1
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Huang X, Huang J, Li X, Fan J, Zhou D, Qu HQ, Glessner JT, Ji D, Jia Q, Ding Z, Wang N, Wei W, Lyu X, Li MJ, Liu Z, Liu W, Wei Y, Hakonarson H, Xia Q, Li J. Target genes regulated by CLEC16A intronic region associated with common variable immunodeficiency. J Allergy Clin Immunol 2024; 153:1668-1680. [PMID: 38191060 DOI: 10.1016/j.jaci.2023.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND CLEC16A intron 19 has been identified as a candidate locus for common variable immunodeficiency (CVID). OBJECTIVES This study sought to elucidate the molecular mechanism by which variants at the CLEC16A intronic locus may contribute to the pathogenesis of CVID. METHODS The investigators performed fine-mapping of the CLEC16A locus in a CVID cohort, then deleted the candidate functional SNP in T-cell lines by the CRISPR-Cas9 technique and conducted RNA-sequencing to identify target gene(s). The interactions between the CLEC16A locus and its target genes were identified using circular chromosome conformation capture. The transcription factor complexes mediating the chromatin interactions were determined by proteomic approach. The molecular pathways regulated by the CLEC16A locus were examined by RNA-sequencing and reverse phase protein array. RESULTS This study showed that the CLEC16A locus is an enhancer regulating expression of multiple target genes including a distant gene ATF7IP2 through chromatin interactions. Distinct transcription factor complexes mediate the chromatin interactions in an allele-specific manner. Disruption of the CLEC16A locus affects the AKT signaling pathway, as well as the molecular response of CD4+ T cells to immune stimulation. CONCLUSIONS Through multiomics and targeted experimental approaches, this study elucidated the underlying target genes and signaling pathways involved in the genetic association of CLEC16A with CVID, and highlighted plausible molecular targets for developing novel therapeutics.
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Affiliation(s)
- Xubo Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinxia Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiumei Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jingxian Fan
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Desheng Zhou
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hui-Qi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Dandan Ji
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qi Jia
- International School of Information Science Engineering, Dalian University of Technology, Dalian, China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan, China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan, China
| | - Wei Wei
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xing Lyu
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Liu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Yongjie Wei
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Qianghua Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Jin Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China.
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2
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Lee KH, Kim J, Kim JH. 3D epigenomics and 3D epigenopathies. BMB Rep 2024; 57:216-231. [PMID: 38627948 PMCID: PMC11139681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 03/18/2024] [Indexed: 05/25/2024] Open
Abstract
Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies. [BMB Reports 2024; 57(5): 216-231].
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Affiliation(s)
- Kyung-Hwan Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jungyu Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Ji Hun Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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3
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Pandey R, Bakay M, Hakonarson H. SOCS-JAK-STAT inhibitors and SOCS mimetics as treatment options for autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis. Front Immunol 2023; 14:1271102. [PMID: 38022642 PMCID: PMC10643230 DOI: 10.3389/fimmu.2023.1271102] [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: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Autoimmune diseases arise from atypical immune responses that attack self-tissue epitopes, and their development is intricately connected to the disruption of the JAK-STAT signaling pathway, where SOCS proteins play crucial roles. Conditions such as autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis exhibit immune system dysfunctions associated with JAK-STAT signaling dysregulation. Emerging therapeutic strategies utilize JAK-STAT inhibitors and SOCS mimetics to modulate immune responses and alleviate autoimmune manifestations. Although more research and clinical studies are required to assess their effectiveness, safety profiles, and potential for personalized therapeutic approaches in autoimmune conditions, JAK-STAT inhibitors and SOCS mimetics show promise as potential treatment options. This review explores the action, effectiveness, safety profiles, and future prospects of JAK inhibitors and SOCS mimetics as therapeutic agents for psoriasis, autoimmune uveitis, systemic lupus erythematosus, and autoimmune encephalitis. The findings underscore the importance of investigating these targeted therapies to advance treatment options for individuals suffering from autoimmune diseases.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA, United States
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4
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Pandey R, Bakay M, Hakonarson H. CLEC16A-An Emerging Master Regulator of Autoimmunity and Neurodegeneration. Int J Mol Sci 2023; 24:ijms24098224. [PMID: 37175930 PMCID: PMC10179542 DOI: 10.3390/ijms24098224] [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: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
CLEC16A is emerging as an important genetic risk factor for several autoimmune disorders and for Parkinson disease (PD), opening new avenues for translational research and therapeutic development. While the exact role of CLEC16A in health and disease is still being elucidated, the gene plays a critical role in the regulation of autophagy, mitophagy, endocytosis, intracellular trafficking, immune function, and in biological processes such as insulin secretion and others that are important to cellular homeostasis. As shown in both human and animal modeling studies, CLEC16A hypofunction predisposes to both autoinflammatory phenotype and neurodegeneration. While the two are clearly related, further functional studies are needed to fully understand the mechanisms involved for optimized therapeutic interventions. Based on recent data, mitophagy-inducing drugs may be warranted, and such therapy should be tested in clinical trials as these drugs would tackle the underlying pathogenic mechanism (s) and could treat or prevent symptoms of autoimmunity and neurodegeneration in individuals with CLEC16A risk variants. Accordingly, interventions directed at reversing the dysregulated mitophagy and the consequences of loss of function of CLEC16A without activating other detrimental cellular pathways could present an effective therapy. This review presents the emerging role of CLEC16A in health and disease and provides an update on the disease processes that are attributed to variants located in the CLEC16A gene, which are responsible for autoimmune disorders and neurodegeneration with emphasis on how this information is being translated into practical and effective applications in the clinic.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA 19104-4318, USA
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5
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Manuel AM, Dai Y, Jia P, Freeman LA, Zhao Z. A gene regulatory network approach harmonizes genetic and epigenetic signals and reveals repurposable drug candidates for multiple sclerosis. Hum Mol Genet 2023; 32:998-1009. [PMID: 36282535 PMCID: PMC9991005 DOI: 10.1093/hmg/ddac265] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/14/2022] [Accepted: 10/20/2022] [Indexed: 02/02/2023] Open
Abstract
Multiple sclerosis (MS) is a complex dysimmune disorder of the central nervous system. Genome-wide association studies (GWAS) have identified 233 genetic variations associated with MS at the genome-wide significant level. Epigenetic studies have pinpointed differentially methylated CpG sites in MS patients. However, the interplay between genetic risk factors and epigenetic regulation remains elusive. Here, we employed a network model to integrate GWAS summary statistics of 14 802 MS cases and 26 703 controls with DNA methylation profiles from 140 MS cases and 139 controls and the human interactome. We identified differentially methylated genes by aggregating additive effects of differentially methylated CpG sites within promoter regions. We reconstructed a gene regulatory network (GRN) using literature-curated transcription factor knowledge. Colocalization of the MS GWAS and methylation quantitative trait loci (mQTL) was performed to assess the GRN. The resultant MS-associated GRN highlighted several single nucleotide polymorphisms with GWAS-mQTL colocalization: rs6032663, rs6065926 and rs2024568 of CD40 locus, rs9913597 of STAT3 locus, and rs887864 and rs741175 of CIITA locus. Moreover, synergistic mQTL and expression QTL signals were identified in CD40, suggesting gene expression alteration was likely induced by epigenetic changes. Web-based Cell-type Specific Enrichment Analysis of Genes (WebCSEA) indicated that the GRN was enriched in T follicular helper cells (P-value = 0.0016). Drug target enrichment analysis of annotations from the Therapeutic Target Database revealed the GRN was also enriched with drug target genes (P-value = 3.89 × 10-4), revealing repurposable candidates for MS treatment. These candidates included vorinostat (HDAC1 inhibitor) and sivelestat (ELANE inhibitor), which warrant further investigation.
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Affiliation(s)
- Astrid M Manuel
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Peilin Jia
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX 77030, USA
| | - Leorah A Freeman
- Department of Neurology, Dell Medical School, The University of Texas, Austin, TX 78712, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center, Houston, TX 77030, USA
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6
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Davidson C, Wordsworth BP, Cohen CJ, Knight JC, Vecellio M. Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis. Front Genet 2023; 14:1129207. [PMID: 36760998 PMCID: PMC9905691 DOI: 10.3389/fgene.2023.1129207] [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: 12/21/2022] [Accepted: 01/16/2023] [Indexed: 01/26/2023] Open
Abstract
Ankylosing Spondylitis (AS) is a chronic inflammatory arthritis of the spine exhibiting a strong genetic background. The mechanistic and functional understanding of the AS-associated genomic loci, identified with Genome Wide Association Studies (GWAS), remains challenging. Chromosome conformation capture (3C) and derivatives are recent techniques which are of great help in elucidating the spatial genome organization and of enormous support in uncover a mechanistic explanation for disease-associated genetic variants. The perturbation of three-dimensional (3D) genome hierarchy may lead to a plethora of human diseases, including rheumatological disorders. Here we illustrate the latest approaches and related findings on the field of genome organization, highlighting how the instability of 3D genome conformation may be among the causes of rheumatological disease phenotypes. We suggest a new perspective on the inclusive potential of a 3C approach to inform GWAS results in rheumatic diseases. 3D genome organization may ultimately lead to a more precise and comprehensive functional interpretation of AS association, which is the starting point for emerging and more specific therapies.
