg Hamann
- Neuroimmunology Research Group, Netherlands Institute for Neuroscience, Amsterdam, The Netherlands.
- Department of Experimental Immunology, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Center, Amsterdam, The Netherlands.
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3
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Abbas M, Diallo A, Goodney G, Gaye A. Leveraging the transcriptome to further our understanding of GWAS findings: eQTLs associated with genes related to LDL and LDL subclasses, in a cohort of African Americans. Front Genet 2024; 15:1345541. [PMID: 38384714 PMCID: PMC10879560 DOI: 10.3389/fgene.2024.1345541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/16/2024] [Indexed: 02/23/2024] Open
Abstract
Background: GWAS discoveries often pose a significant challenge in terms of understanding their underlying mechanisms. Further research, such as an integration with expression quantitative trait locus (eQTL) analyses, are required to decipher the mechanisms connecting GWAS variants to phenotypes. An eQTL analysis was conducted on genes associated with low-density lipoprotein (LDL) cholesterol and its subclasses, with the aim of pinpointing genetic variants previously implicated in GWAS studies focused on lipid-related traits. Notably, the study cohort consisted of African Americans, a population characterized by a heightened prevalence of hypercholesterolemia. Methods: A comprehensive differential expression (DE) analysis was undertaken, with a dataset of 17,948 protein-coding mRNA transcripts extracted from the whole-blood transcriptomes of 416 samples to identify mRNA transcripts associated with LDL, with further granularity delineated between small LDL and large LDL subclasses. Subsequently, eQTL analysis was conducted with a subset of 242 samples for which whole-genome sequencing data were available to identify single-nucleotide polymorphisms (SNPs) associated with the LDL-related mRNA transcripts. Lastly, plausible functional connections were established between the identified eQTLs and genetic variants reported in the GWAS catalogue. Results: DE analysis revealed 1,048, 284, and 94 mRNA transcripts that exhibited differential expression in response to LDL, small LDL, and large LDL, respectively. The eQTL analysis identified a total of 9,950 significant SNP-mRNA associations involving 6,955 SNPs including a subset 101 SNPs previously documented in GWAS of LDL and LDL-related traits. Conclusion: Through comprehensive differential expression analysis, we identified numerous mRNA transcripts responsive to LDL, small LDL, and large LDL. Subsequent eQTL analysis revealed a rich landscape of eQTL-mRNA associations, including a subset of eQTL reported in GWAS studies of LDL and related traits. The study serves as a testament to the important role of integrative genomics in unraveling the enigmatic GWAS relationships between genetic variants and the complex fabric of human traits and diseases.
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Affiliation(s)
- Malak Abbas
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ana Diallo
- School of Nursing, Virginia Commonwealth University, Richmond, VA, United States
| | - Gabriel Goodney
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Amadou Gaye
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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4
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Wang C, Ramasamy A, Verduzco-Gutierrez M, Brode WM, Melamed E. Acute and post-acute sequelae of SARS-CoV-2 infection: a review of risk factors and social determinants. Virol J 2023; 20:124. [PMID: 37328773 PMCID: PMC10276420 DOI: 10.1186/s12985-023-02061-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 05/02/2023] [Indexed: 06/18/2023] Open
Abstract
SARS-CoV-2 infection leading to Coronavirus Disease 2019 (COVID-19) has caused more than 762 million infections worldwide, with 10-30% of patients suffering from post-acute sequelae of SARS-CoV-2 infections (PASC). Initially thought to primarily affect the respiratory system, it is now known that SARS-CoV-2 infection and PASC can cause dysfunction in multiple organs, both during the acute and chronic stages of infection. There are also multiple risk factors that may predispose patients to worse outcomes from acute SARS-CoV-2 infection and contribute to PASC, including genetics, sex differences, age, reactivation of chronic viruses such as Epstein Barr Virus (EBV), gut microbiome dysbiosis, and behavioral and lifestyle factors, including patients' diet, alcohol use, smoking, exercise, and sleep patterns. In addition, there are important social determinants of health, such as race and ethnicity, barriers to health equity, differential cultural perspectives and biases that influence patients' access to health services and disease outcomes from acute COVID-19 and PASC. Here, we review risk factors in acute SARS-CoV-2 infection and PASC and highlight social determinants of health and their impact on patients affected with acute and chronic sequelae of COVID-19.
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Affiliation(s)
- Chumeng Wang
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Akshara Ramasamy
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Monica Verduzco-Gutierrez
- Department of Physical Medicine and Rehabilitation, University of Texas at San Antonio, San Antonio, TX, USA
| | - W Michael Brode
- Department of Internal Medicine, Dell Medical School, University of Texas at Austin, Austin, TX, USA
| | - Esther Melamed
- Department of Neurology, Dell Medical School, University of Texas at Austin, Austin, TX, USA.
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5
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Zhang HG, McDermott G, Seyok T, Huang S, Dahal K, L'Yi S, Lea-Bonzel C, Stratton J, Weisenfeld D, Monach P, Raychaudhuri S, Yu KH, Cai T, Cui J, Hong C, Cai T, Liao KP. Identifying shared genetic architecture between rheumatoid arthritis and other conditions: a phenome-wide association study with genetic risk scores. EBioMedicine 2023; 92:104581. [PMID: 37121095 PMCID: PMC10173154 DOI: 10.1016/j.ebiom.2023.104581] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 03/19/2023] [Accepted: 04/05/2023] [Indexed: 05/02/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) shares genetic variants with other autoimmune conditions, but existing studies test the association between RA variants with a pre-defined set of phenotypes. The objective of this study was to perform a large-scale, systemic screen to determine phenotypes that share genetic architecture with RA to inform our understanding of shared pathways. METHODS In the UK Biobank (UKB), we constructed RA genetic risk scores (GRS) incorporating human leukocyte antigen (HLA) and non-HLA risk alleles. Phenotypes were defined using groupings of International Classification of Diseases (ICD) codes. Patients with an RA code were excluded to mitigate the possibility of associations being driven by the diagnosis or management of RA. We performed a phenome-wide association study, testing the association between the RA GRS with phenotypes using multivariate generalized estimating equations that adjusted for age, sex, and first five principal components. Statistical significance was defined using Bonferroni correction. Results were replicated in an independent cohort and replicated phenotypes were validated using medical record review of patients. FINDINGS We studied n = 316,166 subjects from UKB without evidence of RA and screened for association between the RA GRS and n = 1317 phenotypes. In the UKB, 20 phenotypes were significantly associated with the RA GRS, of which 13 (65%) were immune mediated conditions including polymyalgia rheumatica, granulomatosis with polyangiitis (GPA), type 1 diabetes, and multiple sclerosis. We further identified a novel association in Celiac disease where the HLA and non-HLA alleles had strong associations in opposite directions. Strikingly, we observed that the non-HLA GRS was exclusively associated with greater risk of the validated conditions, suggesting shared underlying pathways outside the HLA region. INTERPRETATION This study replicated and identified novel autoimmune phenotypes verified by medical record review that share immune pathways with RA and may inform opportunities for shared treatment targets, as well as risk assessment for conditions with a paucity of genomic data, such as GPA. FUNDING This research was funded by the US National Institutes of Health (P30AR072577, R21AR078339, R35GM142879, T32AR007530) and the Harold and DuVal Bowen Fund.
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Affiliation(s)
- Harrison G Zhang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Greg McDermott
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Thany Seyok
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sicong Huang
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kumar Dahal
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sehi L'Yi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Clara Lea-Bonzel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jacklyn Stratton
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dana Weisenfeld
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul Monach
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Center for Data Science, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Kun-Hsing Yu
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tianrun Cai
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Chuan Hong
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC, USA
| | - Tianxi Cai
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; VA Boston Healthcare System, Boston, MA, USA.
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6
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Li K, Wang M, Zhao L, Liu Y, Zhang X. ACPA-negative rheumatoid arthritis: From immune mechanisms to clinical translation. EBioMedicine 2022; 83:104233. [PMID: 36027873 PMCID: PMC9404277 DOI: 10.1016/j.ebiom.2022.104233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/13/2022] [Accepted: 08/05/2022] [Indexed: 11/28/2022] Open
Abstract
The presence of anti-citrullinated protein autoantibodies (ACPA) is a hallmark feature of rheumatoid arthritis (RA), which causes chronic joint destruction and systemic inflammation. Based on ACPA status, RA patients can be sub-grouped into two major subsets: ACPA-positive RA (ACPA+ RA) and ACPA-negative RA (ACPA– RA). Accumulating evidence have suggested that ACPA+ RA and ACPA– RA are two distinct disease entities with different underlying pathophysiology. In contrast to the well-characterized pathogenic mechanisms of ACPA+ RA, the etiology of ACPA– RA remains largely unknown. In this review, we summarized current knowledge about the primary drivers of ACPA– RA, particularly focusing on the serological, cellular, and molecular aspects of immune mechanisms. A better understanding of the immunopathogenesis in ACPA– RA will help in designing more precisely targeting strategies, and paving the road to personalized treatment. In addition, identification of novel biomarkers in ACPA– RA will substantially promote early treatment and improve the outcomes.
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Affiliation(s)
- Ketian Li
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Min Wang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Lidan Zhao
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China
| | - Yudong Liu
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China; The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing 100730, PR China.
| | - Xuan Zhang
- Department of Rheumatology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Clinical Immunology Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, PR China.
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Akel O, Zhao LP, Geraghty DE, Lind A. High-resolution HLA class II sequencing of Swedish multiple sclerosis patients. Int J Immunogenet 2022; 49:333-339. [PMID: 35959717 PMCID: PMC9545082 DOI: 10.1111/iji.12594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/20/2022] [Accepted: 07/29/2022] [Indexed: 11/28/2022]
Abstract
Multiple sclerosis (MS) is a chronic neurological disease believed to be caused by autoimmune pathogenesis. The aetiology is likely explained by a complex interplay between inherited and environmental factors. Genetic investigations into MS have been conducted for over 50 years, yielding >100 associations to date. Globally, the strongest linkage is with the human leukocyte antigen (HLA) HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01 haplotype. Here, high-resolution sequencing of HLA was used to determine the alleles of DRB3, DRB4, DRB5, DRB1, DQA1, DQB1, DPA1 and DPB1 as well as their extended haplotypes and genotypes in 100 Swedish MS patients. Results were compared to 636 population controls. The heterogeneity in HLA associations with MS was demonstrated; among 100 patients, 69 extended HLA-DR-DQ genotypes were found. Three extended HLA-DR-DQ genotypes were found to be correlated to MS; HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01 haplotype together with (A) HLA-DRB4*01:01:01//DRB4*01:01:01:01-DRB1*07:01:01-DQA1*02:01//02:01:01-DQB1*02:02:01, (B) HLA-DRBX*null-DRB1*08:01:01-DQA1*04:01:01-DQB1*04:02:01, and (C) HLA-DRB3*01:01:02-DRB1*03:01:01-DQA1*05:01:01-DQB1*02:01:01. At the allelic level, HLA-DRB3*01:01:02 was considered protective against MS. However, when combined with HLA-DRB3*01:01:02-DRB1*03:01:01-DQA1*05:01:01-DQB1*02:01:01, this extended haplotype was considered a predisposing risk factor. This highlights the limitations as included with investigations of single alleles relative to those of extended haplotypes/genotypes. In conclusion, with 69 genotypes presented among 100 patients, high-resolution sequencing was conducted to underscore the wide polymorphisms present among MS patients. Additional studies in larger cohorts will be of importance to define MS among the patient group not associated with HLA-DRB5*01:01:01-DRB1*15:01:01-DQA1*01:02:01-DQB1*06:02:01.
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Affiliation(s)
- Omar Akel
- Department of Clinical Sciences Malmö, Clinical Research Centre, Lund University, Skåne University Hospital SUS, Malmö, Sweden
| | - Lue Ping Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Daniel E Geraghty
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Alexander Lind
- Department of Clinical Sciences Malmö, Clinical Research Centre, Lund University, Skåne University Hospital SUS, Malmö, Sweden
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van Olst L, Coenen L, Nieuwland JM, Rodriguez-Mogeda C, de Wit NM, Kamermans A, Middeldorp J, de Vries HE. Crossing borders in Alzheimer's disease: A T cell's perspective. Adv Drug Deliv Rev 2022; 188:114398. [PMID: 35780907 DOI: 10.1016/j.addr.2022.114398] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is the most common form of dementia affecting millions of people worldwide. While different immunotherapies are imminent, currently only disease-modifying medications are available and a cure is lacking. Over the past decade, immunological interfaces of the central nervous system (CNS) and their role in neurodegenerative diseases received increasing attention. Specifically, emerging evidence shows that subsets of circulating CD8+ T cells cross the brain barriers and associate with AD pathology. To gain more insight into how the adaptive immune system is involved in disease pathogenesis, we here provide a comprehensive overview of the contribution of T cells to AD pathology, incorporating changes at the brain barriers. In addition, we review studies that provide translation of these findings by targeting T cells to combat AD pathology and cognitive decline. Importantly, these data show that immunological changes in AD are not confined to the CNS and that AD-associated systemic immune changes appear to affect brain homeostasis.
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Affiliation(s)
- L van Olst
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - L Coenen
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands; Department of Neurobiology and Aging, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - J M Nieuwland
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands; Department of Neurobiology and Aging, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - C Rodriguez-Mogeda
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - N M de Wit
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - A Kamermans
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - J Middeldorp
- Department of Neurobiology and Aging, Biomedical Primate Research Centre, Rijswijk, The Netherlands
| | - H E de Vries
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC location Vrije Universiteit Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands.
