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Aydemir Ö, Noble JA, Bailey JA, Lernmark Å, Marsh P, Andersson Svärd A, Bearoff F, Blankenhorn EP, Mordes JP. Genetic Variation Within the HLA-DRA1 Gene Modulates Susceptibility to Type 1 Diabetes in HLA-DR3 Homozygotes. Diabetes 2019; 68:1523-1527. [PMID: 30962219 PMCID: PMC6609989 DOI: 10.2337/db18-1128] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
Abstract
Type 1 diabetes (T1D) involves the interaction of multiple gene variants, environmental factors, and immunoregulatory dysfunction. Major T1D genetic risk loci encode HLA-DR and -DQ. Genetic heterogeneity and linkage disequilibrium in the highly polymorphic HLA region confound attempts to identify additional T1D susceptibility loci. To minimize HLA heterogeneity, T1D patients (N = 365) and control subjects (N = 668) homozygous for the HLA-DR3 high-risk haplotype were selected from multiple large T1D studies and examined to identify new T1D susceptibility loci using molecular inversion probe sequencing technology. We report that risk for T1D in HLA-DR3 homozygotes is increased significantly by a previously unreported haplotype of three single nucleotide polymorphisms (SNPs) within the first intron of HLA-DRA1. The homozygous risk haplotype has an odds ratio of 4.65 relative to the protective homozygous haplotype in our sample. Individually, these SNPs reportedly function as "expression quantitative trait loci," modulating HLA-DR and -DQ expression. From our analysis of available data, we conclude that the tri-SNP haplotype within HLA-DRA1 may modulate class II expression, suggesting that increased T1D risk could be attributable to regulated expression of class II genes. These findings could help clarify the role of HLA in T1D susceptibility and improve diabetes risk assessment, particularly in high-risk HLA-DR3 homozygous individuals.
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Affiliation(s)
- Özkan Aydemir
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | | | - Jeffrey A Bailey
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Patrick Marsh
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
| | - Agnes Andersson Svärd
- Department of Clinical Sciences, Lund University/CRC, Skåne University Hospital, Malmö, Sweden
| | - Frank Bearoff
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - John P Mordes
- Division of Endocrinology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA
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Graves JS, Barcellos LF, Simpson S, Belman A, Lin R, Taylor BV, Ponsonby AL, Dwyer T, Krupp L, Waubant E, van der Mei IAF. The multiple sclerosis risk allele within the AHI1 gene is associated with relapses in children and adults. Mult Scler Relat Disord 2017; 19:161-165. [PMID: 29409597 DOI: 10.1016/j.msard.2017.10.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/12/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND While common variant non-HLA (human leukocyte antigen) alleles have been associated with MS risk, their role in disease course is less clear. We sought to determine whether established multiple sclerosis (MS) genetic susceptibility factors are associated with relapse rate in children and an independent cohort of adults with MS. METHODS Genotyping was performed for 182 children with MS or clinically isolated syndrome with high risk for MS from two Pediatric MS Centers. They were prospectively followed for relapses. Fifty-two non-HLA MS susceptibility single nucleotide polymorphisms (SNPs) were evaluated for association with relapse rate. Cox regression models were adjusted for sex, genetic ancestry, disease-modifying therapy (DMT), 25-OH vitamin D level and HLA-DRB1*15:01/03 status. Investigation of pediatric subject SNP results was performed using a second cohort of 141 adult MS subjects of Northern European ancestry from the Southern Tasmanian Multiple Sclerosis Longitudinal Study. RESULTS For pediatric subjects, 408 relapses were captured over 622 patient-years of follow-up. Four non-HLA risk SNPs (rs11154801, rs650258, rs12212193, rs2303759) were associated with relapses (p < 0.01) in the pediatric subjects. After adjustment for genetic ancestry, sex, age, vitamin D level, DMT use and HLA-DRB1*15 status, having two copies of the MS risk allele within AHI1 (rs11154801) was associated with increased relapses among children (HR = 1.75,95%CI = 1.18-2.48, p = 0.006) and this result was also observed among adults (HR = 1.81,95%CI = 1.05-3.03, p = 0.026). CONCLUSIONS Our results suggest that the MS genetic risk variant within the gene AHI1 may contribute to disease course in addition to disease susceptibility.