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Affiliation(s)
- Connor Davidson
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Carla J. Cohen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute for Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Julian C. Knight
- Wellcome Centre of Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
- Centro Ricerche Fondazione Italiana Ricerca Sull’Artrite (FIRA), Fondazione Pisana x la Scienza ONLUS, San Giuliano Terme, Italy
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7
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Chandrasekaran V, Oparina N, Garcia-Bonete MJ, Wasén C, Erlandsson MC, Malmhäll-Bah E, Andersson KME, Jensen M, Silfverswärd ST, Katona G, Bokarewa MI. Cohesin-Mediated Chromatin Interactions and Autoimmunity. Front Immunol 2022; 13:840002. [PMID: 35222432 PMCID: PMC8866859 DOI: 10.3389/fimmu.2022.840002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 11/23/2022] Open
Abstract
Proper physiological functioning of any cell type requires ordered chromatin organization. In this context, cohesin complex performs important functions preventing premature separation of sister chromatids after DNA replication. In partnership with CCCTC-binding factor, it ensures insulator activity to organize enhancers and promoters within regulatory chromatin. Homozygous mutations and dysfunction of individual cohesin proteins are embryonically lethal in humans and mice, which limits in vivo research work to embryonic stem cells and progenitors. Conditional alleles of cohesin complex proteins have been generated to investigate their functional roles in greater detail at later developmental stages. Thus, genome regulation enabled by action of cohesin proteins is potentially crucial in lineage cell development, including immune homeostasis. In this review, we provide current knowledge on the role of cohesin complex in leukocyte maturation and adaptive immunity. Conditional knockout and shRNA-mediated inhibition of individual cohesin proteins in mice demonstrated their importance in haematopoiesis, adipogenesis and inflammation. Notably, these effects occur rather through changes in transcriptional gene regulation than through expected cell cycle defects. This positions cohesin at the crossroad of immune pathways including NF-kB, IL-6, and IFNγ signaling. Cohesin proteins emerged as vital regulators at early developmental stages of thymocytes and B cells and after antigen challenge. Human genome-wide association studies are remarkably concordant with these findings and present associations between cohesin and rheumatoid arthritis, multiple sclerosis and HLA-B27 related chronic inflammatory conditions. Furthermore, bioinformatic prediction based on protein-protein interactions reveal a tight connection between the cohesin complex and immune relevant processes supporting the notion that cohesin will unearth new clues in regulation of autoimmunity.
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Affiliation(s)
- Venkataragavan Chandrasekaran
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Nina Oparina
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria-Jose Garcia-Bonete
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Caroline Wasén
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women’s Hospital, Boston, MA, United States
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Malin C. Erlandsson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Eric Malmhäll-Bah
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Karin M. E. Andersson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Maja Jensen
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Sofia T. Silfverswärd
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Maria I. Bokarewa
- Department of Rheumatology and Inflammation Research, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
- Rheumatology Clinic, Sahlgrenska University Hospital, Gothenburg, Sweden
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8
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Zarzuelo-Romero MJ, Pérez-Ramírez C, Cura Y, Carrasco-Campos MI, Marangoni-Iglecias LM, Ramírez-Tortosa MC, Jiménez-Morales A. Influence of Genetic Polymorphisms on Clinical Outcomes of Glatiramer Acetate in Multiple Sclerosis Patients. J Pers Med 2021; 11:jpm11101032. [PMID: 34683173 PMCID: PMC8540092 DOI: 10.3390/jpm11101032] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/04/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic, inflammatory, demyelinating disease of autoimmune origin, in which inflammation and demyelination lead to neurodegeneration and progressive disability. Treatment is aimed at slowing down the course of the disease and mitigating its symptoms. One of the first-line treatments used in patients with MS is glatiramer acetate (GA). However, in clinical practice, a response rate of between 30% and 55% is observed. This variability in the effectiveness of the medication may be influenced by genetic factors such as polymorphisms in the genes involved in the pathogenesis of MS. Therefore, this review assesses the impact of genetic variants on the response to GA therapy in patients diagnosed with MS. The results suggest that a relationship exists between the effectiveness of the treatment with GA and the presence of polymorphisms in the following genes: CD86, CLEC16A, CTSS, EOMES, MBP, FAS, TRBC1, IL1R1, IL12RB2, IL22RA2, PTPRT, PVT1, ALOX5AP, MAGI2, ZAK, RFPL3, UVRAG, SLC1A4, and HLA-DRB1*1501. Consequently, the identification of polymorphisms in these genes can be used in the future as a predictive marker of the response to GA treatment in patients diagnosed with MS. Nevertheless, there is a lack of evidence for this and more validation studies need to be conducted to apply this information to clinical practice.
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Affiliation(s)
- María José Zarzuelo-Romero
- Department of Pharmacy and Pharmaceutical Technology, Faculty of Pharmacy, University of Granada, 18001 Granada, Spain;
| | - Cristina Pérez-Ramírez
- Center of Biomedical Research, Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Avda. del Conocimiento s/n., 18016 Armilla, Granada, Spain;
- Pharmacogenetics Unit, Pharmacy Service, Virgen de las Nieves University Hospital, 18012 Granada, Spain; (Y.C.); (M.I.C.-C.); (L.M.M.-I.); (A.J.-M.)
- Correspondence:
| | - Yasmín Cura
- Pharmacogenetics Unit, Pharmacy Service, Virgen de las Nieves University Hospital, 18012 Granada, Spain; (Y.C.); (M.I.C.-C.); (L.M.M.-I.); (A.J.-M.)
| | - María Isabel Carrasco-Campos
- Pharmacogenetics Unit, Pharmacy Service, Virgen de las Nieves University Hospital, 18012 Granada, Spain; (Y.C.); (M.I.C.-C.); (L.M.M.-I.); (A.J.-M.)
| | - Luciana María Marangoni-Iglecias
- Pharmacogenetics Unit, Pharmacy Service, Virgen de las Nieves University Hospital, 18012 Granada, Spain; (Y.C.); (M.I.C.-C.); (L.M.M.-I.); (A.J.-M.)
| | - María Carmen Ramírez-Tortosa
- Center of Biomedical Research, Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Avda. del Conocimiento s/n., 18016 Armilla, Granada, Spain;
| | - Alberto Jiménez-Morales
- Pharmacogenetics Unit, Pharmacy Service, Virgen de las Nieves University Hospital, 18012 Granada, Spain; (Y.C.); (M.I.C.-C.); (L.M.M.-I.); (A.J.-M.)
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9
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Eriksson AM, Leikfoss IS, Abrahamsen G, Sundvold V, Isom MM, Keshari PK, Rognes T, Landsverk OJB, Bos SD, Harbo HF, Spurkland A, Berge T. Exploring the role of the multiple sclerosis susceptibility gene CLEC16A in T cells. Scand J Immunol 2021; 94:e13050. [PMID: 34643957 DOI: 10.1111/sji.13050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
C-type lectin-like domain family 16 member A (CLEC16A) is associated with autoimmune disorders, including multiple sclerosis (MS), but its functional relevance is not completely understood. CLEC16A is expressed in several immune cells, where it affects autophagic processes and receptor expression. Recently, we reported that the risk genotype of an MS-associated single nucleotide polymorphism in CLEC16A intron 19 is associated with higher expression of CLEC16A in CD4+ T cells. Here, we show that CLEC16A expression is induced in CD4+ T cells upon T cell activation. By the use of imaging flow cytometry and confocal microscopy, we demonstrate that CLEC16A is located in Rab4a-positive recycling endosomes in Jurkat TAg T cells. CLEC16A knock-down in Jurkat cells resulted in lower cell surface expression of the T cell receptor, however, this did not have a major impact on T cell activation response in vitro in Jurkat nor in human, primary CD4+ T cells.