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9
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Krovi SH, Kuchroo VK. Activation pathways that drive CD4 + T cells to break tolerance in autoimmune diseases . Immunol Rev 2022; 307:161-190. [PMID: 35142369 PMCID: PMC9255211 DOI: 10.1111/imr.13071] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/11/2022]
Abstract
Autoimmune diseases are characterized by dysfunctional immune systems that misrecognize self as non-self and cause tissue destruction. Several cell types have been implicated in triggering and sustaining disease. Due to a strong association of major histocompatibility complex II (MHC-II) proteins with various autoimmune diseases, CD4+ T lymphocytes have been thoroughly investigated for their roles in dictating disease course. CD4+ T cell activation is a coordinated process that requires three distinct signals: Signal 1, which is mediated by antigen recognition on MHC-II molecules; Signal 2, which boosts signal 1 in a costimulatory manner; and Signal 3, which helps to differentiate the activated cells into functionally relevant subsets. These signals are disrupted during autoimmunity and prompt CD4+ T cells to break tolerance. Herein, we review our current understanding of how each of the three signals plays a role in three different autoimmune diseases and highlight the genetic polymorphisms that predispose individuals to autoimmunity. We also discuss the drawbacks of existing therapies and how they can be addressed to achieve lasting tolerance in patients.
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Affiliation(s)
- Sai Harsha Krovi
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, Massachusetts, USA
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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Doroszkiewicz J, Groblewska M, Mroczko B. Molecular Biomarkers and Their Implications for the Early Diagnosis of Selected Neurodegenerative Diseases. Int J Mol Sci 2022; 23:ijms23094610. [PMID: 35563001 PMCID: PMC9100918 DOI: 10.3390/ijms23094610] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/15/2022] [Accepted: 04/20/2022] [Indexed: 02/07/2023] Open
Abstract
The degeneration and dysfunction of neurons are key features of neurodegenerative diseases (NDs). Currently, one of the main challenges facing researchers and clinicians is the ability to obtain reliable diagnostic tools that will allow for the diagnosis of NDs as early as possible and the detection of neuronal dysfunction, preferably in the presymptomatic stage. Additionally, better tools for assessing disease progression in this group of disorders are also being sought. The ideal biomarker must have high sensitivity and specificity, be easy to measure, give reproducible results, and reflect the disease progression. Molecular biomarkers include miRNAs and extracellular microvesicles known as exosomes. They may be measured in two extracellular fluids of the highest importance in NDs, i.e., cerebrospinal fluid (CSF) and blood. The aim of the current review is to summarize the pathophysiology of the four most frequent NDs—i.e., Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), and multiple sclerosis (MS)—as well as current progress in the research into miRNAs as biomarkers in these major neurodegenerative diseases. In addition, we discuss the possibility of using miRNA-based therapies in the treatment of neurodegenerative diseases, and present the limitations of this type of therapy.
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Affiliation(s)
- Julia Doroszkiewicz
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland;
- Correspondence: ; Tel.: +48-85-686-51-68
| | - Magdalena Groblewska
- Department of Biochemical Diagnostics, University Hospital in Białystok, 15-269 Bialystok, Poland;
| | - Barbara Mroczko
- Department of Neurodegeneration Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland;
- Department of Biochemical Diagnostics, Medical University of Bialystok, 15-269 Bialystok, Poland
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11
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Nath SR, Grewal P, Cho T, Mao-Draayer Y. Familial multiple sclerosis in patients with Von Hippel-Lindau disease. BMC Neurol 2022; 22:80. [PMID: 35260109 PMCID: PMC8902760 DOI: 10.1186/s12883-022-02604-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/24/2022] [Indexed: 11/17/2022] Open
Abstract
Background Multiple sclerosis (MS) is a progressive autoimmune demyelinating disorder. Recent studies suggest that a combination of genetic susceptibility and environmental insult contributes to its pathogenesis. Many candidate genes have been discovered to modulate susceptibility for developing MS by genome wide association studies (GWAS); these include major histocompatibility complex (MHC) genes and non-MHC genes. MS cases in the context of genetic diseases may provide different approaches and clues towards identifying novel genes and pathways involved in MS pathogenesis. Here, we present a case series of two related patients with concomitant Von Hippel-Lindau disease (VHLD) and MS. Case presentation We present two patients, a mother (case 1) and daughter (case 2), who developed superimposed relapsing-remitting multiple sclerosis in the background of the autosomal dominant genetic disorder VHLD. Several tumors characteristic of VHLD developed in both cases with pancreatic and renal neoplasms and cerebellar hemangioblastomas. In addition, both patients developed clinical symptoms consistent with multiple sclerosis, supported by radiologic lesions disseminating in time and space. Conclusion Though non-MHC susceptibility genes remain elusive in MS, we present the striking finding of superimposed multiple sclerosis in a mother and daughter with VHLD. The VHL gene is known to be the primary regulator of Nrf2, the well-established target of the FDA-approved therapeutic dimethyl fumarate. These cases provide support for further studies to determine whether VHLD pathway related genes represent a novel genetic link in multiple sclerosis.
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Affiliation(s)
- Samir R Nath
- Medical Scientist Training Program, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Prabhjot Grewal
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Thomas Cho
- Department of Neurology, Clinical Autoimmunity Center of Excellence, University of Michigan Medical School, 4015 A. Alfred Taubman Biomedical Sciences Research Building 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA
| | - Yang Mao-Draayer
- Department of Neurology, Clinical Autoimmunity Center of Excellence, University of Michigan Medical School, 4015 A. Alfred Taubman Biomedical Sciences Research Building 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA. .,Graduate Program in Immunology, Program in Biomedical Sciences, University of Michigan Medical School, 4015 A. Alfred Taubman Biomedical Sciences Research Building 109 Zina Pitcher Place, Ann Arbor, MI, 48109-2200, USA.
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Kaabinejadian S, Barra C, Alvarez B, Yari H, Hildebrand WH, Nielsen M. Accurate MHC Motif Deconvolution of Immunopeptidomics Data Reveals a Significant Contribution of DRB3, 4 and 5 to the Total DR Immunopeptidome. Front Immunol 2022; 13:835454. [PMID: 35154160 PMCID: PMC8826445 DOI: 10.3389/fimmu.2022.835454] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 01/23/2023] Open
Abstract
Mass spectrometry (MS) based immunopeptidomics is used in several biomedical applications including neo-epitope discovery in oncology, next-generation vaccine development and protein-drug immunogenicity assessment. Immunopeptidome data are highly complex given the expression of multiple HLA alleles on the cell membrane and presence of co-immunoprecipitated contaminants. The absence of tools that deal with these challenges effectively and guide the analysis and interpretation of this complex type of data is currently a major bottleneck for the large-scale application of this technique. To resolve this, we here present the MHCMotifDecon that benefits from state-of-the-art HLA class-I and class-II predictions to accurately deconvolute immunopeptidome datasets and assign individual ligands to the most likely HLA molecule, allowing to identify and characterize HLA binding motifs while discarding co-purified contaminants. We have benchmarked the tool against other state-of-the-art methods and illustrated its application on experimental datasets for HLA-DR demonstrating a previously underappreciated role for HLA-DRB3/4/5 molecules in defining HLA class II immune repertoires. With its ease of use, MHCMotifDecon can efficiently guide interpretation of immunopeptidome datasets, serving the discovery of novel T cell targets. MHCMotifDecon is available at https://services.healthtech.dtu.dk/service.php?MHCMotifDecon-1.0.
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Affiliation(s)
- Saghar Kaabinejadian
- Pure MHC, LLC., Oklahoma City, OK, United States.,Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Carolina Barra
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Bruno Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Hooman Yari
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Morten Nielsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
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Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. Genes (Basel) 2021; 13:genes13010087. [PMID: 35052430 PMCID: PMC8774935 DOI: 10.3390/genes13010087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 11/17/2022] Open
Abstract
Conventional genome-wide association studies (GWASs) of complex traits, such as Multiple Sclerosis (MS), are reliant on per-SNP p-values and are therefore heavily burdened by multiple testing correction. Thus, in order to detect more subtle alterations, ever increasing sample sizes are required, while ignoring potentially valuable information that is readily available in existing datasets. To overcome this, we used penalised regression incorporating elastic net with a stability selection method by iterative subsampling to detect the potential interaction of loci with MS risk. Through re-analysis of the ANZgene dataset (1617 cases and 1988 controls) and an IMSGC dataset as a replication cohort (1313 cases and 1458 controls), we identified new association signals for MS predisposition, including SNPs above and below conventional significance thresholds while targeting two natural killer receptor loci and the well-established HLA loci. For example, rs2844482 (98.1% iterations), otherwise ignored by conventional statistics (p = 0.673) in the same dataset, was independently strongly associated with MS in another GWAS that required more than 40 times the number of cases (~45 K). Further comparison of our hits to those present in a large-scale meta-analysis, confirmed that the majority of SNPs identified by the elastic net model reached conventional statistical GWAS thresholds (p < 5 × 10−8) in this much larger dataset. Moreover, we found that gene variants involved in oxidative stress, in addition to innate immunity, were associated with MS. Overall, this study highlights the benefit of using more advanced statistical methods to (re-)analyse subtle genetic variation among loci that have a biological basis for their contribution to disease risk.
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Bakutenko IY, Haurylchyk ID, Sechko EV, Tchitchko AM, Batyan GM, Sukalo AV, Ryabokon NI. AGER gene variant as a risk factor for juvenile idiopathic arthritis. J Gene Med 2021; 24:e3399. [PMID: 34806241 DOI: 10.1002/jgm.3399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND The AGER gene encodes a cell surface multiligand receptor of advanced glycation end-products that is also capable of binding other molecules and is involved in numerous pathways related to inflammation, apoptosis, immunity and so on. In the present study, we aimed to investigate whether the AGER rs1035798 (G>A) intronic polymorphism, showing an association with multiple sclerosis and rheumatoid arthritis in adults, is related to juvenile idiopathic arthritis (JIA). METHODS Caucasian children from the Belarusian population were enrolled in the study. In total, there were 201 cases with JIA, 37 with juvenile systemic lupus erythematosus, 222 children with the articular syndrome of non-autoimmune etiology (positive control for JIA) and 365 negative controls (children without any autoimmune or inflammatory diseases). Genomic DNA samples from the patients and controls were genotyped by a real-time polymerase chain reaction. RESULTS A marked association of the homozygous AA rs1035798 genotype with JIA (p = 5 × 10-4 ) was found. Allele A was also associated with JIA (p = 0.0058), as well as with the articular syndrome of non-autoimmune etiology (p = 0.0264). The highest frequencies of the AA genotype were found in the subgroups of JIA patients with polyarthritis or severe oligoarthritis. The AA genotype patients also had the smallest mean age of the JIA onset. CONCLUSIONS Our results demonstrate that the AGER rs1035798 AA genotype is a risk factor for JIA in Belarusian children. They also suggest a link between the AGER AA genotype and the risk of JIA early onset and severity. However, the functional relevance of the rs1035798 polymorphism is still unclear.
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Affiliation(s)
- Ivan Yurievich Bakutenko
- Laboratory of Molecular Basis of Genome Stability, Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Irena Dmitrievna Haurylchyk
- Laboratory of Molecular Basis of Genome Stability, Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
| | - Elena Vladimirovna Sechko
- 1st Department of Childhood Diseases, Belarusian State Medical University, Minsk, Republic of Belarus
| | | | - Galina Mihajlovna Batyan
- 1st Department of Childhood Diseases, Belarusian State Medical University, Minsk, Republic of Belarus
| | | | - Nadezhda Ivanovna Ryabokon
- Laboratory of Molecular Basis of Genome Stability, Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Republic of Belarus
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15
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Genetic susceptibility to multiple sclerosis in African Americans. PLoS One 2021; 16:e0254945. [PMID: 34370753 PMCID: PMC8352072 DOI: 10.1371/journal.pone.0254945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 07/06/2021] [Indexed: 12/26/2022] Open
Abstract
Objective To explore the nature of genetic-susceptibility to multiple sclerosis (MS) in African-Americans. Background Recently, the number of genetic-associations with MS has exploded although the MS-associations of specific haplotypes within the major histocompatibility complex (MHC) have been known for decades. For example, the haplotypes HLA-DRB1*15:01~HLA-DQB1*06:02, and HLA-DRB1*03:01~ HLA-DQB1*02:01 have odds ratios (ORs) for an MS-association orders of magnitude stronger than many of these newly-discovered associations. Nevertheless, all these haplotypes are part of much larger conserved extended haplotypes (CEHs), which span both the Class I and Class II MHC regions. African-Americans are at greater risk of developing MS compared to a native Africans but at lesser risk compared to Europeans. It is the purpose of this manuscript to explore the relationship between MS-susceptibility and the CEH make-up of our African-American cohort. Design/methods The African-American (AA) cohort consisted of 1,305 patients with MS and 1,155 controls, who self-identified as being African-American. For comparison, we used the 18,492 controls and 11,144 MS-cases from the predominantly European Wellcome Trust Case Control Consortium (WTCCC) and the 28,557 phased native Africans from the multinational “Be the Match” registry. The WTCCC and the African-Americans were phased at each of five HLA loci (HLA-A, HLA-C, HLA-B, HLA-DRB1 and HLA-DQB1) and the at 11 SNPs (10 of which were in non-coding regions) surrounding the Class II region of the DRB1 gene using previously-published probabilistic phasing algorithms. Results Of the 32 most frequent CEHs, 18 (56%) occurred either more frequently or exclusively in Africans) whereas 9 (28%) occurred more frequently or exclusively in Europeans. The remaining 5 CEHs occurred in neither control group although, likely, these were African in origin. Eight of these CEHs carried the DRB1*15:03~DQB1*06:02~a36 haplotype and three carried the DRB1*15:01~DQB1*06:02~a1 haplotype. In African Americans, a single-copy of the European CEH (03:01_07:02_07:02_15:01_06:02_a1) was associated with considerable MS-risk (OR = 3.30; p = 0.0001)–similar to that observed in the WTCCC (OR = 3.25; p<10−168). By contrast, the MS-risk for the European CEH (02:01_07:02_07:02_15:01_06:02_a1) was less (OR = 1.49; ns)–again, similar to the WTCCC (OR = 2.2; p<10−38). Moreover, four African haplotypes were “protective” relative to a neutral reference, to three European CEHs, and also to the five other African CEHs. Conclusions The common CEHs in African Americans are divisible into those that are either African or European in origin, which are derived without modification from their source population. European CEHs, linked to MS-risk, in general, had similar impacts in African-Americans as they did in Europeans. By contrast, African CEHs had mixed MS-risks. For a few, the MS-risk exceeded that in a neutral-reference group whereas, for many others, these CEHs were “protective”–perhaps providing a partial rationale for the lower MS-risk in African-Americans compared to European-Americans.