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Affiliation(s)
- Jennifer S Graves
- UCSF Pediatric MS Center, San Francisco, CA, USA; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Lisa F Barcellos
- Genetic Epidemiology and Genomics Lab, School of Public Health, and California Institute of Quantitative Biosciences, UC Berkeley, Berkeley, CA, USA; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Steve Simpson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Anita Belman
- National Pediatric MS Center, Stonybrook, NY, USA; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Rui Lin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia; Guangxi Center for Disease Prevention and Control, Nanning, China; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Bruce V Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Terence Dwyer
- Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Australia; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Lauren Krupp
- National Pediatric MS Center, Stonybrook, NY, USA; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Emmanuelle Waubant
- UCSF Pediatric MS Center, San Francisco, CA, USA; School of Medicine, University of Tasmania, Hobart, Australia.
| | - Ingrid A F van der Mei
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia; School of Medicine, University of Tasmania, Hobart, Australia.
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Kreft KL, Van Nierop GP, Scherbeijn SMJ, Janssen M, Verjans GMGM, Hintzen RQ. Elevated EBNA-1 IgG in MS is associated with genetic MS risk variants. NEUROLOGY-NEUROIMMUNOLOGY & NEUROINFLAMMATION 2017; 4:e406. [PMID: 29379819 PMCID: PMC5778394 DOI: 10.1212/nxi.0000000000000406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 07/31/2017] [Indexed: 12/26/2022]
Abstract
Objective: To assess whether MS genetic risk polymorphisms (single nucleotide polymorphism [SNP]) contribute to the enhanced humoral immune response against Epstein-Barr virus (EBV) infection in patients with MS. Methods: Serum anti-EBV nuclear antigen 1 (EBNA-1) and early antigen D (EA-D) immunoglobulin γ (IgG) levels were quantitatively determined in 668 genotyped patients with MS and 147 healthy controls. Anti–varicella-zoster virus (VZV) IgG levels were used as a highly prevalent, non-MS–associated control herpesvirus. Associations between virus-specific IgG levels and MS risk SNPs were analyzed. Results: IgG levels of EBNA-1, but not EA-D and VZV, were increased in patients with MS compared with healthy controls. Increased EBNA-1 IgG levels were significantly associated with risk alleles of SNP rs2744148 (SOX8), rs11154801 (MYB), rs1843938 (CARD11), and rs7200786 (CLEC16A/CIITA) in an interaction model and a trend toward significance for rs3135388 (HLA-DRB1*1501). In addition, risk alleles of rs694739 (PRDX5/BAD) and rs11581062 (VCAM1) were independently associated and interacted with normal EBNA-1 IgG levels. None of these interactions were associated with EA-D and VZV IgG titers. Conclusions: Several MS-associated SNPs significantly correlated with differential IgG levels directed to a latent, but not a lytic EBV protein. The data suggest that the aforementioned immune-related genes orchestrate the aberrant EBNA-1 IgG levels.