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Affiliation(s)
- Anna M Eriksson
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingvild Sørum Leikfoss
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Neuroscience Research Unit, Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
| | - Greger Abrahamsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Vibeke Sundvold
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Pankaj K Keshari
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Steffan D Bos
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anne Spurkland
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Tone Berge
- Neuroscience Research Unit, Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway.,Department of Mechanical, Electronic and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
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10
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Armitage LH, Stimpson SE, Santostefano KE, Sui L, Ogundare S, Newby BN, Castro-Gutierrez R, Huber MK, Taylor JP, Sharma P, Radichev IA, Perry DJ, Fredette NC, Savinov AY, Wallet MA, Terada N, Brusko TM, Russ HA, Chen J, Egli D, Mathews CE. Use of Induced Pluripotent Stem Cells to Build Isogenic Systems and Investigate Type 1 Diabetes. Front Endocrinol (Lausanne) 2021; 12:737276. [PMID: 34858326 PMCID: PMC8630743 DOI: 10.3389/fendo.2021.737276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/05/2021] [Indexed: 11/13/2022] Open
Abstract
Type 1 diabetes (T1D) is a disease that arises due to complex immunogenetic mechanisms. Key cell-cell interactions involved in the pathogenesis of T1D are activation of autoreactive T cells by dendritic cells (DC), migration of T cells across endothelial cells (EC) lining capillary walls into the islets of Langerhans, interaction of T cells with macrophages in the islets, and killing of β-cells by autoreactive CD8+ T cells. Overall, pathogenic cell-cell interactions are likely regulated by the individual's collection of genetic T1D-risk variants. To accurately model the role of genetics, it is essential to build systems to interrogate single candidate genes in isolation during the interactions of cells that are essential for disease development. However, obtaining single-donor matched cells relevant to T1D is a challenge. Sourcing these genetic variants from human induced pluripotent stem cells (iPSC) avoids this limitation. Herein, we have differentiated iPSC from one donor into DC, macrophages, EC, and β-cells. Additionally, we also engineered T cell avatars from the same donor to provide an in vitro platform to study genetic influences on these critical cellular interactions. This proof of concept demonstrates the ability to derive an isogenic system from a single donor to study these relevant cell-cell interactions. Our system constitutes an interdisciplinary approach with a controlled environment that provides a proof-of-concept for future studies to determine the role of disease alleles (e.g. IFIH1, PTPN22, SH2B3, TYK2) in regulating cell-cell interactions and cell-specific contributions to the pathogenesis of T1D.
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Affiliation(s)
- Lucas H. Armitage
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Scott E. Stimpson
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Katherine E. Santostefano
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
- Century Therapeutics, iPSC Biology, Philadelphia, PA, United States
| | - Lina Sui
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, United States
| | - Similoluwa Ogundare
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Brittney N. Newby
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Roberto Castro-Gutierrez
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Mollie K. Huber
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Jared P. Taylor
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Prerana Sharma
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Ilian A. Radichev
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Daniel J. Perry
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Natalie C. Fredette
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Alexei Y. Savinov
- Children’s Health Research Center, Sanford Research, Sioux Falls, SD, United States
| | - Mark A. Wallet
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
- Century Therapeutics, Immunology, Philadelphia, PA, United States
| | - Naohiro Terada
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
| | - Todd M. Brusko
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Holger A. Russ
- Barbara Davis Center for Diabetes, University of Colorado School of Medicine, Aurora, CO, United States
| | - Jing Chen
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
| | - Dieter Egli
- Department of Pediatrics, Naomi Berrie Diabetes Center, Columbia Stem Cell Initiative, Columbia University, New York, NY, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, United States
- University of Florida Diabetes Institute, University of Florida, Gainesville, FL, United States
- Center for Cellular Reprogramming, College of Medicine, University of Florida, Gainesville, FL, United States
- *Correspondence: Clayton E. Mathews,
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11
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Carlo SE, Martinez-Baladejo MT, Santiago-Cornier A, Arciniegas-Medina N. 9q34 & 16p13 chromosome duplications in autism. AME Case Rep 2020; 4:17. [PMID: 32793859 DOI: 10.21037/acr.2020.03.07] [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: 06/03/2019] [Accepted: 02/28/2020] [Indexed: 11/06/2022]
Abstract
Epigenetic mechanisms, genetic factors, and environment influence the diversity of phenotypes developed in various diseases. Duplications in several chromosomes are well characterized in the scientific literature, but partial duplications, in some cases, present with milder forms of a disease and are yet to be understood. Fortunately, the identification of genetic diseases has now become more feasible due to several cytogenetic techniques such as microarray analysis and karyotyping. With these tools, together with other laboratory results and clinical examination, we are able to report the first case in the medical literature of double partial trisomy of chromosome 9q34 and 16p13.
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Affiliation(s)
- Simon E Carlo
- Department of Biochemistry, Ponce Health Sciences University, Ponce.,Department of Medicine, Ponce Health Sciences University, Ponce.,SER de Puerto Rico, Ponce.,Mayagüez Medical Center, Mayaguez, Ponce
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12
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Abstract
PURPOSE OF REVIEW To provide an updated summary of discoveries made to date resulting from genome-wide association study (GWAS) and sequencing studies, and to discuss the latest loci added to the growing repertoire of genetic signals predisposing to type 1 diabetes (T1D). RECENT FINDINGS Genetic studies have identified over 60 loci associated with T1D susceptibility. GWAS alone does not specifically inform on underlying mechanisms, but in combination with other sequencing and omics-data, advances are being made in our understanding of T1D genetic etiology and pathogenesis. Current knowledge indicates that genetic variation operating in both pancreatic β cells and in immune cells is central in mediating T1D risk. One of the main challenges is to determine how these recently discovered GWAS-implicated variants affect the expression and function of gene products. Once we understand the mechanism of action for disease-causing variants, we will be well placed to apply targeted genomic approaches to impede the premature activation of the immune system in an effort to ultimately prevent the onset of T1D.
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Affiliation(s)
- Marina Bakay
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Suite 1216B, Philadelphia, PA, 19104-4318, USA
| | - Rahul Pandey
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Suite 1216B, Philadelphia, PA, 19104-4318, USA
| | - Struan F A Grant
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Suite 1216B, Philadelphia, PA, 19104-4318, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Spatial and Functional Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- The Center for Applied Genomics, Division of Human Genetics, The Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Suite 1216B, Philadelphia, PA, 19104-4318, USA.
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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13
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Dos Santos RS, Marroqui L, Velayos T, Olazagoitia-Garmendia A, Jauregi-Miguel A, Castellanos-Rubio A, Eizirik DL, Castaño L, Santin I. DEXI, a candidate gene for type 1 diabetes, modulates rat and human pancreatic beta cell inflammation via regulation of the type I IFN/STAT signalling pathway. Diabetologia 2019; 62:459-472. [PMID: 30478640 DOI: 10.1007/s00125-018-4782-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/29/2018] [Indexed: 01/09/2023]
Abstract
AIMS/HYPOTHESIS The initial stages of type 1 diabetes are characterised by an aberrant islet inflammation that is in part regulated by the interaction between type 1 diabetes susceptibility genes and environmental factors. Chromosome 16p13 is associated with type 1 diabetes and CLEC16A is thought to be the aetiological gene in the region. Recent gene expression analysis has, however, indicated that SNPs in CLEC16A modulate the expression of a neighbouring gene with unknown function named DEXI, encoding dexamethasone-induced protein (DEXI). We therefore evaluated the role of DEXI in beta cell responses to 'danger signals' and determined the mechanisms involved. METHODS Functional studies based on silencing or overexpression of DEXI were performed in rat and human pancreatic beta cells. Beta cell inflammation and apoptosis, driven by a synthetic viral double-stranded RNA, were evaluated by real-time PCR, western blotting and luciferase assays. RESULTS DEXI-silenced beta cells exposed to a synthetic double-stranded RNA (polyinosinic:polycytidylic acid [PIC], a by-product of viral replication) showed reduced activation of signal transducer and activator of transcription (STAT) 1 and lower production of proinflammatory chemokines that was preceded by a reduction in IFNβ levels. Exposure to PIC increased chromatin-bound DEXI and IFNβ promoter activity. This effect on IFNβ promoter was inhibited in DEXI-silenced beta cells, suggesting that DEXI is implicated in the regulation of IFNβ transcription. In a mirror image of knockdown experiments, DEXI overexpression led to increased levels of STAT1 and proinflammatory chemokines. CONCLUSIONS/INTERPRETATION These observations support DEXI as the aetiological gene in the type 1 diabetes-associated 16p13 genomic region, and provide the first indication of a link between this candidate gene and the regulation of local antiviral immune responses in beta cells. Moreover, our results provide initial information on the function of DEXI.
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Affiliation(s)
- Reinaldo S Dos Santos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Instituto de Biología Molecular y Celular (IBMC), and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Laura Marroqui
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Instituto de Biología Molecular y Celular (IBMC), and Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universitas Miguel Hernández, Elche, Spain
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
| | - Teresa Velayos
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pediatrics, University of the Basque Country, Leioa, Spain
| | - Ane Olazagoitia-Garmendia
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, Leioa, Spain
| | - Amaia Jauregi-Miguel
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, Leioa, Spain
| | - Ainara Castellanos-Rubio
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Genetics, Physical Anthropology and Animal Fisiology, University of the Basque Country, Leioa, Spain
| | - Decio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Luis Castaño
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Pediatrics, University of the Basque Country, Leioa, Spain
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Izortze Santin
- CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
- Biocruces Bizkaia Health Research Institute, Barakaldo, Spain.
- CIBER de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Biochemistry and Molecular Biology, University of the Basque Country, Barrio Sarriena, S/N, 48940, Leioa, Bizkaia, Spain.