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16
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Saadatmand F, Gurdziel K, Jackson L, Kwabi-Addo B, Ruden DM. DNA methylation and exposure to violence among African American young adult males. Brain Behav Immun Health 2021; 14:100247. [PMID: 34589758 PMCID: PMC8474503 DOI: 10.1016/j.bbih.2021.100247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 02/02/2023] Open
Abstract
Exposure to violence (ETV) has been linked to epigenomics mechanisms such as DNA methylation (DNAm). We used epigenetic profiling of blood collected from 32 African American young adult males who lived in Washington DC to determine if changes in DNAm at CpG sites affiliated with nervous and immune system were associated with exposure to violence. Pathway analysis of differentially methylated regions comparing high and low ETV groups revealed an enrichment of gene sets annotated to nervous system and immune ontologies. Many of these genes are known to interact with each other which suggests DNAm alters gene function in the nervous and immune system in response to ETV. Using data from a unique age group, young African American adult males, we provide evidence that lifetime ETV could impact DNA methylation in genes impacted at Central Nervous System and Immune Function sites. METHOD Methylation analysis was performed on DNA collected from the blood of participants classified with either high or low lifetime ETV. Illumina®MethylationEPIC Beadchips (~850k CpG sites) were processed on the iScan System to examine whole-genome methylation differences. Differentially methylated CpG-sites between high (n = 19) and low (n = 13) groups were identified using linear regression with violence and substance abuse as model covariates. Gene ontology analysis was used to identify enrichment categories from probes annotated to the nearest gene. RESULTS A total of 595 probes (279 hypermethylated; 316 hypomethylated) annotated to 383 genes were considered differentially methylated in association with ETV. Males with high ETV showed elevated methylation in several signaling pathways but were most impacted at Central Nervous System and Immune Function affiliated sites. Eight candidate genes were identified that play important biological roles in stress response to violence with HDAC4 (10%), NR4A3 (11%), NR4A2 (12%), DSCAML1(12%), and ELAVL3 (13%) exhibiting higher levels in the low ETV group and DLGAP1 (10%), SHANK2 (10%), and NRG1(11%) having increased methylation in the high ETV group. These findings suggest that individuals subjected to high ETV may be at risk for poor health outcomes that have not been reported previously.
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Affiliation(s)
- Forough Saadatmand
- Department of Pediatrics, College of Medicine, Howard University, Washington, DC, USA
| | - Katherine Gurdziel
- Office of the Vice President of Research, Wayne State University, Detroit, MI, USA
| | - Latifa Jackson
- Department of Pediatrics, College of Medicine, Howard University, Washington, DC, USA
- W. Montague Cobb Research Laboratory, College of Arts and Sciences, Howard University, Washington, DC, USA
| | - Bernard Kwabi-Addo
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, USA
| | - Douglas M. Ruden
- Department of Ob/Gyn, CS Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, MI, USA
- Institutes for Environmental Health Science, Wayne State University School of Medicine, Detroit, MI, USA
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17
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Osoegawa K, Creary LE, Montero-Martín G, Mallempati KC, Gangavarapu S, Caillier SJ, Santaniello A, Isobe N, Hollenbach JA, Hauser SL, Oksenberg JR, Fernández-Viňa MA. High Resolution Haplotype Analyses of Classical HLA Genes in Families With Multiple Sclerosis Highlights the Role of HLA-DP Alleles in Disease Susceptibility. Front Immunol 2021; 12:644838. [PMID: 34211458 PMCID: PMC8240666 DOI: 10.3389/fimmu.2021.644838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Multiple sclerosis (MS) susceptibility shows strong genetic associations with HLA alleles and haplotypes. We genotyped 11 HLA genes in 477 non-Hispanic European MS patients and their 954 unaffected parents using a validated next-generation sequencing (NGS) methodology. HLA haplotypes were assigned unequivocally by tracing HLA allele transmissions. We explored HLA haplotype/allele associations with MS using the genotypic transmission disequilibrium test (gTDT) and multiallelic TDT (mTDT). We also conducted a case-control (CC) study with all patients and 2029 healthy unrelated ethnically matched controls. We performed separate analyses of 54 extended multi-case families by reviewing transmission of haplotype blocks. The haplotype fragment including DRB5*01:01:01~DRB1*15:01:01:01 was significantly associated with predisposition (gTDT: p < 2.20e-16; mTDT: p =1.61e-07; CC: p < 2.22e-16) as reported previously. A second risk allele, DPB1*104:01 (gTDT: p = 3.69e-03; mTDT: p = 2.99e-03; CC: p = 1.00e-02), independent from the haplotype bearing DRB1*15:01 was newly identified. The allele DRB1*01:01:01 showed significant protection (gTDT: p = 8.68e-06; mTDT: p = 4.50e-03; CC: p = 1.96e-06). Two DQB1 alleles, DQB1*03:01 (gTDT: p = 2.86e-03; mTDT: p = 5.56e-02; CC: p = 4.08e-05) and DQB1*03:03 (gTDT: p = 1.17e-02; mTDT: p = 1.16e-02; CC: p = 1.21e-02), defined at two-field level also showed protective effects. The HLA class I block, A*02:01:01:01~C*03:04:01:01~B*40:01:02 (gTDT: p = 5.86e-03; mTDT: p = 3.65e-02; CC: p = 9.69e-03) and the alleles B*27:05 (gTDT: p = 6.28e-04; mTDT: p = 2.15e-03; CC: p = 1.47e-02) and B*38:01 (gTDT: p = 3.20e-03; mTDT: p = 6.14e-03; CC: p = 1.70e-02) showed moderately protective effects independently from each other and from the class II associated factors. By comparing statistical significance of 11 HLA loci and 19 haplotype segments with both untruncated and two-field allele names, we precisely mapped MS candidate alleles/haplotypes while eliminating false signals resulting from 'hitchhiking' alleles. We assessed genetic burden for the HLA allele/haplotype identified in this study. This family-based study including the highest-resolution of HLA alleles proved to be powerful and efficient for precise identification of HLA genotypes associated with both, susceptibility and protection to development of MS.
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Affiliation(s)
- Kazutoyo Osoegawa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Lisa E. Creary
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Gonzalo Montero-Martín
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Kalyan C. Mallempati
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Sridevi Gangavarapu
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
| | - Stacy J. Caillier
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Adam Santaniello
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Noriko Isobe
- Department of Neurology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jill A. Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Stephen L. Hauser
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Jorge R. Oksenberg
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA, United States
| | - Marcelo A. Fernández-Viňa
- Histocompatibility & Immunogenetics Laboratory, Stanford Blood Center, Palo Alto, CA, United States
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, United States
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Martin R, Sospedra M, Eiermann T, Olsson T. Multiple sclerosis: doubling down on MHC. Trends Genet 2021; 37:784-797. [PMID: 34006391 DOI: 10.1016/j.tig.2021.04.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 01/12/2023]
Abstract
Human leukocyte antigen (HLA)-encoded surface molecules present antigenic peptides to T lymphocytes and play a key role in adaptive immune responses. Besides their physiological role of defending the host against infectious pathogens, specific alleles serve as genetic risk factors for autoimmune diseases. For multiple sclerosis (MS), an autoimmune disease that affects the brain and spinal cord, an association with the HLA-DR15 haplotype was described in the early 1970s. This short opinion piece discusses the difficulties of disentangling the details of this association and recent observations about the functional involvement of not only one, but also the second gene of the HLA-DR15 haplotype. This information is not only important for understanding the pathomechanism of MS, but also for antigen-specific therapies.
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Affiliation(s)
- Roland Martin
- Neuroimmunology and Multiple Sclerosis Research, Neurology Clinic, Frauenklinikstrasse 26, 8091 Zurich, University Hospital Zurich, University Zurich, Switzerland.
| | - Mireia Sospedra
- Neuroimmunology and Multiple Sclerosis Research, Neurology Clinic, Frauenklinikstrasse 26, 8091 Zurich, University Hospital Zurich, University Zurich, Switzerland
| | - Thomas Eiermann
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Tomas Olsson
- Neuroimmunology Unit, Department of Clinical Neuroscience, Karolinska Institutet, 17176 Stockholm, Sweden
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Cree BAC, Pradhan A, Pei J, Williams MJ. Efficacy and safety of ocrelizumab vs interferon beta-1a in participants of African descent with relapsing multiple sclerosis in the Phase III OPERA I and OPERA II studies. Mult Scler Relat Disord 2021; 52:103010. [PMID: 34147885 DOI: 10.1016/j.msard.2021.103010] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/05/2021] [Accepted: 04/30/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND People of African descent with multiple sclerosis (MS) appear to have a more severe disease course and may have an attenuated response to some medications compared with people of European descent. METHODS This is a post hoc subgroup analysis of participants of African descent with relapsing forms of MS who were enrolled in the Phase III OPERA I or OPERA II clinical trials and treated with ocrelizumab (OCR) 600 mg every 6 months or interferon beta-1a (IFN β-1a) 44 μg 3 times per week. RESULTS Among the 1,656 participants enrolled in OPERA I and II, 72 (4.3%) were of African descent (OCR, 40; IFN β-1a, 32). A trend for reduction in annualized relapse rate (ARR) was observed in participants of African descent, with an ≈50% reduction with OCR vs IFN β-1a. The relative rate of the mean number of gadolinium-enhancing lesions on magnetic resonance imaging (MRI) was 0.04 (95% CI, 0.01-0.22; p=0.001) in participants of African descent treated with OCR compared with IFN β-1a. Similarly, the relative rate of the number of new or enlarging T2 lesions on MRI was 0.14 (95% CI, 0.06-0.32; p<0.001). In participants of African descent, those treated with OCR were 2.61 times more likely than those who received IFN β-1a to be classified as having no evidence of disease activity (95% CI, 1.24-5.49; p=0.003) and 4.17 times more likely to be classified as having no evidence of disease activity or progression (95% CI, 1.27-13.65; p=0.006). African-descent participants tended to have a greater radiographic burden of disease at baseline, develop more brain lesions when treated with IFN β-1a, and be at greater risk of disability progression than non-African-descent participants. Participants of African descent experienced slightly more adverse events, serious adverse events, and hypersensitivity reactions than non-African-descent participants. CONCLUSION In this small sample of participants of African descent with relapsing MS from the OPERA studies, OCR demonstrated treatment benefits in clinical, MRI, and composite efficacy outcomes vs IFN β-1a, consistent with what was observed in the complete OPERA intention-to-treat cohorts.
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Affiliation(s)
- Bruce A C Cree
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA.
| | | | - Jinglan Pei
- Genentech, Inc., South San Francisco, CA, USA
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20
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Derdelinckx J, Nkansah I, Ooms N, Van Bruggen L, Emonds MP, Daniëls L, Reynders T, Willekens B, Cras P, Berneman ZN, Cools N. HLA Class II Genotype Does Not Affect the Myelin Responsiveness of Multiple Sclerosis Patients. Cells 2020; 9:cells9122703. [PMID: 33348629 PMCID: PMC7766454 DOI: 10.3390/cells9122703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 11/16/2022] Open
Abstract
Background: When aiming to restore myelin tolerance using antigen-specific treatment approaches in MS, the wide variety of myelin-derived antigens towards which immune responses are targeted in multiple sclerosis (MS) patients needs to be taken into account. Uncertainty remains as to whether the myelin reactivity pattern of a specific MS patient can be predicted based upon the human leukocyte antigen (HLA) class II haplotype of the patient. Methods: In this study, we analyzed the reactivity towards myelin oligodendrocyte glycoprotein (MOG), myelin basic protein (MBP) and proteolipid protein (PLP) peptides using direct interferon (IFN)-γ enzyme-linked immune absorbent spot (ELISPOT). Next, the HLA class II haplotype profile was determined by next-generation sequencing. In doing so, we aimed to evaluate the possible association between the precursor frequency of myelin-reactive T cells and the HLA haplotype. Results: Reactivity towards any of the analyzed peptides could be demonstrated in 65.0% (13/20) of MS patients and in 60.0% (6/10) of healthy controls. At least one of the MS risk alleles HLA-DRB1*15:01, HLA-DQA1*01:02 and HLA-DQB1*06:02 was found in 70.0% (14/20) of patients and in 20.0% (2/10) of healthy controls. No difference in the presence of a myelin-specific response, nor in the frequency of myelin peptide-reactive precursor cells could be detected among carriers and non-carriers of these risk alleles. Conclusion: No association between HLA haplotype and myelin reactivity profile was present in our study population. This complicates the development of antigen-specific treatment approaches and implies the need for multi-epitope targeting in an HLA-unrestricted manner to fully address the wide variation in myelin responses and HLA profiles in a heterogeneous group of MS patients.
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Affiliation(s)
- Judith Derdelinckx
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
- Division of Neurology, Antwerp University Hospital, 2650 Edegem, Belgium; (T.R.); (P.C.)
- Correspondence: ; Tel.: +32-3-821-3584; Fax: +32-3-825-1148
| | - Irene Nkansah
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
| | - Naomi Ooms
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
| | - Laura Van Bruggen
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
| | - Marie-Paule Emonds
- Histocompatibility and Immunogenetics Laboratory, Red Cross-Flanders, 2650 Mechelen, Belgium; (M.-P.E.); (L.D.)
| | - Liesbeth Daniëls
- Histocompatibility and Immunogenetics Laboratory, Red Cross-Flanders, 2650 Mechelen, Belgium; (M.-P.E.); (L.D.)
| | - Tatjana Reynders
- Division of Neurology, Antwerp University Hospital, 2650 Edegem, Belgium; (T.R.); (P.C.)
| | - Barbara Willekens
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
- Division of Neurology, Antwerp University Hospital, 2650 Edegem, Belgium; (T.R.); (P.C.)
| | - Patrick Cras
- Division of Neurology, Antwerp University Hospital, 2650 Edegem, Belgium; (T.R.); (P.C.)