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Affiliation(s)
- Karim L Kreft
- Department of Neurology (K.L.K., G.P.V.N., M.J., R.Q.H.), MS Center ErasMS (K.L.K., M.J., R.Q.H.), Department of Viroscience (G.P.V.N., S.M.J.S., G.M.G.M.V.), and Department of Immunology (M.J., R.Q.H.), Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Gijsbert P Van Nierop
- Department of Neurology (K.L.K., G.P.V.N., M.J., R.Q.H.), MS Center ErasMS (K.L.K., M.J., R.Q.H.), Department of Viroscience (G.P.V.N., S.M.J.S., G.M.G.M.V.), and Department of Immunology (M.J., R.Q.H.), Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Sandra M J Scherbeijn
- Department of Neurology (K.L.K., G.P.V.N., M.J., R.Q.H.), MS Center ErasMS (K.L.K., M.J., R.Q.H.), Department of Viroscience (G.P.V.N., S.M.J.S., G.M.G.M.V.), and Department of Immunology (M.J., R.Q.H.), Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Malou Janssen
- Department of Neurology (K.L.K., G.P.V.N., M.J., R.Q.H.), MS Center ErasMS (K.L.K., M.J., R.Q.H.), Department of Viroscience (G.P.V.N., S.M.J.S., G.M.G.M.V.), and Department of Immunology (M.J., R.Q.H.), Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Georges M G M Verjans
- Department of Neurology (K.L.K., G.P.V.N., M.J., R.Q.H.), MS Center ErasMS (K.L.K., M.J., R.Q.H.), Department of Viroscience (G.P.V.N., S.M.J.S., G.M.G.M.V.), and Department of Immunology (M.J., R.Q.H.), Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Rogier Q Hintzen
- Department of Neurology (K.L.K., G.P.V.N., M.J., R.Q.H.), MS Center ErasMS (K.L.K., M.J., R.Q.H.), Department of Viroscience (G.P.V.N., S.M.J.S., G.M.G.M.V.), and Department of Immunology (M.J., R.Q.H.), Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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The distribution and functional relevance analysis of runs of homozygosity (ROHs) in Chinese Han female population. Mol Genet Genomics 2017; 293:197-206. [PMID: 28980070 DOI: 10.1007/s00438-017-1378-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/25/2017] [Indexed: 10/18/2022]
Abstract
Extended homozygosity is a genomic region in which the copies inherited from parents are identical, and has obvious inter-individual differences in length and frequency. Runs of homozygosity (ROHs), regarded as a type of structure variations, may have potential capacity in regulating gene transcription. To learn more about the genome-wide distribution of ROH regions in humans and understand the potential roles, this study applied ROH-based approach to quantify and characterize ROHs in 41 Chinese Han female subjects, and test potential associations between ROHs and mRNA expressions by eQTL analysis to ascertain whether ROHs are relevant to gene transcription in peripheral blood mononuclear cells (PBMCs). 10,884 ROH regions were identified in human genome. The average cumulative length of ROH regions was 217,250 ± 20,241 kb. The number of core segments in each chromosome generally matched the total length of corresponding chromosome, i.e., the longer the chromosome, the more the core segments. Genes located in the core regions of ROH were significantly enriched in multiple basic metabolism pathways. A total of 226 cis-eQTLs and 178 trans-eQTLs were identified. The cis-effect size was mainly concentrated at ± 0.5; and the trans-effect size was mainly concentrated at -1.5 and 1.0. Genes with eQTL effects were significantly enriched in functions related to protein binding, cytosol, nucleoplasm, nuclear membrane, protein binding and citrate metabolic process. This study described comprehensive distributions and characteristics of ROH in Han female Chinese, and recognized the significant role of ROH associated with gene transcription in human PBMC.
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Bykadorov PA, Oparina NY, Fridman MV, Makeev VY. Prevalent function of genome loci associated with development of multiple sclerosis as revealed by GWAS and eQTL analysis. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417090058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Functional relevance for associations between osteoporosis and genetic variants. PLoS One 2017; 12:e0174808. [PMID: 28369098 PMCID: PMC5378394 DOI: 10.1371/journal.pone.0174808] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/15/2017] [Indexed: 11/19/2022] Open
Abstract
Osteoporosis is characterized by increased bone loss and deterioration of bone microarchitecture, which will lead to reduced bone strength and increased risk of fragility fractures. Previous studies have identified many genetic loci associated with osteoporosis, but functional mechanisms underlying the associations have rarely been explored. In order to explore the potential molecular functional mechanisms underlying the associations for osteoporosis, we performed integrative analyses by using the publically available datasets and resources. We searched 128 identified osteoporosis associated SNPs (P<10-6), and 8 SNPs exert cis-regulation effects on 11 eQTL target genes. Among the 8 SNPs, 2 SNPs (RPL31 rs2278729 and LRP5 rs3736228) were confirmed to impact the expression of 3 genes (RPL31, CPT1A and MTL5) that were differentially expressed between human subjects of high BMD group and low BMD group. All of the functional evidence suggested the important functional mechanisms underlying the associations of the 2 SNPs (rs2278729 and rs3736228) and 3 genes (RPL31, CPT1A and MTL5) with osteoporosis. This study may provide novel insights into the functional mechanisms underlying the osteoporosis associated genetic variants, which will help us to comprehend the potential mechanisms underlying the genetic association for osteoporosis.