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14
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Kozin MS, Kulakova OG, Kiselev IS, Balanovsky OP, Boyko AN, Favorova OO. Variants of Mitochondrial Genome and Risk of Multiple Sclerosis Development in Russians. Acta Naturae 2018; 10:79-86. [PMID: 30713765 PMCID: PMC6351038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Indexed: 11/02/2022] Open
Abstract
For the first time in the history of ethnic Russians, an association analysis the development of multiple sclerosis (MS) was performed for the mitochondrial haplogroups H, J, K, and U, as well as for the individual mitochondrial DNA (mtDNA) polymorphisms discriminating these haplogroups (m.1719G > A, m. 7028C > T, m.9055G > A, m.10398A > G, m.12308A > G). A total of 283 unrelated patients with the relapsing-remitting form of MS and 290 healthy controls were enrolled in the study. Association of haplogroup J with MS was observed (P = 0.0055, OR = 2.00 [95% CI 1.21-3.41]). After gender stratification, the association remained significant in women (P = 0.0083, OR = 2.20 [95% CI 1.19-4.03]). A multilocus analysis of the association between combinations of mtDNA haplogroups with variants of 38 nuclear immune-related genes and MS risk was carried out. MS-associated biallelic combinations of haplogroup J with the alleles CCL5 rs2107538*A, PVT1 rs2114358*G, TNFSF14 rs1077667*C, and IL4 rs2243250*C, which were not associated with MS individually, were identified. For the combination of haplogroup J and the CCL5*A allele (P = 0.00043, OR = 5.47 [95% CI 1.85-16.15]), a epistatic (synergistic) interaction between the components was established using two statistical criteria: the PFLINT value in the Fisher-like interaction numeric test and the synergy factor, SF (PFLINT = 0.025, SF = 4.32 [95% CI 1.20-15.60]). The combination of haplogroup J and the PVT1*G allele is characterized by PFLINT = 0.084; SF = 3.05 [95% CI 1.00-9.31] and can also be epistatic. Thus, interaction between nuclear and mitochondrial genome components in the risk of developing MS was demonstrated for the first time.
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Affiliation(s)
- M. S. Kozin
- Pirogov Russian National Research Medical University, Ostrovitjanova Str. 1, Moscow, 117997, Russia
- National Medical Research Center of Cardiology, 3rd Cherepkovskaya Str., 15a, Moscow, 121552 , Russia
| | - O. G. Kulakova
- Pirogov Russian National Research Medical University, Ostrovitjanova Str. 1, Moscow, 117997, Russia
- National Medical Research Center of Cardiology, 3rd Cherepkovskaya Str., 15a, Moscow, 121552 , Russia
| | - I. S. Kiselev
- Pirogov Russian National Research Medical University, Ostrovitjanova Str. 1, Moscow, 117997, Russia
- National Medical Research Center of Cardiology, 3rd Cherepkovskaya Str., 15a, Moscow, 121552 , Russia
| | - O. P. Balanovsky
- Biobank of north Eurasia, Kotlyakovskaya Str., 3, Moscow, 115201, Russia
| | - A. N. Boyko
- Pirogov Russian National Research Medical University, Ostrovitjanova Str. 1, Moscow, 117997, Russia
| | - O. O. Favorova
- Pirogov Russian National Research Medical University, Ostrovitjanova Str. 1, Moscow, 117997, Russia
- National Medical Research Center of Cardiology, 3rd Cherepkovskaya Str., 15a, Moscow, 121552 , Russia
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15
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Genetic variants at the 16p13 locus confer risk for eosinophilic esophagitis. Genes Immun 2018; 20:281-292. [PMID: 29904099 PMCID: PMC6286696 DOI: 10.1038/s41435-018-0034-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/06/2018] [Accepted: 04/11/2018] [Indexed: 02/08/2023]
Abstract
Eosinophilic esophagitis (EoE) is a chronic inflammatory disease of the esophagus triggered by immune hypersensitivity to food. Herein, we tested whether genetic risk factors for known, non-allergic, immune-mediated diseases, particularly those involving autoimmunity, were associated with EoE risk. We used the high-density Immunochip platform, encoding 200,000 genetic variants for major auto-immune disease. Accordingly, 1214 subjects with EoE of European ancestry and 3734 population controls were genotyped and assessed using data directly generated or imputed from the previously published GWAS. We found lack of association of EoE with the genetic variants in the major histocompatibility complex (MHC) class I, II, and III genes and nearly all other loci using a highly powered study design with dense genotyping throughout the locus. Importantly, we identified an EoE risk locus at 16p13 with genome-wide significance (Pcombined=2.05 × 10−9, odds ratio = 0.76−0.81). This region is known to encode for the genes CLEC16A, DEXI, and CIITI, which are expressed in immune cells and esophageal epithelial cells. Suggestive EoE risk were also seen 5q23 (intergenic) and 7p15 (JAZF1). Overall, we have identified an additional EoE risk locus at 16p13 and highlight a shared and unique genetic etiology of EoE with a spectrum of immune-associated diseases.
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16
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Popova EV, Kiselev IS, Boyko AN, Sivertseva SA, Malkova NA, Korobko DS, Spirin NN, Kasatkin DS, Karaeva AV, Turova EL, Spirina NN, Volkova LI, Baulina NM, Bashinskaya VV, Kulakova OG, Favorova OO. [Polymorphic variants of the immune response genes as risk factors for primary progressive multiple sclerosis]. Zh Nevrol Psikhiatr Im S S Korsakova 2017; 117:14-21. [PMID: 28617357 DOI: 10.17116/jnevro20171172214-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
AIM To analyze the involvement of immune response genes in the pathogenesis of primary progressive multiple sclerosis (PPMS). MATERIAL AND METHODS This multicenter study included 111 patients with PPMS from the Russian ethnic group. The association of PPMS with genes of immune system was analyzed by the study of polymorphic variants of genes of cytokines and genes of antigen-presenting cells. RESULTS AND CONCLUSION The genotypes of IL-4 (rs2243250)*C/C and CLEC16A (rs6498169)*G/G were associated with PPMS in Russians. The association between the HLA-DRB1*15 and PPMS found out in other populations was confirmed in Russians.
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Affiliation(s)
- E V Popova
- Interregional Department of Multiple Sclerosis at Moscow Clinical Hospital #24, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - I S Kiselev
- Cardiology research and clinical complex, Moscow, Russia; Tumen Regional Center of Multiple Sclerosis, Tumen, Russia
| | - A N Boyko
- Interregional Department of Multiple Sclerosis at Moscow Clinical Hospital #24, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
| | - S A Sivertseva
- Novosibirsk Regional Center of Multiple Sclerosis and other Autoimmune Diseases 'GNOKB', Novosibirsk, Russia
| | - N A Malkova
- State Medical University, Novosibirsk, Russia
| | - D S Korobko
- State Medical University, Novosibirsk, Russia
| | - N N Spirin
- Yaroslavl State Medical University, Yaroslavl, Russia; Sverdlovsk Regional Clinical Hospital #1, Yekaterinburg, Russia
| | - D S Kasatkin
- Yaroslavl State Medical University, Yaroslavl, Russia; Sverdlovsk Regional Clinical Hospital #1, Yekaterinburg, Russia
| | - A V Karaeva
- Sverdlovsk Regional Clinical Hospital #1, Yekaterinburg, Russia
| | - E L Turova
- Sverdlovsk Regional Clinical Hospital #1, Yekaterinburg, Russia
| | - N N Spirina
- Yaroslavl State Medical University, Yaroslavl, Russia; Sverdlovsk Regional Clinical Hospital #1, Yekaterinburg, Russia
| | - L I Volkova
- Sverdlovsk Regional Clinical Hospital #1, Yekaterinburg, Russia
| | - N M Baulina
- Cardiology research and clinical complex, Moscow, Russia; Tumen Regional Center of Multiple Sclerosis, Tumen, Russia
| | - V V Bashinskaya
- Cardiology research and clinical complex, Moscow, Russia; Tumen Regional Center of Multiple Sclerosis, Tumen, Russia
| | - O G Kulakova
- Cardiology research and clinical complex, Moscow, Russia; Tumen Regional Center of Multiple Sclerosis, Tumen, Russia
| | - O O Favorova
- Cardiology research and clinical complex, Moscow, Russia; Tumen Regional Center of Multiple Sclerosis, Tumen, Russia
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17
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Bos SD, Berge T, Celius EG, Harbo HF. From genetic associations to functional studies in multiple sclerosis. Eur J Neurol 2016; 23:847-53. [PMID: 26948534 DOI: 10.1111/ene.12981] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/18/2016] [Indexed: 12/13/2022]
Abstract
Genetic screens steadily reveal more loci that show robust associations to complex human diseases, including multiple sclerosis (MS). Although some of the identified genetic variants are easily interpreted into a biological function, most of the genetic associations are frequently challenging to interpret. Underlying these difficulties is the fact that chip-based assays typically detect single nucleotide polymorphisms (SNPs) representative of a stretch of DNA containing many genomic variants in linkage disequilibrium. Furthermore, a large proportion of the SNPs with strongest association to MS are located in regions of the DNA that do not directly code for proteins. Here we discuss challenges faced by MS researchers to follow up the large-scale genetic screens that have been published over the past years in search of functional consequences of the identified MS-associated SNPs. We discuss experimental design, tools and methods that may provide the much-needed biological insights in both disease etiology and disease manifestations.