- Born Bunge Institute, Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium
| | - Zwi N. Berneman
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
| | - Nathalie Cools
- Laboratory of Experimental Hematology, Vaccine and Infectious Disease Institute (VaxInfectio), Faculty of Medicine and Health Sciences, University of Antwerp, 2610 Antwerp, Belgium; (I.N.); (N.O.); (L.V.B.); (B.W.); (Z.N.B.); (N.C.)
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, 2650 Edegem, Belgium
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21
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Wang J, Jelcic I, Mühlenbruch L, Haunerdinger V, Toussaint NC, Zhao Y, Cruciani C, Faigle W, Naghavian R, Foege M, Binder TMC, Eiermann T, Opitz L, Fuentes-Font L, Reynolds R, Kwok WW, Nguyen JT, Lee JH, Lutterotti A, Münz C, Rammensee HG, Hauri-Hohl M, Sospedra M, Stevanovic S, Martin R. HLA-DR15 Molecules Jointly Shape an Autoreactive T Cell Repertoire in Multiple Sclerosis. Cell 2020; 183:1264-1281.e20. [PMID: 33091337 PMCID: PMC7707104 DOI: 10.1016/j.cell.2020.09.054] [Citation(s) in RCA: 125] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
The HLA-DR15 haplotype is the strongest genetic risk factor for multiple sclerosis (MS), but our understanding of how it contributes to MS is limited. Because autoreactive CD4+ T cells and B cells as antigen-presenting cells are involved in MS pathogenesis, we characterized the immunopeptidomes of the two HLA-DR15 allomorphs DR2a and DR2b of human primary B cells and monocytes, thymus, and MS brain tissue. Self-peptides from HLA-DR molecules, particularly from DR2a and DR2b themselves, are abundant on B cells and thymic antigen-presenting cells. Furthermore, we identified autoreactive CD4+ T cell clones that can cross-react with HLA-DR-derived self-peptides (HLA-DR-SPs), peptides from MS-associated foreign agents (Epstein-Barr virus and Akkermansia muciniphila), and autoantigens presented by DR2a and DR2b. Thus, both HLA-DR15 allomorphs jointly shape an autoreactive T cell repertoire by serving as antigen-presenting structures and epitope sources and by presenting the same foreign peptides and autoantigens to autoreactive CD4+ T cells in MS. HLA-DR15 present abundant HLA-DR-derived self-peptides on B cells Autoreactive T cells in MS recognize HLA-DR-derived self-peptides/DR15 complexes Foreign peptides/DR15 complexes trigger potential autoreactive T cells in MS HLA-DR15 shape an autoreactive T cell repertoire by cross-reactivity/restriction
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Affiliation(s)
- Jian Wang
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Ivan Jelcic
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Lena Mühlenbruch
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Veronika Haunerdinger
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Nora C Toussaint
- NEXUS Personalized Health Technologies, ETH Zurich, Zurich 8093, Switzerland; Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Yingdong Zhao
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, NCI, NIH, Rockville, MD 20850, USA
| | - Carolina Cruciani
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Wolfgang Faigle
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Reza Naghavian
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Magdalena Foege
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Thomas M C Binder
- HLA Laboratory of the Stefan Morsch Foundation (SMS), Birkenfeld 55765, Germany
| | - Thomas Eiermann
- Department of Transfusion Medicine, University Medical Center Hamburg-Eppendorf, Hamburg 20251, Germany
| | - Lennart Opitz
- Functional Genomics Center Zurich, Swiss Federal Institute of Technology and University of Zurich, Zurich 8057, Switzerland
| | - Laura Fuentes-Font
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - Richard Reynolds
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, UK
| | - William W Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Julie T Nguyen
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Jar-How Lee
- One Lambda, Inc., a part of Transplant Diagnostics Thermo Fisher Scientific, 22801 Roscoe Blvd., West Hills, CA 91304, USA
| | - Andreas Lutterotti
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Christian Münz
- Viral Immunobiology, Institute of Experimental Immunology, University of Zurich, Zurich 8057, Switzerland
| | - Hans-Georg Rammensee
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Mathias Hauri-Hohl
- Pediatric Stem Cell Transplantation, University Children's Hospital Zurich, Zurich 8032, Switzerland
| | - Mireia Sospedra
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland
| | - Stefan Stevanovic
- Department of Immunology, Institute of Cell Biology, University of Tübingen, Tübingen 72076, Germany; German Cancer Consortium (DKTK), Partner Site Tübingen, Tübingen 72076, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies," University of Tübingen, Tübingen 72076, Germany
| | - Roland Martin
- Neuroimmunology and MS Research, Neurology Clinic, University Hospital Zurich, University of Zurich, Zurich 8091, Switzerland.
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22
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Stürner KH, Siembab I, Schön G, Stellmann JP, Heidari N, Fehse B, Heesen C, Eiermann TH, Martin R, Binder TM. Is multiple sclerosis progression associated with the HLA-DR15 haplotype? Mult Scler J Exp Transl Clin 2019; 5:2055217319894615. [PMID: 31839982 PMCID: PMC6902395 DOI: 10.1177/2055217319894615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/04/2019] [Accepted: 11/09/2019] [Indexed: 11/17/2022] Open
Abstract
Background The prevalence of multiple sclerosis is associated with the major histocompatibility complex class II DR15 haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Objective To assess whether multiple sclerosis progression is associated with the main susceptibility haplotype HLA-DRB1*15:01∼HLA-DRB5*01:01. Methods Patients (n = 1230) and healthy controls (n = 2110) were genotyped for HLA-DRB1 and HLA-DRB5. The baseline Expanded Disability Status Scale (EDSS) score was determined and patients were followed for at least 3 years. Results After follow-up of the consecutive cohort 349 patients were classified as having clinical isolated syndrome and 881 patients as having multiple sclerosis. The susceptibility allele HLA-DRB1*15:01 was more frequent in clinical isolated syndrome (odds ratio 1.56) and multiple sclerosis (odds ratio 3.17) compared to controls. HLA- DRB1*15:01 was the only enriched HLA-DRB1 allele in multiple sclerosis patients. Comparison of clinical characteristics between HLA-DRB1*15:01∼HLA-DRB5*01:01 negative and positive patients with multiple sclerosis showed that baseline EDSS score, disease duration and frequency of the category secondary progressive multiple sclerosis with relapse were increased in the HLA-DRB1*15:01∼HLA-DRB5*01:01 positive group. Conclusion The study confirmed HLA-DRB1*15:01 and HLA-DRB5*01:01 as the main susceptibility alleles and showed weak indirect evidence for a role in progression of the disease.
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Affiliation(s)
- Klarissa Hanja Stürner
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Inessa Siembab
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Gerhard Schön
- Department of Medical Biometry and Epidemiology, University Medical Center Hamburg-Eppendorf, Germany
| | - Jan-Patrick Stellmann
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Nika Heidari
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Boris Fehse
- Research Department Cell and Gene Therapy, University Medical Center Hamburg-Eppendorf, Germany
| | - Christoph Heesen
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas H Eiermann
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
| | - Roland Martin
- Institute for Neuroimmunology and Clinical MS Research, University Medical Center Hamburg-Eppendorf, Germany
| | - Thomas Mc Binder
- HLA Laboratory, University Medical Center Hamburg-Eppendorf, Germany
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23
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Barsakis K, Babrzadeh F, Chi A, Mallempati K, Pickle W, Mindrinos M, Fernández-Viña MA. Complete nucleotide sequence characterization of DRB5 alleles reveals a homogeneous allele group that is distinct from other DRB genes. Hum Immunol 2019; 80:437-448. [PMID: 30954494 PMCID: PMC6622178 DOI: 10.1016/j.humimm.2019.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Next Generation Sequencing allows for testing and typing of entire genes of the HLA region. A better and comprehensive sequence assessment can be achieved by the inclusion of full gene sequences of all the common alleles at a given locus. The common alleles of DRB5 are under-characterized with the full exon-intron sequence of two alleles available. In the present study the DRB5 genes from 18 subjects alleles were cloned and sequenced; haplotype analysis showed that 17 of them had a single copy of DRB5 and one consanguineous subject was homozygous at all HLA loci. Methodological approaches including robust and efficient long-range PCR amplification, molecular cloning, nucleotide sequencing and de novo sequence assembly were combined to characterize DRB5 alleles. DRB5 sequences covering from 5'UTR to the end of intron 5 were obtained for DRB5*01:01, 01:02 and 02:02; partial coverage including a segment spanning exon 2 to exon 6 was obtained for DRB5*01:03, 01:08N and 02:03. Phylogenetic analysis of the generated sequences showed that the DRB5 alleles group together and have distinctive differences with other DRB loci. Novel intron variants of DRB5*01:01:01, 01:02 and 02:02 were identified. The newly characterized DRB5 intron variants of each DRB5 allele were found in subjects harboring distinct associations with alleles of DRB1, B and/or ethnicity. The new information provided by this study provides reference sequences for HLA typing methodologies. Extending sequence coverage may lead to identify the disease susceptibility factors of DRB5 containing haplotypes while the unexpected intron variations may shed light on understanding of the evolution of the DRB region.
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Affiliation(s)
- Konstantinos Barsakis
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA; Department of Biology, University of Crete, Heraklion, Crete 71003, Greece
| | - Farbod Babrzadeh
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Anjo Chi
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Kalyan Mallempati
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - William Pickle
- Stanford Blood Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
| | - Michael Mindrinos
- Stanford Genome Technology Center, Stanford University School of Medicine, Palo Alto, CA 94304, USA
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24
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Liguori M, Nuzziello N, Licciulli F, Consiglio A, Simone M, Viterbo RG, Creanza TM, Ancona N, Tortorella C, Margari L, Grillo G, Giordano P, Liuni S, Trojano M. Combined microRNA and mRNA expression analysis in pediatric multiple sclerosis: an integrated approach to uncover novel pathogenic mechanisms of the disease. Hum Mol Genet 2019; 27:66-79. [PMID: 29087462 DOI: 10.1093/hmg/ddx385] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/23/2017] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is a complex disease of the CNS that usually affects young adults, although 3-5% of cases are diagnosed in childhood and adolescence (hence called pediatric MS, PedMS). Genetic predisposition, among other factors, seems to contribute to the risk of the onset, in pediatric as in adult ages, but few studies have investigated the genetic 'environmentally naïve' load of PedMS. The main goal of this study was to identify circulating markers (miRNAs), target genes (mRNAs) and functional pathways associated with PedMS; we also verified the impact of miRNAs on clinical features, i.e. disability and cognitive performances. The investigation was performed in 19 PedMS and 20 pediatric controls (PCs) using a High-Throughput Next-generation Sequencing (HT-NGS) approach followed by an integrated bioinformatics/biostatistics analysis. Twelve miRNAs were significantly upregulated (let-7a-5p, let-7b-5p, miR-25-3p, miR-125a-5p, miR-942-5p, miR-221-3p, miR-652-3p, miR-182-5p, miR-185-5p, miR-181a-5p, miR-320a, miR-99b-5p) and 1 miRNA was downregulated (miR-148b-3p) in PedMS compared with PCs. The interactions between the significant miRNAs and their targets uncovered predicted genes (i.e. TNFSF13B, TLR2, BACH2, KLF4) related to immunological functions, as well as genes involved in autophagy-related processes (i.e. ATG16L1, SORT1, LAMP2) and ATPase activity (i.e. ABCA1, GPX3). No significant molecular profiles were associated with any PedMS demographic/clinical features. Both miRNAs and mRNA expressions predicted the phenotypes (PedMS-PC) with an accuracy of 92% and 91%, respectively. In our view, this original strategy of contemporary miRNA/mRNA analysis may help to shed light in the genetic background of the disease, suggesting further molecular investigations in novel pathogenic mechanisms.
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Affiliation(s)
- Maria Liguori
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Nicoletta Nuzziello
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy.,Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Flavio Licciulli
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Arianna Consiglio
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Marta Simone
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Rosa Gemma Viterbo
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Teresa Maria Creanza
- National Research Council of Italy, Department of Engineering, ICT and Technology for Energy and Transportation, Institute of Intelligent Systems for Automation, 70125 Bari, Italy
| | - Nicola Ancona
- National Research Council of Italy, Department of Engineering, ICT and Technology for Energy and Transportation, Institute of Intelligent Systems for Automation, 70125 Bari, Italy
| | - Carla Tortorella
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy.,Department of Neurosciences, San Camillo Forlanini Hospital, 00185 Rome, Italy
| | - Lucia Margari
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
| | - Giorgio Grillo
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Paola Giordano
- General Paediatric Unit "B. Trambusti", Azienda Policlinico-Giovanni XXIII and University of Bari, 70125 Bari, Italy
| | - Sabino Liuni
- National Research Council of Italy, Department of Biomedicine, Institute of Biomedical Technologies, Bari Section, 70125 Bari, Italy
| | - Maria Trojano
- Department of Basic Sciences, Neurosciences and Sense Organs, University of Bari, 70125 Bari, Italy
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25
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Delfan N, Galehdari H, Shafiei M, Ghanbari-Mardasi F, Latifi T, Majdinasab N, Seifi T. Association of human leukocyte antigen-DRB haplotype in multiple sclerosis population of Khuzestan, Iran. IRANIAN JOURNAL OF NEUROLOGY 2018; 17:154-160. [PMID: 31210899 PMCID: PMC6555884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Background: One of the demyelinating and inflammatory diseases of the central nervous system (CNS) is multiple sclerosis (MS). Though pathogenesis of MS is still unknown, both genetic and environmental factors are involved. The human leukocyte antigen (HLA) class-II alleles including HLA-DRB5*01, DQB1*0602, DRB1*1501, and DQA1*0102 may have remarkable effect in MS risk although it is controversial in studies. As there is no data with respect to the HLA-DRB1*1501-DRB5*01 correlation with MS in Khuzestan Province, Iran, the goal of the survey was to investigate the association of this haplotype with MS in this population. Methods: The study focused on DRB5*01-DRB1*1501 haplotype association with MS in 200 patients and 200 healthy individuals. Typing of HLA was carried out by polymerase chain reaction (PCR) amplification with sequence-specific primers (SSP) method. SPSS software was used for the statistical analyses. Results: No association between DRB5*01+-DRB1*1501+ and MS was found (P = 0.156). Distribution of DRB1*1501+-DRB5*01- (carrying DRB1*1501+ but not DRB5*01-) and DRB1*1501--DRB5*01- haplotypes was statistically different between patients and controls (29.73% vs. 11.81%, P < 0.001) and (42.16% vs. 68.50%, P < 0.001), respectively. However, DRB1*1501--DRB5*01+ revealed no association with MS (15.13% vs. 11.81%, P = 0.403). HLA-DRB1*1501--DRB5*01+ was significantly more frequent among female patients with MS (16.19% vs. 6.12%, P = 0.019) and Persian group (17.11% vs. 5.79%, P = 0.027). Positive correlation of HLA-DRB1*1501+-DRB5*01- haplotype with the expanded disability status scale (EDSS) steps from 5 to 10 was observed (62.50% vs. 25.76%, P = 0.026). Moreover, no meaningful association was shown among the haplotypes with EDSS, course of MS, ethnicity, and gender. Conclusion: Our findings suggest that DRB1*1501+-DRB5*01- and DRB1*1501--DRB5*01- haplotypes may have positive association with MS risk. Also, this survey indicates that HLA-DRB1*1501--DRB5*01+ is involved in susceptibility of the disease among women and Persians. DRB1*1501+-DRB5*01- genotype frequency may have a key role in MS developing.