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Krausz C, Escamilla AR, Chianese C. Genetics of male infertility: from research to clinic. Reproduction 2016; 150:R159-74. [PMID: 26447148 DOI: 10.1530/rep-15-0261] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Male infertility is a multifactorial complex disease with highly heterogeneous phenotypic representation and in at least 15% of cases, this condition is related to known genetic disorders, including both chromosomal and single-gene alterations. In about 40% of primary testicular failure, the etiology remains unknown and a portion of them is likely to be caused by not yet identified genetic anomalies. During the last 10 years, the search for 'hidden' genetic factors was largely unsuccessful in identifying recurrent genetic factors with potential clinical application. The armamentarium of diagnostic tests has been implemented only by the screening for Y chromosome-linked gr/gr deletion in those populations for which consistent data with risk estimate are available. On the other hand, it is clearly demonstrated by both single nucleotide polymorphisms and comparative genomic hybridization arrays, that there is a rare variant burden (especially relevant concerning deletions) in men with impaired spermatogenesis. In the era of next generation sequencing (NGS), we expect to expand our diagnostic skills, since mutations in several hundred genes can potentially lead to infertility and each of them is likely responsible for only a small fraction of cases. In this regard, system biology, which allows revealing possible gene interactions and common biological pathways, will provide an informative tool for NGS data interpretation. Although these novel approaches will certainly help in discovering 'hidden' genetic factors, a more comprehensive picture of the etiopathogenesis of idiopathic male infertility will only be achieved by a parallel investigation of the complex world of gene environmental interaction and epigenetics.
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Affiliation(s)
- Csilla Krausz
- Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Antoni Riera Escamilla
- Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Chiara Chianese
- Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain Department of Experimental and Clinical Biomedical SciencesCentre of Excellence DeNothe, University of Florence, Viale Gaetano Pieraccini, 6, 50139, Florence, Italy and Andrology ServiceFundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Universitat Autònoma de Barcelona, Catalonia, Spain
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Scattering Month and Day of Baby Delivery in a Retrospective Survey Linked to 1484 Patients With Multiple Sclerosis. ARCHIVES OF NEUROSCIENCE 2015. [DOI: 10.5812/archneurosci.27292v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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de Andrade Pereira B, Ackermann M, Chaudhary S, Vogel R, Vogt B, Dresch C, Fraefel C. Tolerance of activated pathogenic CD4+ T cells by transcriptional targeting of dendritic cells. Gene Ther 2015; 22:382-90. [PMID: 25739989 DOI: 10.1038/gt.2015.6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 12/02/2014] [Accepted: 01/15/2015] [Indexed: 01/30/2023]
Abstract
We have recently shown that targeted expression of myelin oligodendrocyte glycoprotein (MOG) to dendritic cells with self-inactivating-lentivirus vectors induces antigen-specific tolerance in naive antigen-specific CD4+ T cells and protects mice from experimental autoimmune encephalomyelitis (EAE). In the present study, we demonstrate that this approach also induces tolerance of activated antigen-specific CD4+ T cells and completely protects mice from passive EAE induction. Tolerance induction did not correlate with the depletion of the preactivated antigen-specific CD4+ T cells. However, upon isolation and in vitro re-stimulation at day 6 after adoptive transfer the MOG-specific CD4+ T cells from the non-tolerized mice produced large amounts of inflammatory cytokines, whereas those from tolerized mice did not. This unresponsiveness correlated with the upregulation of regulatory molecules associated with anergy and regulatory T cells (Tregs). The in vivo depletion of Tregs resulted in EAE susceptibility of the tolerized animals, suggesting that these cells have indeed a role in tolerance induction/maintenance.
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Affiliation(s)
| | - M Ackermann
- Institute of Virology, University of Zürich, Zürich, Switzerland
| | - S Chaudhary
- Institute of Virology, University of Zürich, Zürich, Switzerland
| | - R Vogel
- Institute of Virology, University of Zürich, Zürich, Switzerland
| | - B Vogt
- Institute of Virology, University of Zürich, Zürich, Switzerland
| | - C Dresch
- Institute of Virology, University of Zürich, Zürich, Switzerland
| | - C Fraefel
- Institute of Virology, University of Zürich, Zürich, Switzerland
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