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Affiliation(s)
- S D Bos
- Institute of Clinical Medicine, University of Oslo, Oslo.,Department of Neurology, Oslo University Hospital, Oslo
| | - T Berge
- Institute of Clinical Medicine, University of Oslo, Oslo.,Department of Neurology, Oslo University Hospital, Oslo
| | - E G Celius
- Department of Neurology, Oslo University Hospital, Oslo.,Institute of Health and Society, University of Oslo, Oslo, Norway
| | - H F Harbo
- Institute of Clinical Medicine, University of Oslo, Oslo.,Department of Neurology, Oslo University Hospital, Oslo
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18
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Multiple Sclerosis Risk Allele in CLEC16A Acts as an Expression Quantitative Trait Locus for CLEC16A and SOCS1 in CD4+ T Cells. PLoS One 2015. [PMID: 26203907 PMCID: PMC4512731 DOI: 10.1371/journal.pone.0132957] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
For multiple sclerosis, genome wide association studies and follow up studies have identified susceptibility single nucleotide polymorphisms located in or near CLEC16A at chromosome 16p13.13, encompassing among others CIITA, DEXI and SOCS1 in addition to CLEC16A. These genetic variants are located in intronic or intergenic regions and display strong linkage disequilibrium with each other, complicating the understanding of their functional contribution and the identification of the direct causal variant(s). Previous studies have shown that multiple sclerosis-associated risk variants in CLEC16A act as expression quantitative trait loci for CLEC16A itself in human pancreatic β-cells, for DEXI and SOCS1 in thymic tissue samples, and for DEXI in monocytes and lymphoblastoid cell lines. Since T cells are major players in multiple sclerosis pathogenesis, we have performed expression analyses of the CIITA-DEXI-CLEC16A-SOCS1 gene cluster in CD4+ and CD8+ T cells isolated from multiple sclerosis patients and healthy controls. We observed a higher expression of SOCS1 and CLEC16A in CD4+ T cells in samples homozygous for the risk allele of CLEC16A rs12927355. Pair-wise linear regression analysis revealed high correlation in gene expression in peripheral T cells of CIITA, DEXI, CLEC16A and SOCS1. Our data imply a possible regulatory role for the multiple sclerosis-associated rs12927355 in CLEC16A.
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19
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Paradela ER, Alves-Leon SV, Figueiredo ALS, Pereira VCSR, Malfetano F, Mansur LF, Scherpenhuijzen S, Agostinho LA, Rocha CF, Rueda-Lopes F, Gasparetto E, Paiva CLA. The CIITA genetic polymorphism rs4774*C in combination with the HLA-DRB1*15:01 allele as a putative susceptibility factor to multiple sclerosis in Brazilian females. ARQUIVOS DE NEURO-PSIQUIATRIA 2015; 73:283-8. [PMID: 25992516 DOI: 10.1590/0004-282x20150012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 12/09/2014] [Indexed: 11/21/2022]
Abstract
The objective of this study was to investigate the association between the HLA alleles at the DQA1, DQB1 and DRB1 loci, the CIITA genetic polymorphisms -168A/G and +1614G/C, and susceptibility to multiple sclerosis (MS) in a sample from Rio de Janeiro State, Brazil. Furthermore, we wished to determine whether any of these associations might be more significant in women compared with men. DNA samples from 52 relapsing-remitting MS (RRMS) patients and 126 healthy controls matched for sex and age were analyzed. We identified a significant HLA-DRB1*15:01-MS association that was female-specific (Odds Ratio (OR) = 4.78; p = 0.001). Furthermore, we observed that the +1614G/C mutation in combination with the HLA-DRB1*15:01 allele increased susceptibility to MS in females (OR = 4.55; p = 0.01). Together, these findings highlight the polygenic nature of MS.
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Affiliation(s)
- Eduardo R Paradela
- Departamento de Neurologia, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Soniza V Alves-Leon
- Departamento de Neurologia, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - André L S Figueiredo
- Departamento de Neurologia, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Valéria C S R Pereira
- Centro de Referência em Esclerose Múltipla e outras Doenças Inflamatórias Desmielinizantes do Sistema Nervoso Central,, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fabíola Malfetano
- Centro de Referência em Esclerose Múltipla e outras Doenças Inflamatórias Desmielinizantes do Sistema Nervoso Central,, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Letícia F Mansur
- Centro de Referência em Esclerose Múltipla e outras Doenças Inflamatórias Desmielinizantes do Sistema Nervoso Central,, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Simone Scherpenhuijzen
- Centro de Referência em Esclerose Múltipla e outras Doenças Inflamatórias Desmielinizantes do Sistema Nervoso Central,, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Luciana A Agostinho
- Departamento de Neurologia, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Catielly F Rocha
- Departamento de Neurologia, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernanda Rueda-Lopes
- Centro de Referência em Esclerose Múltipla e outras Doenças Inflamatórias Desmielinizantes do Sistema Nervoso Central,, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Emerson Gasparetto
- Centro de Referência em Esclerose Múltipla e outras Doenças Inflamatórias Desmielinizantes do Sistema Nervoso Central,, Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carmen L A Paiva
- Departamento de Neurologia, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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20
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Benveniste EN, Liu Y, McFarland BC, Qin H. Involvement of the janus kinase/signal transducer and activator of transcription signaling pathway in multiple sclerosis and the animal model of experimental autoimmune encephalomyelitis. J Interferon Cytokine Res 2015; 34:577-88. [PMID: 25084174 DOI: 10.1089/jir.2014.0012] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Multiple sclerosis (MS) and its animal model of experimental autoimmune encephalomyelitis (EAE) are characterized by focal inflammatory infiltrates into the central nervous system, demyelinating lesions, axonal damage, and abundant production of cytokines that activate immune cells and damage neurons and oligodendrocytes, including interleukin-12 (IL-12), IL-6, IL-17, IL-21, IL-23, granulocyte macrophage-colony stimulating factor, and interferon-gamma. The Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) signaling pathway mediates the biological activities of these cytokines and is essential for the development and regulation of immune responses. Dysregulation of the JAK/STAT pathway contributes to numerous autoimmune diseases, including MS/EAE. The JAK/STAT pathway is aberrantly activated in MS/EAE because of excessive production of cytokines, loss of expression of negative regulators such as suppressors of cytokine signaling proteins, and significant enrichment of genes encoding components of the JAK/STAT pathway, including STAT3. Specific JAK/STAT inhibitors have been used in numerous preclinical models of MS and demonstrate beneficial effects on the clinical course of disease and attenuation of innate and adaptive immune responses. In addition, other drugs such as statins, glatiramer acetate, laquinimod, and fumarates have beneficial effects that involve inhibition of the JAK/STAT pathway. We conclude by discussing the feasibility of the JAK/STAT pathway as a target for neuroinflammatory diseases.
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Affiliation(s)
- Etty N Benveniste
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham , Birmingham, Alabama
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21
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van Luijn MM, Kreft KL, Jongsma ML, Mes SW, Wierenga-Wolf AF, van Meurs M, Melief MJ, der Kant RV, Janssen L, Janssen H, Tan R, Priatel JJ, Neefjes J, Laman JD, Hintzen RQ. Multiple sclerosis-associated CLEC16A controls HLA class II expression via late endosome biogenesis. Brain 2015; 138:1531-47. [PMID: 25823473 DOI: 10.1093/brain/awv080] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 01/26/2015] [Indexed: 01/20/2023] Open
Abstract
C-type lectins are key players in immune regulation by driving distinct functions of antigen-presenting cells. The C-type lectin CLEC16A gene is located at 16p13, a susceptibility locus for several autoimmune diseases, including multiple sclerosis. However, the function of this gene and its potential contribution to these diseases in humans are poorly understood. In this study, we found a strong upregulation of CLEC16A expression in the white matter of multiple sclerosis patients (n = 14) compared to non-demented controls (n = 11), mainly in perivascular leukocyte infiltrates. Moreover, CLEC16A levels were significantly enhanced in peripheral blood mononuclear cells of multiple sclerosis patients (n = 69) versus healthy controls (n = 46). In peripheral blood mononuclear cells, CLEC16A was most abundant in monocyte-derived dendritic cells, in which it strongly co-localized with human leukocyte antigen class II. Treatment of these professional antigen-presenting cells with vitamin D, a key protective environmental factor in multiple sclerosis, downmodulated CLEC16A in parallel with human leukocyte antigen class II. Knockdown of CLEC16A in distinct types of model and primary antigen-presenting cells resulted in severely impaired cytoplasmic distribution and formation of human leucocyte antigen class II-positive late endosomes, as determined by immunofluorescence and electron microscopy. Mechanistically, CLEC16A participated in the molecular machinery of human leukocyte antigen class II-positive late endosome formation and trafficking to perinuclear regions, involving the dynein motor complex. By performing co-immunoprecipitations, we found that CLEC16A directly binds to two critical members of this complex, RILP and the HOPS complex. CLEC16A silencing in antigen-presenting cells disturbed RILP-mediated recruitment of human leukocyte antigen class II-positive late endosomes to perinuclear regions. Together, we identify CLEC16A as a pivotal gene in multiple sclerosis that serves as a direct regulator of the human leukocyte antigen class II pathway in antigen-presenting cells. These findings are a first step in coupling multiple sclerosis-associated genes to the regulation of the strongest genetic factor in multiple sclerosis, human leukocyte antigen class II.