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Affiliation(s)
- Nooshin Delfan
- Department of Genetics, School of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hamid Galehdari
- Department of Genetics, School of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mohammad Shafiei
- Department of Genetics, School of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Tahereh Latifi
- Department of Genetics, School of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Nastaran Majdinasab
- Multiple Sclerosis Society, School of Rehabilitation, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Tahereh Seifi
- Department of Genetics, School of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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26
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Thorstenson YR, Creary LE, Huang H, Rozot V, Nguyen TT, Babrzadeh F, Kancharla S, Fukushima M, Kuehn R, Wang C, Li M, Krishnakumar S, Mindrinos M, Fernandez Viña MA, Scriba TJ, Davis MM. Allelic resolution NGS HLA typing of Class I and Class II loci and haplotypes in Cape Town, South Africa. Hum Immunol 2018; 79:839-847. [PMID: 30240896 DOI: 10.1016/j.humimm.2018.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/23/2018] [Accepted: 09/17/2018] [Indexed: 11/18/2022]
Abstract
The development of next-generation sequencing (NGS) methods for HLA genotyping has already had an impact on the scope and precision of HLA research. In this study, allelic resolution HLA typing was obtained for 402 individuals from Cape Town, South Africa. The data were produced by high-throughput NGS sequencing as part of a study of T-cell responses to Mycobacterium tuberculosis in collaboration with the University of Cape Town and Stanford University. All samples were genotyped for 11 HLA loci, namely HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3, -DRB4, and -DRB5. NGS HLA typing of samples from Cape Town inhabitants revealed a unique cohort, including unusual haplotypes, and 22 novel alleles not previously reported in the IPD-IMGT/HLA Database. Eight novel alleles were in Class I loci and 14 were in Class II. There were 62 different alleles of HLA-A, 72 of HLA-B, and 47 of HLA-C. Alleles A∗23:17, A∗43:01, A∗29:11, A∗68:27:01, A∗01:23, B∗14:01:01, B∗15:10:01, B∗39:10:01, B∗45:07, B∗82:02:01 and C∗08:04:01 were notably more frequent in Cape Town compared to other populations reported in the literature. Class II loci had 21 different alleles of DPA1, 46 of DPB1, 27 of DQA1, 26 of DQB1, 41 of DRB1, 5 of DRB3, 4 of DRB4 and 6 of DRB5. The Cape Town cohort exhibited high degrees of HLA diversity and relatively high heterozygosity at most loci. Genetic distances between Cape Town and five other sub-Saharan African populations were also calculated and compared to European Americans.
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Affiliation(s)
| | - Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Huang Huang
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | | | | | | | | | - Raquel Kuehn
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Chunlin Wang
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | - Ming Li
- Immucor, Sirona Genomics, Mountain View, CA, USA
| | | | | | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Mark M Davis
- Stanford University and Howard Hughes Medical Institute, Stanford, CA
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Vaccination with RSV M 209-223 peptide promotes a protective immune response associated with reduced pulmonary inflammation. Antiviral Res 2018; 157:102-110. [DOI: 10.1016/j.antiviral.2018.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 07/02/2018] [Accepted: 07/06/2018] [Indexed: 12/29/2022]
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Association of MMP-2 (⁻1306 C/T) Gene Polymorphism with Predisposition to Optic Neuritis and Optic Neuritis Together with Multiple Sclerosis. ACTA ACUST UNITED AC 2018; 54:medicina54020029. [PMID: 30344260 PMCID: PMC6037261 DOI: 10.3390/medicina54020029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/02/2018] [Accepted: 05/04/2018] [Indexed: 11/25/2022]
Abstract
Background and objective: Optic neuritis (ON) is characterized by painful, usually monocular vision loss with decreased visual acuity and defects of the visual field and color vision. The etiology and pathophysiology of ON is not completely clear. It is thought that a matrix metalloproteinase 2 (MMP-2) gene plays an essential role in this autoimmune inflammatory disease. The aim of this study was to determine the relationship between the MMP-2 (-1306 C/T)rs243865 gene polymorphism and ON, and that of ON with multiple sclerosis. Materials and methods: Patients with ON/ON and multiple sclerosis and a control group of healthy individuals were enrolled in this study. The genotyping test of the MMP-2 (-1306 C/T) was carried out using a real-time polymerase chain reaction (PCR) method. Results: Analysis revealed that T allele at the MMP-2 (-1306 C/T) was less frequent in the ON group compared to the control group (14.5% vs. 23.3%, p = 0.031), and was associated with decreased likelihood of ON development (OR = 0.566; 95% CI: 0.333-0.962; p = 0.036). No significant associations were revealed while comparing the subgroups of ON patients with and without multiple sclerosis. Conclusion: The MMP-2 (-1306 C/T) gene polymorphism was found to be associated with ON development.
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Creary LE, Mallempati KC, Gangavarapu S, Caillier SJ, Oksenberg JR, Fernández-Viňa MA. Deconstruction of HLA-DRB1*04:01:01 and HLA-DRB1*15:01:01 class II haplotypes using next-generation sequencing in European-Americans with multiple sclerosis. Mult Scler 2018; 25:772-782. [PMID: 29683085 DOI: 10.1177/1352458518770019] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND The association between HLA-DRB1*15:01 with multiple sclerosis (MS) susceptibility is well established, but the contribution of the tightly associated HLA-DRB5*01:01 allele has not yet been completely ascertained. Similarly, the effects of HLA-DRB1*04:01 alleles and haplotypes, defined at the full-gene resolution level with MS risk remains to be elucidated. OBJECTIVES To characterize the molecular architecture of class II HLA-DR15 and HLA-DR4 haplotypes associated with MS. METHODS Next-generation sequencing was used to determine HLA-DQB1, HLA-DQA1, and HLA-DRB1/4/5 alleles in 1403 unrelated European-American patients and 1425 healthy unrelated controls. Effect sizes of HLA alleles and haplotypes on MS risk were measured by odds ratio (OR) with 95% confidence intervals. RESULTS HLA-DRB1*15:01:01:01SG (OR = 3.20, p < 2.2E-16), HLA-DRB5*01:01:01 (OR = 2.96, p < 2.2E-16), and HLA-DRB5*01:01:01v1_STR1 (OR = 8.18, p = 4.3E-05) alleles all occurred at significantly higher frequencies in MS patients compared to controls. The most significant predis-posing haplotypes were HLA-DQB1*06:02:01~ HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01 and HLA-DQB1*06:02:01~HLA-DQA1*01:02:01:01SG~HLA-DRB1*15:01:01:01SG~HLA-DRB5*01:01:01v1_STR1 (OR = 3.19, p < 2.2E-16; OR = 9.30, p = 9.7E-05, respectively). Analyses of the HLA-DRB1*04 cohort in the absence of HLA-DRB1*15:01 haplotypes revealed that the HLA-DQB1*03:01:01:01~HLA-DQA1*03:03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was protective (OR = 0.64, p = 0.028), whereas the HLA-DQB1*03:02:01~HLA-DQA1*03:01:01~HLA-DRB1*04:01:01:01SG~HLA-DRB4*01:03:01:01 haplotype was associated with MS susceptibility (OR = 1.66, p = 4.9E-03). CONCLUSION HLA-DR15 haplotypes, including genomic variants of HLA-DRB5, and HLA-DR4 haplotypes affect MS risk.
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Affiliation(s)
- Lisa E Creary
- Department of Pathology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Kalyan C Mallempati
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Sridevi Gangavarapu
- Histocompatibility, Immunogenetics and Disease Profiling Laboratory, Stanford Blood Center, Palo Alto, CA, USA
| | - Stacy J Caillier
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Jorge R Oksenberg
- Department of Neurology, University of California, San Francisco, CA, USA
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Derk J, MacLean M, Juranek J, Schmidt AM. The Receptor for Advanced Glycation Endproducts (RAGE) and Mediation of Inflammatory Neurodegeneration. JOURNAL OF ALZHEIMER'S DISEASE & PARKINSONISM 2018; 8:421. [PMID: 30560011 PMCID: PMC6293973 DOI: 10.4172/2161-0460.1000421] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Julia Derk
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU School of Medicine, 550 First Avenue, Smilow 906, New York, NY, 10016, USA
| | - Michael MacLean
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU School of Medicine, 550 First Avenue, Smilow 906, New York, NY, 10016, USA
| | - Judyta Juranek
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU School of Medicine, 550 First Avenue, Smilow 906, New York, NY, 10016, USA
| | - Ann Marie Schmidt
- Diabetes Research Program, Division of Endocrinology, Diabetes and Metabolism, NYU School of Medicine, 550 First Avenue, Smilow 906, New York, NY, 10016, USA
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Transcriptional dysregulation of Interferome in experimental and human Multiple Sclerosis. Sci Rep 2017; 7:8981. [PMID: 28827704 PMCID: PMC5566335 DOI: 10.1038/s41598-017-09286-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 07/18/2017] [Indexed: 11/10/2022] Open
Abstract
Recent evidence indicates that single multiple sclerosis (MS) susceptibility genes involved in interferon (IFN) signaling display altered transcript levels in peripheral blood of untreated MS subjects, suggesting that responsiveness to endogenous IFN is dysregulated during neuroinflammation. To prove this hypothesis we exploited the systematic collection of IFN regulated genes (IRG) provided by the Interferome database and mapped Interferome changes in experimental and human MS. Indeed, central nervous system tissue and encephalitogenic CD4 T cells during experimental autoimmune encephalomyelitis were characterized by massive changes in Interferome transcription. Further, the analysis of almost 500 human blood transcriptomes showed that (i) several IRG changed expression at distinct MS stages with a core of 21 transcripts concordantly dysregulated in all MS forms compared with healthy subjects; (ii) 100 differentially expressed IRG were validated in independent case-control cohorts; and (iii) 53 out of 100 dysregulated IRG were targeted by IFN-beta treatment in vivo. Finally, ex vivo and in vitro experiments established that IFN-beta administration modulated expression of two IRG, ARRB1 and CHP1, in immune cells. Our study confirms the impairment of Interferome in experimental and human MS, and describes IRG signatures at distinct disease stages which can represent novel therapeutic targets in MS.
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Boghozian R, McKenzie BA, Saito LB, Mehta N, Branton WG, Lu J, Baker GB, Noorbakhsh F, Power C. Suppressed oligodendrocyte steroidogenesis in multiple sclerosis: Implications for regulation of neuroinflammation. Glia 2017; 65:1590-1606. [PMID: 28707358 DOI: 10.1002/glia.23179] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 05/26/2017] [Accepted: 05/26/2017] [Indexed: 12/11/2022]
Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease of the central nervous system (CNS). Neurosteroids are reported to exert anti-inflammatory effects in several neurological disorders. We investigated the expression and actions of the neurosteroid, dehydroepiandrosterone (DHEA), and its more stable 3β-sulphated ester, DHEA-S, in MS and associated experimental models. CNS tissues from patients with MS and animals with experimental autoimmune encephalomyelitis (EAE) displayed reduced DHEA concentrations, accompanied by diminished expression of the DHEA-synthesizing enzyme CYP17A1 in oligodendrocytes (ODCs), in association with increased expression of inflammatory genes including interferon (IFN)-γ and interleukin (IL)-1β. CYP17A1 was expressed variably in different human neural cell types but IFN-γ exposure selectively reduced CYP17A1 detection in ODCs. DHEA-S treatment reduced IL-1β and -6 release from activated human myeloid cells with minimal effect on lymphocyte viability. Animals with EAE receiving DHEA-S treatment showed reduced Il1b and Ifng transcript levels in spinal cord compared to vehicle-treated animals with EAE. DHEA-S treatment also preserved myelin basic protein immunoreactivity and reduced axonal loss in animals with EAE, relative to vehicle-treated EAE animals. Neurobehavioral deficits were reduced in DHEA-S-treated EAE animals compared with vehicle-treated animals with EAE. Thus, CYP17A1 expression in ODCs and its product DHEA were downregulated in the CNS during inflammatory demyelination while DHEA-S provision suppressed neuroinflammation, demyelination, and axonal injury that was evident as improved neurobehavioral performance. These findings indicate that DHEA production is an immunoregulatory pathway within the CNS and its restoration represents a novel treatment approach for neuroinflammatory diseases.
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Affiliation(s)
- Roobina Boghozian
- Department of Medical Microbiology & Immunology, University of Alberta Edmonton, Alberta, Canada.,Department of Medical Microbiology & Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Brienne A McKenzie
- Department of Medical Microbiology & Immunology, University of Alberta Edmonton, Alberta, Canada
| | - Leina B Saito
- Department of Medical Microbiology & Immunology, University of Alberta Edmonton, Alberta, Canada
| | - Ninad Mehta
- Department of Medical Microbiology & Immunology, University of Alberta Edmonton, Alberta, Canada
| | - William G Branton
- Department of, Medicine, University of Alberta Edmonton, Alberta, Canada
| | - JianQiang Lu
- Department of Laboratory Medicine & Pathology, University of Alberta Edmonton, Alberta, Canada
| | - Glen B Baker
- Depatment of Psychiatry, University of Alberta Edmonton, Alberta, Canada
| | - Farshid Noorbakhsh
- Department of Medical Microbiology & Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Christopher Power
- Department of Medical Microbiology & Immunology, University of Alberta Edmonton, Alberta, Canada.,Department of, Medicine, University of Alberta Edmonton, Alberta, Canada.,Depatment of Psychiatry, University of Alberta Edmonton, Alberta, Canada
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Restrepo NA, Butkiewicz M, McGrath JA, Crawford DC. Shared Genetic Etiology of Autoimmune Diseases in Patients from a Biorepository Linked to De-identified Electronic Health Records. Front Genet 2016; 7:185. [PMID: 27812365 PMCID: PMC5071319 DOI: 10.3389/fgene.2016.00185] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 10/03/2016] [Indexed: 01/15/2023] Open
Abstract
Autoimmune diseases represent a significant medical burden affecting up to 5–8% of the U.S. population. While genetics is known to play a role, studies of common autoimmune diseases are complicated by phenotype heterogeneity, limited sample sizes, and a single disease approach. Here we performed a targeted genetic association study for cases of multiple sclerosis (MS), rheumatoid arthritis (RA), and Crohn's disease (CD) to assess which common genetic variants contribute individually and pleiotropically to disease risk. Joint modeling and pathway analysis combining the three phenotypes were performed to identify common underlying mechanisms of risk of autoimmune conditions. European American cases of MS, RA, and CD, (n = 119, 53, and 129, respectively) and 1924 controls were identified using de-identified electronic health records (EHRs) through a combination of International Classification of Diseases, Ninth Revision, Clinical Modification (ICD-9-CM) billing codes, Current Procedural Terminology (CPT) codes, medication lists, and text matching. As expected, hallmark SNPs in MS, such as DQA1 rs9271366 (OR = 1.91; p = 0.008), replicated in the present study. Both MS and CD were associated with TIMMDC1 rs2293370 (OR = 0.27, p = 0.01; OR = 0.25, p = 0.02; respectively). Additionally, PDE2A rs3781913 was significantly associated with both CD and RA (OR = 0.46, p = 0.02; OR = 0.32, p = 0.02; respectively). Joint modeling and pathway analysis identified variants within the KEGG NOD-like receptor signaling pathway and Shigellosis pathway as being correlated with the combined autoimmune phenotype. Our study replicated previously-reported genetic associations for MS and CD in a population derived from de-identified EHRs. We found evidence to support a shared genetic etiology between CD/MS and CD/RA outside of the major histocompatibility complex region and identified KEGG pathways indicative of a bacterial pathogenesis risk for autoimmunity in a joint model. Future work to elucidate this shared etiology will be key in the development of risk models as envisioned in the era of precision medicine.
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Affiliation(s)
- Nicole A Restrepo
- Department of Epidemiology and Biostatistics, Case Western Reserve University Cleveland, OH, USA
| | - Mariusz Butkiewicz
- Department of Epidemiology and Biostatistics, Case Western Reserve University Cleveland, OH, USA
| | - Josephine A McGrath
- Vanderbilt Eye Institute, Vanderbilt University Medical Center Nashville, TN, USA
| | - Dana C Crawford
- Department of Epidemiology and Biostatistics, Case Western Reserve UniversityCleveland, OH, USA; Institute for Computational Biology, Case Western Reserve UniversityCleveland, OH, USA
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The killer immunoglobulin-like receptor KIR3DL1 in combination with HLA-Bw4 is protective against multiple sclerosis in African Americans. Genes Immun 2016; 17:199-202. [PMID: 26866467 PMCID: PMC5105680 DOI: 10.1038/gene.2016.5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 12/16/2015] [Accepted: 12/21/2015] [Indexed: 01/29/2023]
Abstract
We investigated the role of the KIR loci and their HLA class I ligands in a large cohort of African American MS patients (N=907) and controls (N=1456). No significant differences in carrier frequencies for any KIR locus or haplotype were observed between cases and controls. However, examination of KIR in the context of their cognate HLA ligands revealed a strong protective effect for KIR3DL1 in combination with HLA-A and –B alleles bearing the Bw4 motif (p=10−8; OR=0.60, CI=0.50–0.71) and the Bw4 ligand alone (Table 3; p<10−6; OR=0.63, CI=0.53–0.75). The observed effect cannot be explained by either a specific HLA-B allele or by linkage disequilibrium with HLA-DRB1 or HLA-A. The protective effect was observed only in individuals who were not positive for the MS risk allele HLA-DRB1*15:01 (p<10−6; OR=0.61, CI=0.51–0.74). Our study, the first investigation of KIR and MS in African Americans, confirms and refines previous findings in a European cohort.
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35
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Dankowski T, Buck D, Andlauer TFM, Antony G, Bayas A, Bechmann L, Berthele A, Bettecken T, Chan A, Franke A, Gold R, Graetz C, Haas J, Hecker M, Herms S, Infante-Duarte C, Jöckel KH, Kieseier BC, Knier B, Knop M, Kümpfel T, Lichtner P, Lieb W, Lill CM, Limmroth V, Linker RA, Loleit V, Meuth SG, Moebus S, Müller-Myhsok B, Nischwitz S, Nöthen MM, Paul F, Pütz M, Ruck T, Salmen A, Stangel M, Stellmann JP, Strauch K, Stürner KH, Tackenberg B, Then Bergh F, Tumani H, Waldenberger M, Weber F, Wiendl H, Wildemann B, Zettl UK, Ziemann U, Zipp F, Hemmer B, Ziegler A. Successful Replication of GWAS Hits for Multiple Sclerosis in 10,000 Germans Using the Exome Array. Genet Epidemiol 2015; 39:601-8. [PMID: 26497834 DOI: 10.1002/gepi.21933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 09/01/2015] [Accepted: 09/02/2015] [Indexed: 12/20/2022]
Abstract
Genome-wide association studies (GWAS) successfully identified various chromosomal regions to be associated with multiple sclerosis (MS). The primary aim of this study was to replicate reported associations from GWAS using an exome array in a large German study. German MS cases (n = 4,476) and German controls (n = 5,714) were genotyped using the Illumina HumanExome v1-Chip. Genotype calling was performed with the Illumina Genome Studio(TM) Genotyping Module, followed by zCall. Single-nucleotide polymorphisms (SNPs) in seven regions outside the human leukocyte antigen (HLA) region showed genome-wide significant associations with MS (P values < 5 × 10(-8) ). These associations have been reported previously. In addition, SNPs in three previously reported regions outside the HLA region yielded P values < 10(-5) . The effect of nine SNPs in the HLA region remained (P < 10(-5) ) after adjustment for other significant SNPs in the HLA region. All of these findings have been reported before or are driven by known risk loci. In summary, findings from previous GWAS for MS could be successfully replicated. We conclude that the regions identified in previous GWAS are also associated in the German population. This reassures the need for detailed investigations of the functional mechanisms underlying the replicated associations.
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Affiliation(s)
- Theresa Dankowski
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Dorothea Buck
- Department of Neurology, Technische Universität München, Munich, Germany
| | | | - Gisela Antony
- Central Information Office (CIO), Philipps University Marburg, Marburg, Germany
| | - Antonios Bayas
- Department of Neurology, Klinikum Augsburg, Augsburg, Germany
| | - Lukas Bechmann
- Department of Neurology, University of Leipzig, Leipzig, Germany.,Institute of Medical Microbiology, Otto-von-Guericke University, Magdeburg, Germany
| | - Achim Berthele
- Department of Neurology, Technische Universität München, Munich, Germany
| | | | - Andrew Chan
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Ralf Gold
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Christiane Graetz
- Department of Neurology, University Medical Center Mainz, Mainz, Germany
| | - Jürgen Haas
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Hecker
- Department of Neurology, University of Rostock, Rostock, Germany
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany.,Division of Medical Genetics, University Hospital, Basel, Switzerland.,Human Genetics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Bernd C Kieseier
- Department of Neurology, Heinrich Heine University, Düsseldorf, Germany
| | - Benjamin Knier
- Department of Neurology, Technische Universität München, Munich, Germany
| | - Matthias Knop
- Department of Neurology, MPI of Psychiatry, Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, Ludwigs-Maximilians-Universität, Munich, Germany
| | - Peter Lichtner
- Institute of Human Genetics, Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank popgen, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Christina M Lill
- Department of Neurology, University Medical Center Mainz, Mainz, Germany.,Platform for Genome Analytics, Institutes of Neurogenetics, & for Integrative and Experimental Genomics, University of Lübeck, Lübeck, Germany
| | - Volker Limmroth
- Department of Neurology, Hospital Köln-Merheim, Köln, Germany
| | - Ralf A Linker
- Department of Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Verena Loleit
- Department of Neurology, Technische Universität München, Munich, Germany
| | - Sven G Meuth
- Department für Neurologie, Klinik für Allgemeine Neurologie, Münster, Germany
| | - Susanne Moebus
- Institute of Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | | | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany.,Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Friedemann Paul
- Department of Neurology, Charité University Medicine Berlin, Berlin, Germany.,NeuroCure Clinical Research Center, Experimental and Clinical Research Center, Max Delbrueck Center for Molecular Medicine and, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Pütz
- Department of Neurology, Philipps-University of Marburg, Marburg, Germany
| | - Tobias Ruck
- Department für Neurologie, Klinik für Allgemeine Neurologie, Münster, Germany
| | - Anke Salmen
- Department of Neurology, St. Josef Hospital, Ruhr-University Bochum, Bochum, Germany
| | - Martin Stangel
- Clinical Neuroimmunology and Neurochemistry, Department of Neurology, Hannover Medical School, Hannover, Germany
| | - Jan-Patrick Stellmann
- Department of Neurology and, Institute of Neuroimmunology and MS (INIMS), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Klarissa H Stürner
- Department of Neurology and, Institute of Neuroimmunology and MS (INIMS), University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Tackenberg
- Department of Neurology, Philipps-University of Marburg, Marburg, Germany
| | - Florian Then Bergh
- Department of Neurology and Translational Center for Regenerative Medicine, University of Leipzig, Leipzig, Germany
| | | | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Frank Weber
- Department of Neurology, MPI of Psychiatry, Munich, Germany.,Neurological Clinic, Medical Park, Bad Camberg, Germany
| | - Heinz Wiendl
- Department für Neurologie, Klinik für Allgemeine Neurologie, Münster, Germany
| | - Brigitte Wildemann
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Uwe K Zettl
- Department of Neurology, University of Rostock, Rostock, Germany
| | - Ulf Ziemann
- Department of Neurology, University Hospital, Eberhard-Karls-Universität Tübingen, Tübingen, Germany
| | - Frauke Zipp
- Department of Neurology, University Medical Center Mainz, Mainz, Germany
| | - Bernhard Hemmer
- Department of Neurology, Technische Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Andreas Ziegler
- Institut für Medizinische Biometrie und Statistik, Universität zu Lübeck, Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,Zentrum für Klinische Studien, Universität zu Lübeck, Lübeck, Germany.,School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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Association between the Advanced Glycosylation End Product-Specific Receptor Gene and Cardiovascular Death in Older Men. PLoS One 2015; 10:e0134475. [PMID: 26226616 PMCID: PMC4520603 DOI: 10.1371/journal.pone.0134475] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/10/2015] [Indexed: 01/11/2023] Open
Abstract
Advanced glycosylation end product-specific receptor (AGER) signaling has been implicated in atherosclerosis. The aim of this study was to evaluate whether a common genetic variation in the AGER gene is associated with cardiovascular (CV) death. We included 1304 older men who were genotyped for rs1035798:C>T, which is a single nucleotide polymorphism (SNP) mapped to the third intron of AGER. Cox proportional hazard analysis was used to estimate the association of rs1035798:C>T with CV death. In addition we analyzed total RNA extracted from carotid atherosclerosis biopsies of 18 patients that did or did not have recent symptoms of cerebral embolization by quantitative real-time reverse transcription PCR (qRT-PCR). The minor T-allele of rs1035798:C>T was found to be associated with CV death under dominant (HR = 1.43, 95% CI: 1.01–2.02, P = 0.04) and recessive (HR = 2.05, 95% CI: 1.11–3.81, P = 0.02) models of inheritance even after adjustment for traditional cardiovascular risk factors. No association was found between rs1035798:C>T and non-CV death. qRT-PCR results suggested that median relative expression of AGER isoform 1 and isoform 6 transcripts were approximately 6- (P = 0.01) and 2-fold (P = 0.02) greater, respectively, within carotid biopsies of symptomatic compared to asymptomatic patients. These data suggest that the minor (T) allele of rs1035798:C>T represents an independent susceptibility factor for CV death. The expression of AGER isoforms is different in atheroma from patients with recent symptoms. Further studies are needed to investigate if rs1035798:C>T influences the alternative splicing of AGER.