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Affiliation(s)
- Marvin M van Luijn
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Karim L Kreft
- 2 Department of Neurology and MS Center ErasMS, Erasmus MC, University Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
| | - Marlieke L Jongsma
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Steven W Mes
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Annet F Wierenga-Wolf
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marjan van Meurs
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Marie-José Melief
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Rik van der Kant
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Lennert Janssen
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Hans Janssen
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Rusung Tan
- 4 Department of Pathology, Sidra Medical and Research Center, Doha, Qatar 5 BC Children's Hospital and Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - John J Priatel
- 5 BC Children's Hospital and Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada
| | - Jacques Neefjes
- 3 Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Jon D Laman
- 1 Department of Immunology and MS Center ErasMS, Erasmus MC, University Medical Center, Wytemaweg 80, 3015 CN Rotterdam, The Netherlands
| | - Rogier Q Hintzen
- 2 Department of Neurology and MS Center ErasMS, Erasmus MC, University Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
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22
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Bashinskaya VV, Kulakova OG, Kiselev IS, Baulina NM, Favorov AV, Boyko AN, Tsareva EY, Favorova OO. GWAS-identified multiple sclerosis risk loci involved in immune response: validation in Russians. J Neuroimmunol 2015; 282:85-91. [PMID: 25903733 DOI: 10.1016/j.jneuroim.2015.03.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/15/2015] [Accepted: 03/16/2015] [Indexed: 01/01/2023]
Abstract
Multiple sclerosis (MS) is a chronic neuro-inflammatory disease of complex etiology. The results of GWAS, a high-throughput method to discover genetic architecture of MS, require replication in independent ethnic groups. We performed a replication study of nine GWAS-identified SNPs in immune response in Russians. Associations of CLEC16A and IL2RA with MS were validated. Besides, we observed the associations of CLEC16A and IRF8 in women, and IL7RA and CD58 in men. With multi-locus association analysis two protective biallelic combinations: (TNFRSF1A*T+CLEC16A*A) and (TNFRSF1A*T+IRF8*A) were identified in women. Associations of CLEC16A*G/G and both biallelic combinations in women with MS survived the permutation test.
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Affiliation(s)
- V V Bashinskaya
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia.
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia
| | - I S Kiselev
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
| | - N M Baulina
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
| | - A V Favorov
- Johns Hopkins School of Medicine, 550 North Broadway, Baltimore, MD 21205, USA; Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, 119333 Moscow, Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
| | - E Yu Tsareva
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia
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23
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Lopez de Lapuente A, Pinto-Medel MJ, Astobiza I, Alloza I, Comabella M, Malhotra S, Montalban X, Zettl UK, Rodríguez-Antigüedad A, Fernández O, Vandenbroeck K. Cell-specific effects in different immune subsets associated with SOCS1 genotypes in multiple sclerosis. Mult Scler 2015; 21:1498-512. [PMID: 25623250 DOI: 10.1177/1352458514566418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 11/19/2014] [Indexed: 11/15/2022]
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) near SOCS1 are associated with multiple sclerosis (MS), but the most important SNPs in the area and mechanisms by which they influence the disease are unknown. METHODS A haplotype-tagging association study was performed covering 60.5kbp around SOCS1, and the index SNP was validated in a total of 2292 individuals. mRNA expression of SOCS1 and nearby genes was measured in MS patients with different disease courses and healthy controls. SOCS1 protein expression was studied by flow cytometry in a separate cohort of patients and controls. Differentiation and maturation of monocyte-derived dendritic cells (moDCs) were also studied. RESULTS One SNP, rs423674, reached genome-wide significance. No genotype-specific mRNA expression differences were seen, but, by flow cytometry, significant interactions were observed between genotypes for rs423674 and disease activity (relapse or remission) in B cells and regulatory T cells. Furthermore, homozygotes for the risk allele (GG) showed higher levels of CD1a and CD86 than carriers of the protective allele (GT) in immature moDCs and a greater increase of HLA-DR+ cell percentage than GT heterozygotes upon maturation. CONCLUSIONS rs423674, or its genetic proxies, may influence MS risk by modulating SOCS1 expression in a cell-specific manner and by influencing dendritic cell function.
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Affiliation(s)
- Aitzkoa Lopez de Lapuente
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/Achucarro Basque Center for Neuroscience, Spain
| | - María Jesús Pinto-Medel
- Research Laboratory, Clinical Neurosciences Institute, Hospital Regional Universitario Carlos Haya and Fundación IMABIS
| | - Ianire Astobiza
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/Achucarro Basque Center for Neuroscience, Spain
| | - Iraide Alloza
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/ Achucarro Basque Center for Neuroscience, Spain/ IKERBASQUE, Basque Foundation for Science, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d'Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d'Hebron (VHIR), Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Spain
| | - Uwe K Zettl
- University of Rostock, Department of Neurology, Germany
| | | | - Oscar Fernández
- Research Laboratory, Clinical Neurosciences Institute, Hospital Regional Universitario Carlos Haya and Fundación IMABIS
| | - Koen Vandenbroeck
- Neurogenomiks Group, Universidad del País Vasco (UPV/EHU), Spain/ Achucarro Basque Center for Neuroscience, Spain/ IKERBASQUE, Basque Foundation for Science, Spain
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24
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Duluc D, Banchereau R, Gannevat J, Thompson-Snipes L, Blanck JP, Zurawski S, Zurawski G, Hong S, Rossello-Urgell J, Pascual V, Baldwin N, Stecher J, Carley M, Boreham M, Oh S. Transcriptional fingerprints of antigen-presenting cell subsets in the human vaginal mucosa and skin reflect tissue-specific immune microenvironments. Genome Med 2014; 6:98. [PMID: 25520755 PMCID: PMC4268898 DOI: 10.1186/s13073-014-0098-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 10/28/2014] [Indexed: 12/30/2022] Open
Abstract
Background Dendritic cells localize throughout the body, where they can sense
and capture invading pathogens to induce protective immunity. Hence, harnessing
the biology of tissue-resident dendritic cells is fundamental for the rational
design of vaccines against pathogens. Methods Herein, we characterized the transcriptomes of four
antigen-presenting cell subsets from the human vagina (Langerhans cells,
CD14- and CD14+ dendritic
cells, macrophages) by microarray, at both the transcript and network level, and
compared them to those of three skin dendritic cell subsets and blood myeloid
dendritic cells. Results We found that genomic fingerprints of antigen-presenting cells are
significantly influenced by the tissue of origin as well as by individual subsets.
Nonetheless, CD14+ populations from both vagina and
skin are geared towards innate immunity and pro-inflammatory responses, whereas
CD14- populations, particularly skin and vaginal
Langerhans cells, and vaginal CD14- dendritic cells,
display both Th2-inducing and regulatory phenotypes. We also identified new
phenotypic and functional biomarkers of vaginal antigen-presenting cell
subsets. Conclusions We provide a transcriptional database of 87 microarray samples
spanning eight antigen-presenting cell populations in the human vagina, skin and
blood. Altogether, these data provide molecular information that will further help
characterize human tissue antigen-presenting cell lineages and their functions.
Data from this study can guide the design of mucosal vaccines against sexually
transmitted pathogens. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0098-y) contains supplementary material, which is available to authorized
users.
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Affiliation(s)
- Dorothée Duluc
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Romain Banchereau
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Julien Gannevat
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | | | - Jean-Philippe Blanck
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Sandra Zurawski
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Gerard Zurawski
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Seunghee Hong
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Jose Rossello-Urgell
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Virginia Pascual
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Nicole Baldwin
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
| | - Jack Stecher
- Department of Obstetrics and Gynecology, Baylor University Medical Center, 3600 Gaston Ave, Dallas, TX 75246 USA
| | - Michael Carley
- Department of Obstetrics and Gynecology, Baylor University Medical Center, 3600 Gaston Ave, Dallas, TX 75246 USA
| | - Muriel Boreham
- Department of Obstetrics and Gynecology, Baylor University Medical Center, 3600 Gaston Ave, Dallas, TX 75246 USA
| | - SangKon Oh
- Baylor Institute for Immunology Research, 3434 Live Oak St, Dallas, TX 75204 USA
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25
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Association of the C-type lectin-like domain family-16A (CLEC16A) gene polymorphisms with acute coronary syndrome in Mexican patients. Immunol Lett 2014; 162:247-51. [PMID: 25447402 DOI: 10.1016/j.imlet.2014.10.003] [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: 07/15/2014] [Revised: 09/22/2014] [Accepted: 10/06/2014] [Indexed: 11/23/2022]
Abstract
The CLEC16A gene has an important role in the immune activation and regulation inflammatory. This gene encodes to C-type lectin domain that is involved in the recognition of DAMPS. The aim of this study was assess the CLEC16A gene polymorphisms in the risk of developing ACS in a group of patients. Four rs12708716, rs12917716, rs6498142 and rs9925481 (positions 146529 A>G, 155804 G>C, 47905 C>G and 64135 C>T, respectively) single nucleotide polymorphisms of CLEC16A gene were analyzed by TaqMan assays in a group of 452 patients with ACS and 456 healthy controls. The analysis was performed on the total group of individuals and then in groups of men and women separately. Under co-dominant model adjusted by cardiovascular risk factors the rs12708716 (146529 A>G) and rs12917716 (155804 G>C) polymorphisms were significantly associated with decrease risk of ACS in men (OR=0.16, PCo-dom=0.027 and OR=0.37, PCo-dom=0.016, respectively). In summary, our data suggests that two polymorphisms of the CLEC16A gene play an important role in the developing of ACS in men.
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26
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Gyllenberg A, Piehl F, Alfredsson L, Hillert J, Bomfim IL, Padyukov L, Orho-Melander M, Lindholm E, Landin-Olsson M, Lernmark Å, Olsson T, Kockum I. Variability in the CIITA gene interacts with HLA in multiple sclerosis. Genes Immun 2014; 15:162-7. [DOI: 10.1038/gene.2013.71] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 11/12/2013] [Accepted: 12/03/2013] [Indexed: 11/10/2022]
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27
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Bakay M, Pandey R, Hakonarson H. Genes involved in type 1 diabetes: an update. Genes (Basel) 2013; 4:499-521. [PMID: 24705215 PMCID: PMC3924830 DOI: 10.3390/genes4030499] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 08/26/2013] [Accepted: 09/05/2013] [Indexed: 01/06/2023] Open
Abstract
Type 1 Diabetes (T1D) is a chronic multifactorial disease with a strong genetic component, which, through interactions with specific environmental factors, triggers disease onset. T1D typically manifests in early to mid childhood through the autoimmune destruction of pancreatic β cells resulting in a lack of insulin production. Historically, prior to genome-wide association studies (GWAS), six loci in the genome were fully established to be associated with T1D. With the advent of high-throughput single nucleotide polymorphism (SNP) genotyping array technologies, enabling investigators to perform high-density GWAS, many additional T1D susceptibility genes have been discovered. Indeed, recent meta-analyses of multiple datasets from independent investigators have brought the tally of well-validated T1D disease genes to almost 60. In this mini-review, we address recent advances in the genetics of T1D and provide an update on the latest susceptibility loci added to the list of genes involved in the pathogenesis of T1D.
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Affiliation(s)
- Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
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28
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Swaminathan B, Cuapio A, Alloza I, Matesanz F, Alcina A, García-Barcina M, Fedetz M, Fernández Ó, Lucas M, Órpez T, Pinto-Medel MJ, Otaegui D, Olascoaga J, Urcelay E, Ortiz MA, Arroyo R, Oksenberg JR, Antigüedad A, Tolosa E, Vandenbroeck K. Fine mapping and functional analysis of the multiple sclerosis risk gene CD6. PLoS One 2013; 8:e62376. [PMID: 23638056 PMCID: PMC3634811 DOI: 10.1371/journal.pone.0062376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 03/22/2013] [Indexed: 12/18/2022] Open
Abstract
CD6 has recently been identified and validated as risk gene for multiple sclerosis (MS), based on the association of a single nucleotide polymorphism (SNP), rs17824933, located in intron 1. CD6 is a cell surface scavenger receptor involved in T-cell activation and proliferation, as well as in thymocyte differentiation. In this study, we performed a haptag SNP screen of the CD6 gene locus using a total of thirteen tagging SNPs, of which three were non-synonymous SNPs, and replicated the recently reported GWAS SNP rs650258 in a Spanish-Basque collection of 814 controls and 823 cases. Validation of the six most strongly associated SNPs was performed in an independent collection of 2265 MS patients and 2600 healthy controls. We identified association of haplotypes composed of two non-synonymous SNPs [rs11230563 (R225W) and rs2074225 (A257V)] in the 2nd SRCR domain with susceptibility to MS (Pmax(T) permutation = 1×10−4). The effect of these haplotypes on CD6 surface expression and cytokine secretion was also tested. The analysis showed significantly different CD6 expression patterns in the distinct cell subsets, i.e. – CD4+ naïve cells, P = 0.0001; CD8+ naïve cells, P<0.0001; CD4+ and CD8+ central memory cells, P = 0.01 and 0.05, respectively; and natural killer T (NKT) cells, P = 0.02; with the protective haplotype (RA) showing higher expression of CD6. However, no significant changes were observed in natural killer (NK) cells, effector memory and terminally differentiated effector memory T cells. Our findings reveal that this new MS-associated CD6 risk haplotype significantly modifies expression of CD6 on CD4+ and CD8+ T cells.
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MESH Headings
- Adult
- Antigens, CD/chemistry
- Antigens, CD/genetics
- Antigens, CD/metabolism
- Antigens, Differentiation, T-Lymphocyte/chemistry
- Antigens, Differentiation, T-Lymphocyte/genetics
- Antigens, Differentiation, T-Lymphocyte/metabolism
- CD4-Positive T-Lymphocytes/metabolism
- CD8-Positive T-Lymphocytes/metabolism
- Chromosome Mapping
- Cluster Analysis
- Cytokines/metabolism
- Female
- Gene Order
- Genetic Loci
- Genetic Predisposition to Disease
- Haplotypes
- Humans
- Linkage Disequilibrium
- Lymphocyte Activation/immunology
- Male
- Multiple Sclerosis/genetics
- Multiple Sclerosis/metabolism
- Polymorphism, Single Nucleotide
- Protein Interaction Domains and Motifs
- Spain
- White People/genetics
- Young Adult
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Affiliation(s)
- Bhairavi Swaminathan
- Neurogenomiks Laboratory, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Angélica Cuapio
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Iraide Alloza
- Neurogenomiks Laboratory, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Fuencisla Matesanz
- Instituto de Parasitología y Biomedicina “López Neyra” Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Antonio Alcina
- Instituto de Parasitología y Biomedicina “López Neyra” Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Maria Fedetz
- Instituto de Parasitología y Biomedicina “López Neyra” Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Óscar Fernández
- Department of Neurology, Institute of Clinical Neurosciences, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - Miguel Lucas
- Unidad de Esclerosis Múltiple, Hospital Virgen Macarena, Sevilla, Spain
| | - Teresa Órpez
- Research Laboratory, Institute of Clinical Neurosciences, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - Mª Jesus Pinto-Medel
- Research Laboratory, Institute of Clinical Neurosciences, Hospital Regional Universitario Carlos Haya, Málaga, Spain
| | - David Otaegui
- Área de Neurociencias, Instituto de Investigación Sanitaria Biodonostia, San Sebastián, Spain
| | - Javier Olascoaga
- Servicio de Neurología, Unidad de Esclerosis Múltiple, Hospital Donostia, San Sebastián, Spain
| | - Elena Urcelay
- Immunology Department H. Clínico S. Carlos, Instituto de Investigación Sanitaria S. Carlos (IdISSC), Madrid, Spain
| | - Miguel A. Ortiz
- Immunology Department H. Clínico S. Carlos, Instituto de Investigación Sanitaria S. Carlos (IdISSC), Madrid, Spain
| | - Rafael Arroyo
- Multiple Sclerosis Unit, Neurology Department H. Clínico S. Carlos, Instituto de Investigación Sanitaria S. Carlos (IdISSC), Madrid, Spain
| | - Jorge R. Oksenberg
- Department of Neurology, University of California San Francisco, San Francisco, California, United States of America
| | | | - Eva Tolosa
- Department of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Koen Vandenbroeck
- Neurogenomiks Laboratory, University of the Basque Country (UPV/EHU), Leioa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- * E-mail:
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Berge T, Sørum Leikfoss I, Harbo HF. From Identification to Characterization of the Multiple Sclerosis Susceptibility Gene CLEC16A. Int J Mol Sci 2013; 14:4476-97. [PMID: 23439554 PMCID: PMC3634488 DOI: 10.3390/ijms14034476] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 02/05/2013] [Accepted: 02/15/2013] [Indexed: 12/16/2022] Open
Abstract
Multiple sclerosis (MS) is an inflammatory, demyelinating disorder of the central nervous system that develops in genetically susceptible individuals, probably triggered by common environmental factors. Human leukocyte antigen (HLA) loci were early shown to confer the strongest genetic associations in MS. Now, more than 50 non-HLA MS susceptibility loci are identified, of which the majority are located in immune-regulatory genes. Single nucleotide polymorphisms (SNPs) in the C-type lectin-like domain family 16A (CLEC16A) gene were among the first non-HLA genetic variants that were confirmed to be associated with MS. Fine-mapping has indicated a primary association in MS and also other autoimmune diseases to intronic CLEC16A SNPs. Here, we review the identification of MS susceptibility variants in the CLEC16A gene region, functional studies of the CLEC16A molecule and the recent progress in understanding the implications thereof for MS development. This may serve as an example of the importance for further molecular investigation of the loci identified in genetic studies, with the aim to translate this knowledge into the clinic.
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Affiliation(s)
- Tone Berge
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo 0407, Norway; E-Mails: (I.S.L.); (H.F.H.)
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo 0317, Norway
| | - Ingvild Sørum Leikfoss
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo 0407, Norway; E-Mails: (I.S.L.); (H.F.H.)