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Hollenbach JA, Oksenberg JR. The immunogenetics of multiple sclerosis: A comprehensive review. J Autoimmun 2015; 64:13-25. [PMID: 26142251 DOI: 10.1016/j.jaut.2015.06.010] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 06/23/2015] [Indexed: 12/21/2022]
Abstract
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system and common cause of non-traumatic neurological disability in young adults. The likelihood for an individual to develop MS is strongly influenced by her or his ethnic background and family history of disease, suggesting that genetic susceptibility is a key determinant of risk. Over 100 loci have been firmly associated with susceptibility, whereas the main signal genome-wide maps to the class II region of the human leukocyte antigen (HLA) gene cluster and explains up to 10.5% of the genetic variance underlying risk. HLA-DRB1*15:01 has the strongest effect with an average odds ratio of 3.08. However, complex allelic hierarchical lineages, cis/trans haplotypic effects, and independent protective signals in the class I region of the locus have been described as well. Despite the remarkable molecular dissection of the HLA region in MS, further studies are needed to generate unifying models to account for the role of the MHC in disease pathogenesis. Driven by the discovery of combinatorial associations of Killer-cell Immunoglobulin-like Receptor (KIR) and HLA alleles with infectious, autoimmune diseases, transplantation outcome and pregnancy, multi-locus immunogenomic research is now thriving. Central to immunity and critically important for human health, KIR molecules and their HLA ligands are encoded by complex genetic systems with extraordinarily high levels of sequence and structural variation and complex expression patterns. However, studies to-date of KIR in MS have been few and limited to very low resolution genotyping. Application of modern sequencing methodologies coupled with state of the art bioinformatics and analytical approaches will permit us to fully appreciate the impact of HLA and KIR variation in MS.
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Affiliation(s)
- Jill A Hollenbach
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA.
| | - Jorge R Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
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Tosca L, Feraud O, Magniez A, Bas C, Griscelli F, Bennaceur-Griscelli A, Tachdjian G. Genomic instability of human embryonic stem cell lines using different passaging culture methods. Mol Cytogenet 2015; 8:30. [PMID: 26052346 PMCID: PMC4456787 DOI: 10.1186/s13039-015-0133-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 04/07/2015] [Indexed: 12/22/2022] Open
Abstract
Background Human embryonic stem cells exhibit genomic instability that can be related to culture duration or to the passaging methods used for cell dissociation. In order to study the impact of cell dissociation techniques on human embryonic stem cells genomic instability, we cultured H1 and H9 human embryonic stem cells lines using mechanical/manual or enzymatic/collagenase-IV dissociation methods. Genomic instability was evaluated at early (<p60) and late (>p60) passages by using oligonucleotide based array-comparative genomic hybridization 105 K with a mean resolution of 50 Kb. Results DNA variations were mainly located on subtelomeric and pericentromeric regions with sizes <100 Kb. In this study, 9 recurrent genomic variations were acquired during culture including the well known duplication 20q11.21. When comparing cell dissociation methods, we found no significant differences between DNA variations number and size, DNA gain or DNA loss frequencies, homozygous loss frequencies and no significant difference on the content of genes involved in development, cell cycle tumorigenesis and syndrome disease. In addition, we have never found any malignant tissue in 4 different teratoma representative of the two independent stem cell lines. Conclusions These results show that the occurrence of genomic instability in human embryonic stem cells is similar using mechanical or collagenase IV-based enzymatic cell culture dissociation methods. All the observed genomic variations have no impact on the development of malignancy. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0133-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lucie Tosca
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpitaux Universitaires Paris Sud, Clamart, F-92141 France ; Université Paris Sud, Le Kremlin-Bicêtre, F-94275 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Olivier Feraud
- Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Aurélie Magniez
- Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Cécile Bas
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpitaux Universitaires Paris Sud, Clamart, F-92141 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
| | - Frank Griscelli
- Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France ; Université Paris Descartes, Sorbonne Paris Cité, F-75006 France
| | - Annelise Bennaceur-Griscelli
- Université Paris Sud, Le Kremlin-Bicêtre, F-94275 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France ; AP-HP, Hématologie, Hôpitaux Universitaires Paris Sud, Villejuif, F-94801 France
| | - Gérard Tachdjian
- AP-HP, Histologie-Embryologie-Cytogénétique, Hôpitaux Universitaires Paris Sud, Clamart, F-92141 France ; Université Paris Sud, Le Kremlin-Bicêtre, F-94275 France ; Esteam Paris Sud INSERM UMR-S 935, Villejuif, F-94801 France
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Boullerne AI, Skias D, Hartman EM, Testai FD, Kalinin S, Polak PE, Feinstein DL. A single-nucleotide polymorphism in serine-threonine kinase 11, the gene encoding liver kinase B1, is a risk factor for multiple sclerosis. ASN Neuro 2015; 7:1759091415568914. [PMID: 25694554 PMCID: PMC4342367 DOI: 10.1177/1759091415568914] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We identified a family in which five siblings were diagnosed with multiple sclerosis (MS) or clinically isolated syndrome. Several women in the maternal lineage have comorbidities typically associated with Peutz Jeghers Syndrome, a rare autosomal-dominant disease caused by mutations in the serine-threonine-kinase 11 (STK11) gene, which encodes liver kinase B1. Sequence analysis of DNA from one sibling identified a single-nucleotide polymorphism (SNP) within STK11 intron 5. This SNP (dbSNP ID: rs9282860) was identified by TaqMan polymerase chain reaction (PCR) assays in DNA samples available from two other siblings. Further screening was carried out in samples from 654 relapsing-remitting MS patients, 100 primary progressive MS patients, and 661 controls. The STK11-SNP has increased frequency in all female patients versus controls (odds ratio = 1.66, 95% CI = 1.05, 2.64, p = .032). The STK11-SNP was not associated with disease duration or onset; however, it was significantly associated with reduced severity (assessed by MS severity scores), with the lowest scores in patients who also harbored the HLA-DRB1*1501 allele. In vitro studies showed that peripheral blood mononuclear cells from members of the family were more sensitive to the mitochondrial inhibitor metformin than cells from MS patients with the major STK11 allele. The increased association of SNP rs9282860 in women with MS defines this variant as a genetic risk factor. The lower disease severity observed in the context of HLA-DRB1*1501 combined with limited in vitro studies raises the provocative possibility that cells harboring the STK11-SNP could be targeted by drugs which increase metabolic stress.
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Affiliation(s)
- Anne I Boullerne
- Department of Anesthesiology, University of Illinois at Chicago, IL, USA
| | - Demetrios Skias
- Department of Veterans Affairs, Jesse Brown VA Medical Center, Chicago, IL, USA Department of Neurology, University of Illinois at Chicago, IL, USA
| | | | | | - Sergey Kalinin
- Department of Anesthesiology, University of Illinois at Chicago, IL, USA
| | - Paul E Polak
- Department of Anesthesiology, University of Illinois at Chicago, IL, USA
| | - Douglas L Feinstein
- Department of Anesthesiology, University of Illinois at Chicago, IL, USA Department of Veterans Affairs, Jesse Brown VA Medical Center, Chicago, IL, USA
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40
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Abstract
One of the most consistent findings in multiple sclerosis (MS) is that development of MS is linked with carriage of the class II human leucocyte antigen (HLA) molecule HLA-DRB1*15:01; around 60 % of Caucasian MS patients carry this allele compared to 25-30 % of ethnically matched healthy individuals. However, other HLA molecules have also been linked to the development of MS. In this chapter, the association between different HLA types and susceptibility to MS will be reviewed, and other linkages between the carriage of specific HLA molecules and clinical and experimental findings in MS will be considered.
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Affiliation(s)
- Judith M Greer
- The University of Queensland, UQ Centre for Clinical Research, Building 71/918 Riyal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia.
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41
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Alexander T, Bondanza A, Muraro PA, Greco R, Saccardi R, Daikeler T, Kazmi M, Hawkey C, Simoes BP, Leblanc K, Fibbe WE, Moore J, Snarski E, Martin T, Hiepe F, Velardi A, Toubert A, Snowden JA, Farge D. SCT for severe autoimmune diseases: consensus guidelines of the European Society for Blood and Marrow Transplantation for immune monitoring and biobanking. Bone Marrow Transplant 2014; 50:173-80. [PMID: 25387090 PMCID: PMC4317973 DOI: 10.1038/bmt.2014.251] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/01/2014] [Indexed: 12/19/2022]
Abstract
Over the past 15 years, SCT has emerged as a promising treatment option for patients with severe autoimmune diseases (ADs). Mechanistic studies recently provided the proof-of-concept that restoration of immunological tolerance can be achieved by haematopoietic SCT in chronic autoimmunity through eradication of the pathologic, immunologic memory and profound reconfiguration of the immune system, that is, immune ‘resetting'. Nevertheless, a number of areas remain unresolved and warrant further investigation to refine our understanding of the underlying mechanisms of action and to optimize clinical SCT protocols. Due to the low number of patients transplanted in each centre, it is essential to adequately collect and analyse biological samples in a larger cohort of patients under standardized conditions. The European society for blood and marrow transplantation Autoimmune Diseases and Immunobiology Working Parties have, therefore, undertaken a joint initiative to develop and implement guidelines for ‘good laboratory practice' in relation to procurement, processing, storage and analysis of biological specimens for immune reconstitution studies in AD patients before, during and after SCT. The aim of this document is to provide practical recommendations for biobanking of samples and laboratory immune monitoring in patients with ADs undergoing SCT, both for routine supportive care purposes and investigational studies.
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Affiliation(s)
- T Alexander
- Department of Rheumatology and Clinical Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - A Bondanza
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - P A Muraro
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - R Greco
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milano, Italy
| | - R Saccardi
- Cord Blood Bank, Haematology department, Careggi University Hospital, Florence, Italy
| | - T Daikeler
- Department of Rheumatology, University Hospital Basel, Basel, Switzerland
| | - M Kazmi
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - C Hawkey
- Nottingham Digestive Diseases Centre, Nottingham, UK
| | - B P Simoes
- Department of Clinical Medicine, School of Medicine, University of Sao Paulo, Ribeirao Preto, Brazil
| | - K Leblanc
- Department of Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - W E Fibbe
- Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
| | - J Moore
- Department of Haematology, St Vincent's Hospital, Darlinghurst, Sydney, Australia
| | - E Snarski
- Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Warsaw, Poland
| | - T Martin
- Strasbourg University Hospital, Strasbourg, France
| | - F Hiepe
- Department of Rheumatology and Clinical Immunology, Charité-University Medicine Berlin, Berlin, Germany
| | - A Velardi
- Department of Medicine, Division of Haematology, University of Perugia, Perugia, Italy
| | - A Toubert
- Inserm U1160, Université Paris Diderot, Sorbonne Paris Cité, AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie, Paris, France
| | - J A Snowden
- Department of Haematology, Sheffield Teaching Hospitals NHS Foundation Trust & University of Sheffield, Sheffield, UK
| | - D Farge
- Saint Louis Hospital, Unité de Médecine interne et Pathologie Vasculaire, Assistance Publique des Hôpitaux de Paris, Paris 7 University, INSERM U1160, Paris, France
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Sollid LM, Pos W, Wucherpfennig KW. Molecular mechanisms for contribution of MHC molecules to autoimmune diseases. Curr Opin Immunol 2014; 31:24-30. [PMID: 25216261 DOI: 10.1016/j.coi.2014.08.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 08/01/2014] [Accepted: 08/24/2014] [Indexed: 12/11/2022]
Abstract
It will soon be 50 years since the first MHC associations with human disease were described. These seminal studies opened a flourishing area of research, yet much remains to be discovered. Genome-wide association studies of autoimmune diseases have demonstrated that the MHC region has effect sizes that supersede those for any non-MHC locus for most diseases. Thus, an understanding of how particular MHC alleles confer susceptibility will be essential for a comprehensive understanding of autoimmune disease pathogenesis. Here we review recent exciting findings in this important field.
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Affiliation(s)
- Ludvig M Sollid
- Centre for Immune Regulation, Department of Immunology, University of Oslo and Oslo University Hospital - Rikshospitalet, 0372 Oslo, Norway.
| | - Wouter Pos
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA.
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Wu L, Guo S, Yang D, Ma Y, Ji H, Chen Y, Zhang J, Wang Y, Jin L, Wang J, Liu J. Copy number variations of HLA-DRB5 is associated with systemic lupus erythematosus risk in Chinese Han population. Acta Biochim Biophys Sin (Shanghai) 2014; 46:155-60. [PMID: 24366815 DOI: 10.1093/abbs/gmt137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a polygenic, systemic, autoimmune disease. Copy number variants (CNVS) have been discovered to be associated with a number of complex disorders. We undertook the current study to explore the potential associations between genomic CNVS and SLE in Chinese Han population. In the discovery stage, seven SLE patients were examined with the high-density comparative genomic hybridization microarrays in the screening test for SLE associated CNVS. Then, in the validation stage, 135 SLE patients and 219 matched healthy subjects were investigated for the CNVS of gene HLA-DRB5 by AccuCopy™ technology. Quantitative polymerase chain reaction was carried out to determine the copy number (CN) and mRNA level of HLA-DRB5 in SLE patients. Although the mRNA level of HLA-DRB5 between the CN deletion group and the CN normal group in SLE patients was not statistically positive (P = 0.46), our results still showed more CN of HLA-DRB5 in SLE patients than in healthy controls (P = 3.98 × 10(-6)). Odds ratio for CN deletion was 0.38 (95% confidence interval (CI), 0.23-0.61, P = 7.79 × 10(-5)) and for CN duplication was 1.89 (95% CI, 0.56-7.66, P = 0.37), respectively. These findings indicated that CNVS of HLA-DRB5 was associated with the risk of SLE, and CN deletion appeared to be protective for SLE.
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Affiliation(s)
- Lijun Wu
- Department of Digestive Diseases of Huashan Hospital, Fudan University, Shanghai 200040, China
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Abstract
Familial aggregation and the studies of twins indicate that heredity contributes to multiple sclerosis (MS) risk. Immunologic studies of leukocyte antigens subsequently followed by gene-mapping techniques identified the primary MS susceptibility locus to be within the major histocompatibility complex (MHC). The primary risk allele is HLA-DRB1*15, although other alleles of this gene also influence MS susceptibility. Other genes within the MHC also contribute to MS susceptibility. Genome-wide association studies have identified over 50 additional common variants of genes across the genome. Estimates suggest that there may be as many as 200 genes involved in MS susceptibility. In addition to these common polymorphisms, studies have identified several rare risk alleles in some families. Interestingly, the majority of the genes identified have known immunologic functions and many contribute to the risk of inheriting other autoimmune diseases. Genetic variants in the vitamin D metabolic pathway have also been identified. That vitamin D contributes to MS susceptibility as both an environmental as well as genetic risk factor underscores the importance of this metabolic pathway in disease pathogenesis. Current efforts are focused on understanding how the myriad of genetic risk alleles interact within networks to influence MS risk at family level as well as within populations.
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Affiliation(s)
- Bruce A C Cree
- Department of Neurology, University of California, San Francisco, USA.
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45
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Mohme M, Hotz C, Stevanovic S, Binder T, Lee JH, Okoniewski M, Eiermann T, Sospedra M, Rammensee HG, Martin R. HLA-DR15-derived self-peptides are involved in increased autologous T cell proliferation in multiple sclerosis. ACTA ACUST UNITED AC 2013; 136:1783-98. [PMID: 23739916 DOI: 10.1093/brain/awt108] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The HLA-DR15 haplotype confers the largest part of the genetic risk to develop multiple sclerosis, a prototypic CD4+ T cell-mediated autoimmune disease. The mechanisms how certain HLA-class II molecules functionally contribute to autoimmune diseases are still poorly understood, but probably involve shaping an autoimmune-prone T cell repertoire during central tolerance in the thymus and subsequently maintaining or even expanding it in the peripheral immune system. Self-peptides that are presented by disease-associated HLA-class II molecules most likely play important roles during both processes. Here, we examined the functional involvement of the HLA-DR15 haplotype in autologous proliferation in multiple sclerosis and the contribution of HLA-DR15 haplotype-derived self-peptides in an in vitro system. We observe increased autologous T cell proliferation in patients with multiple sclerosis in relation to the multiple sclerosis risk-associated HLA-DR15 haplotype. Assuming that the spectrum of self-peptides that is presented by the two HLA-DR15 allelic products is important for sustaining autologous proliferation we performed peptide elution and identification experiments from the multiple sclerosis-associated DR15 molecules and a systematic analysis of a DR15 haplotype-derived self-peptide library. We identify HLA-derived self-peptides as potential mediators of altered autologous proliferation. Our data provide novel insights about perturbed T cell repertoire dynamics and the functional involvement of the major genetic risk factor, the HLA-DR15 haplotype, in multiple sclerosis.
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Affiliation(s)
- Malte Mohme
- Institute for Neuroimmunology and Clinical Multiple Sclerosis Research, Centre for Molecular Neurobiology Hamburg, University Medical Centre Eppendorf, 20251 Hamburg, Germany
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46
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Paltser G, Liu XJ, Yantha J, Winer S, Tsui H, Wu P, Maezawa Y, Cahill LS, Laliberté CL, Ramagopalan SV, DeLuca GC, Sadovnick AD, Astsaturov I, Ebers GC, Henkelman RM, Salter MW, Dosch HM. TRPV1 gates tissue access and sustains pathogenicity in autoimmune encephalitis. Mol Med 2013; 19:149-59. [PMID: 23689362 DOI: 10.2119/molmed.2012.00329] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 05/08/2013] [Indexed: 01/03/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic progressive, demyelinating condition whose therapeutic needs are unmet, and whose pathoetiology is elusive. We report that transient receptor potential vanilloid-1 (TRPV1) expressed in a major sensory neuron subset, controls severity and progression of experimental autoimmune encephalomyelitis (EAE) in mice and likely in primary progressive MS. TRPV1-/- B6 congenics are protected from EAE. Increased survival reflects reduced central nervous systems (CNS) infiltration, despite indistinguishable T cell autoreactivity and pathogenicity in the periphery of TRPV1-sufficient and -deficient mice. The TRPV1+ neurovascular complex defining the blood-CNS barriers promoted invasion of pathogenic lymphocytes without the contribution of TRPV1-dependent neuropeptides such as substance P. In MS patients, we found a selective risk-association of the missense rs877610 TRPV1 single nucleotide polymorphism (SNP) in primary progressive disease. Our findings indicate that TRPV1 is a critical disease modifier in EAE, and we identify a predictor of severe disease course and a novel target for MS therapy.
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Affiliation(s)
- Geoffrey Paltser
- Neuroscience and Mental Health Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
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47
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Isobe N, Gourraud PA, Harbo HF, Caillier SJ, Santaniello A, Khankhanian P, Maiers M, Spellman S, Cereb N, Yang S, Pando MJ, Piccio L, Cross AH, De Jager PL, Cree BAC, Hauser SL, Oksenberg JR. Genetic risk variants in African Americans with multiple sclerosis. Neurology 2013; 81:219-27. [PMID: 23771490 PMCID: PMC3770164 DOI: 10.1212/wnl.0b013e31829bfe2f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/04/2013] [Indexed: 01/26/2023] Open
Abstract
OBJECTIVES To assess the association of established multiple sclerosis (MS) risk variants in 3,254 African Americans (1,162 cases and 2,092 controls). METHODS Human leukocyte antigen (HLA)-DRB1, HLA-DQB1, and HLA-A alleles were typed by molecular techniques. Single nucleotide polymorphism (SNP) genotyping was conducted for 76 MS-associated SNPs and 52 ancestry informative marker SNPs selected throughout the genome. Self-declared ancestry was refined by principal component analysis of the ancestry informative marker SNPs. An ancestry-adjusted multivariate model was applied to assess genetic associations. RESULTS The following major histocompatibility complex risk alleles were replicated: HLA-DRB1*15:01 (odds ratio [OR] = 2.02 [95% confidence interval: 1.54-2.63], p = 2.50e-07), HLA-DRB1*03:01 (OR = 1.58 [1.29-1.94], p = 1.11e-05), as well as HLA-DRB1*04:05 (OR = 2.35 [1.26-4.37], p = 0.007) and the African-specific risk allele of HLA-DRB1*15:03 (OR = 1.26 [1.05-1.51], p = 0.012). The protective association of HLA-A*02:01 was confirmed (OR = 0.72 [0.55-0.93], p = 0.013). None of the HLA-DQB1 alleles were associated with MS. Using a significance threshold of p < 0.01, outside the major histocompatibility complex region, 8 MS SNPs were also found to be associated with MS in African Americans. CONCLUSION MS genetic risk in African Americans only partially overlaps with that of Europeans and could explain the difference of MS prevalence between populations.
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Affiliation(s)
- Noriko Isobe
- Department of Neurology, School of Medicine, University of California, San Francisco, CA, USA
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48
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Croes K, De Coster S, De Galan S, Morrens B, Loots I, Van de Mieroop E, Nelen V, Sioen I, Bruckers L, Nawrot T, Colles A, Den Hond E, Schoeters G, van Larebeke N, Baeyens W, Gao Y. Health effects in the Flemish population in relation to low levels of mercury exposure: from organ to transcriptome level. Int J Hyg Environ Health 2013; 217:239-47. [PMID: 23920476 DOI: 10.1016/j.ijheh.2013.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/29/2013] [Accepted: 06/04/2013] [Indexed: 11/30/2022]
Abstract
Due to possible health risks, quantification of mercury accumulation in humans was included in the Flemish biomonitoring programmes FLEHS I (2002-2006) and FLEHS II (2007-2011). The general objective of FLEHS I was to assess regional exposure levels in order to link possible differences in these internal exposure levels to different types of local environmental pressure. Therefore, Hg and MMHg (methylmercury) were only measured in pooled blood samples per region and per age class. In FLEHS II, mercury concentrations were measured in hair of each participant. About 200 adolescents and 250 mothers (reference group) and two times 200 adolescents (2 hotspots) were screened. The main objectives of the FLEHS II study were: (1) to determine reference levels of mercury in hair for Flanders; (2) to assess relations between mercury exposure and possible sources like fish consumption; (3) to assess dose-effect relations between mercury exposure and health effect markers. The results showed that mercury concentrations in the Flemish population were rather low compared to other studies. Mercury levels in the Flemish populations were strongly related to the age of the participants and consumption of fish. Significant negative associations were observed between mercury in hair and asthma, having received breast feeding as a newborn, age at menarche in girls, allergy for animals and free testosterone levels. Significant correlations were also observed between mercury in hair and genes JAK2, ARID4A, Hist1HA4L (boys) and HLAdrb5, PIAS2, MANN1B1, GIT and ABCA1 (girls).
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Affiliation(s)
- Kim Croes
- Free University of Brussels (VUB), Department of Analytical and Environmental Chemistry (ANCH), Pleinlaan 2, 1050 Brussels, Belgium
| | - Sam De Coster
- Ghent University Hospital, Study Centre for Carcinogenesis and Primary Prevention of Cancer, De Pintelaan 185, 9000 Ghent, Belgium
| | - Sandra De Galan
- Free University of Brussels (VUB), Department of Analytical and Environmental Chemistry (ANCH), Pleinlaan 2, 1050 Brussels, Belgium
| | - Bert Morrens
- University of Antwerp, Faculty of Political and Social Sciences, Department of Sociology, Sint Jacobstraat 2, 2000 Antwerp, Belgium
| | - Ilse Loots
- University of Antwerp, Faculty of Political and Social Sciences, Department of Sociology, Sint Jacobstraat 2, 2000 Antwerp, Belgium
| | - Els Van de Mieroop
- Provincial Institute for Hygiene, Kronenburgstraat 45, 2000 Antwerp, Belgium
| | - Vera Nelen
- Provincial Institute for Hygiene, Kronenburgstraat 45, 2000 Antwerp, Belgium
| | - Isabelle Sioen
- Ghent University, Department of Public Health, UZ-2 Blok A, De Pintelaan 185, 9000 Ghent, Belgium; Research Foundation - Flanders, Egmontstraat 5, 1000 Brussels, Belgium
| | - Liesbeth Bruckers
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Martelarenlaan 42, 3500 Hasselt, Belgium
| | - Tim Nawrot
- School of Public Health, Occupational & Environmental Medicine, K.U. Leuven, Herestraat 49 (O&N 706), 3000 Leuven, Belgium; Centre for Environmental Sciences, Hasselt University, Agoralaan Gebouw D, 3590 Diepenbeek, Belgium
| | - Ann Colles
- Flemish Institute for Technological Research (VITO), Environmental Health and Risk, Boeretang 200, 2400 Mol, Belgium
| | - Elly Den Hond
- Flemish Institute for Technological Research (VITO), Environmental Health and Risk, Boeretang 200, 2400 Mol, Belgium
| | - Greet Schoeters
- Flemish Institute for Technological Research (VITO), Environmental Health and Risk, Boeretang 200, 2400 Mol, Belgium
| | - Nicolas van Larebeke
- Ghent University Hospital, Study Centre for Carcinogenesis and Primary Prevention of Cancer, De Pintelaan 185, 9000 Ghent, Belgium
| | - Willy Baeyens
- Free University of Brussels (VUB), Department of Analytical and Environmental Chemistry (ANCH), Pleinlaan 2, 1050 Brussels, Belgium
| | - Yue Gao
- Free University of Brussels (VUB), Department of Analytical and Environmental Chemistry (ANCH), Pleinlaan 2, 1050 Brussels, Belgium.
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Abstract
RAGE (receptor for advanced glycation end products) is a multi-ligand receptor that belongs to the immunoglobulin superfamily of transmembrane proteins. RAGE binds AGEs (advanced glycation end products), HMGB1 (high-mobility group box-1; also designated as amphoterin), members of the S100 protein family, glycosaminoglycans and amyloid β peptides. Recent studies using tools of structural biology have started to unravel common molecular patterns in the diverse set of ligands recognized by RAGE. The distal Ig domain (V1 domain) of RAGE has a positively charged patch, the geometry of which fits to anionic surfaces displayed at least in a proportion of RAGE ligands. Association of RAGE to itself, to HSPGs (heparan sulfate proteoglycans), and to Toll-like receptors in the cell membrane plays a key role in cell signaling initiated by RAGE ligation. Ligation of RAGE activates cell signaling pathways that regulate migration of several cell types. Furthermore, RAGE ligation has profound effects on the transcriptional profile of cells. RAGE signaling has been mainly studied as a pathogenetic factor of several diseases, where acute or chronic inflammation plays a role. Recent studies have suggested a physiological role for RAGE in normal lung function and in neuronal signaling.
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Affiliation(s)
- Ari Rouhiainen
- Neuroscience Center, University of Helsinki, Helsinki, Finland.
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Apperson ML, Tian Y, Stamova B, Ander BP, Jickling GC, Agius MA, Sharp FR. Genome wide differences of gene expression associated with HLA-DRB1 genotype in multiple sclerosis: a pilot study. J Neuroimmunol 2013; 257:90-6. [PMID: 23477965 DOI: 10.1016/j.jneuroim.2013.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Revised: 02/11/2013] [Accepted: 02/13/2013] [Indexed: 01/21/2023]
Abstract
Using two microarray platforms, we identify HLA-DRB5 as the most highly expressed gene in MS compared to healthy subjects. As expected, HLA-DRB5 expression was associated with the HLA-DRB1*1501 MS susceptibility allele. Besides HLA-DRB5, there were 1219 differentially expressed exons (p<0.01, |fold change (FC)|>1.2) that differed between HLA-DRB1*1501 Positive multiple sclerosis subjects (MSP) compared to HLA-DRB1*1501 negative multiple sclerosis subjects (MSN). Analysis of the regulated genes revealed significantly different immune signaling pathways including IL-4 and IL-17 in these two MS genotypes. Different risk alleles appear to be associated with different patterns of gene expression that may reflect differences in pathophysiology of these two MS subtypes. These preliminary data will need to be confirmed in future studies.
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Affiliation(s)
- Michelle L Apperson
- Department of Neurology and the M.I.N.D. Institute, University of California at Davis, Sacramento, CA 95817, USA.
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