- Department of Anatomy, Institute of Basic Medical Sciences, University of Oslo, Oslo 0317, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo 0450, Norway
| | - Hanne F. Harbo
- Department of Neurology, Oslo University Hospital, Ullevål, Oslo 0407, Norway; E-Mails: (I.S.L.); (H.F.H.)
- Institute of Clinical Medicine, University of Oslo, Oslo 0450, Norway
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30
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Toumi A, Abida O, Ben Ayed M, Masmoudi A, Turki H, Masmoudi H. Cytokine gene polymorphisms in Tunisian endemic pemphigus foliaceus: a possible role of il-4 variants. Hum Immunol 2013; 74:658-65. [PMID: 23376457 DOI: 10.1016/j.humimm.2013.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 12/19/2012] [Accepted: 01/14/2013] [Indexed: 01/17/2023]
Abstract
Polymorphism in the genes of TH2 cytokines and/or theirs receptors can influence serum cytokine levels in and the switch to the pathologic IgG4 auto-antibodies. In order to underline the role of these genes in the aethiopathogenesis of Pemphigus Foliaceus, we conduct a familial and a case control studies including 80 Tunisian patients, 147 related subjects and 160 matched healthy controls. We investigated, by PCR-RFLP technique, seven nucleotide polymorphisms: rs2243250 in promoter region of IL4 gene, rs47877948, rs3024530 and rs30246223 in the IL4R gene, rs1881457and rs205412 SNPs in IL13 gene and rs535036 in IL13RA2 gene. After Bonferroni adjustment, T allele and the TT genotype of IL4-590 were significantly increased in the PF patients group compared to healthy controls. This association was confirmed by the family study. Interestingly, the serum IL-4 levels were significantly increased in patients with the TT genotype compared to CT or CC genotypes. Interestingly, the IL4/IL13:T-A-C haplotype exhibited a significant effect on PF susceptibility. In addition, a significant gene-gene interaction between the IL4/IL4R (TACA) significantly increases in PF patients as compared to controls. These findings assess the role of the IL4/IL4R axis in the aethiopathogenesis of Tunisian endemic PF by the induction of a high transcriptional activity which could enhance the T-cell balance and inducing immunoglobulin isotype switching.
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Affiliation(s)
- Amina Toumi
- Immunology Department, Habib Bourguiba University Hospital, Sfax, Tunisia.
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31
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Leikfoss IS, Mero IL, Dahle MK, Lie BA, Harbo HF, Spurkland A, Berge T. Multiple sclerosis-associated single-nucleotide polymorphisms in CLEC16A correlate with reduced SOCS1 and DEXI expression in the thymus. Genes Immun 2013; 14:62-6. [PMID: 23151489 DOI: 10.1038/gene.2012.52] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 09/04/2012] [Accepted: 10/03/2012] [Indexed: 11/08/2022]
Abstract
Genome-wide association studies have revealed that the 16p13 chromosomal region, including CLEC16A, DEXI, CIITA and SOCS1, is associated with susceptibility to autoimmune diseases. As non-coding single-nucleotide polymorphisms (SNPs) may confer susceptibility to disease by affecting expression of nearby genes, we examined whether autoimmune-associated intronic CLEC16A SNPs (rs12708716, rs6498169 and rs7206912) correlate with the expression of CLEC16A itself as well as neighboring genes in whole-blood and thymic samples. Real-time quantitative PCR analyses show that SOCS1 and DEXI expression was lower in thymic samples carrying at least one of the CLEC16A risk alleles compared with non-carriers of the risk allele. Linear regression analysis revealed a significant correlation between the expression level of CLEC16A and that of SOCS1 and DEXI in thymic samples. These data indicate a possible regulatory role for multiple sclerosis-associated non-coding CLEC16A SNPs and a common control mechanism for the expression of CLEC16A, SOCS1 and DEXI.
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Affiliation(s)
- I S Leikfoss
- Department of Neurology, Oslo University Hospital, Oslo, Norway
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32
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Baxter AG, Jordan MA. From markers to molecular mechanisms: type 1 diabetes in the post-GWAS era. Rev Diabet Stud 2012; 9:201-23. [PMID: 23804261 DOI: 10.1900/rds.2012.9.201] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
By the year 2000, a draft of the human genome sequence was completed. Millions of single-nucleotide polymorphisms (SNPs) had been deposited into public databases, and high throughput technologies were under development for SNP genotyping. At that time, it was predicted that large case control association studies would provide far better resolution and power than genome-wide linkage studies. Type 1 diabetes was one of the first phenotypes to be examined by genome-wide association studies (GWAS), and to date over 50 genomic regions have been associated with the disease. In general, the great majority of these loci individually contribute a relatively small degree of risk, and most loci lie outside of coding sequences. The identification of molecular mechanisms from these genomic data therefore remains a significant challenge. Here, we summarize genetic candidate, linkage, and association studies of type 1 diabetes and discuss a potential strategy to identify mechanisms of disease from genomic data.
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Affiliation(s)
- Alan G Baxter
- Comparative Genomics Centre, Molecular Sciences Building 21, James Cook University, Townsville QLD 4811, Australia.
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33
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Harbo HF, Mero IL. From genes to characteristics of multiple sclerosis. Acta Neurol Scand 2012:76-83. [PMID: 23278661 DOI: 10.1111/ane.12027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2012] [Indexed: 02/03/2023]
Abstract
Multiple sclerosis (MS) is an inflammatory, demyelinating heterogeneous disease of the central nervous system, probably caused by an interaction of common genetic and environmental factors. Much progress has been made through the last few years in genetic studies of MS, and a growing list of genetic risk factors is now available. Biobanking and large collaborations have been prerequisites for this research, and detailed genetic and molecular characterizations are underway, with hopes for to translating new knowledge about MS pathogenesis and characteristics of the disease to personalized, better treatment options for each patient with MS.
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Affiliation(s)
- H F Harbo
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
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34
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Polymorphisms in the inflammatory genes CIITA, CLEC16A and IFNG influence BMD, bone loss and fracture in elderly women. PLoS One 2012; 7:e47964. [PMID: 23133532 PMCID: PMC3485004 DOI: 10.1371/journal.pone.0047964] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 09/25/2012] [Indexed: 12/26/2022] Open
Abstract
Osteoclast activity and the fine balance between bone formation and resorption is affected by inflammatory factors such as cytokines and T lymphocyte activity, mediated by major histocompatibility complex (MHC) molecules, in turn regulated by the MHC class II transactivator (MHC2TA). We investigated the effect of functional polymorphisms in the MHC2TA gene (CIITA), and two additional genes; C-type lectin domain 16A (CLEC16A), in linkage disequilibrium with CIITA and Interferon-γ (IFNG), an inducer of CIITA; on bone density, bone resorption markers, bone loss and fracture risk in 75 year-old women followed for up to 10 years (OPRA n = 1003) and in young adult women (PEAK-25 n = 999). CIITA was associated with BMD at age 75 (lumbar spine p = 0.011; femoral neck (FN) p = 0.049) and age 80 (total body p = 0.015; total hip p = 0.042; FN p = 0.028). Carriers of the CIITA rs3087456(G) allele had 1.8–3.4% higher BMD and displayed increased rate of bone loss between age 75 and 80 (FN p = 0.013; total hip p = 0.030; total body p = 3.8E−5). Despite increasing bone loss, the rs3087456(G) allele was protective against incident fracture overall (p = 0.002), osteoporotic fracture and hip fracture. Carriers of CLEC16A and IFNG variant alleles had lower BMD (p<0.05) and ultrasound parameters and a lower risk of incident fracture (CLEC16A, p = 0.011). In 25-year old women, none of the genes were associated with BMD. In conclusion, variation in inflammatory genes CIITA, CLEC-16A and INFG appear to contribute to bone phenotypes in elderly women and suggest a role for low-grade inflammation and MHC class II expression for osteoporosis pathogenesis.
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35
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Gourraud PA, Harbo HF, Hauser SL, Baranzini SE. The genetics of multiple sclerosis: an up-to-date review. Immunol Rev 2012. [PMID: 22725956 DOI: 10.1111/j.1600-065x.2012.01134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Multiple sclerosis (MS) is a prevalent inflammatory disease of the central nervous system that often leads to disability in young adults. Treatment options are limited and often only partly effective. The disease is likely caused by a complex interaction between multiple genes and environmental factors, leading to inflammatory-mediated central nervous system deterioration. A series of genomic studies have confirmed a central role for the immune system in the development of MS, including genetic association studies that have now dramatically expanded the roster of MS susceptibility genes beyond the longstanding human leukocyte antigen (HLA) association in MS first identified nearly 40 years ago. Advances in technology together with novel models for collaboration across research groups have enabled the discovery of more than 50 non-HLA genetic risk factors associated with MS. However, with a large proportion of the disease heritability still unaccounted for, current studies are now geared towards identification of causal alleles, associated pathways, epigenetic mechanisms, and gene-environment interactions. This article reviews recent efforts in addressing the genetics of MS and the challenges posed by an ever increasing amount of analyzable data, which is spearheading development of novel statistical methods necessary to cope with such complexity.
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Affiliation(s)
- Pierre-Antoine Gourraud
- Department of Neurology, University of California San Francisco, San Francisco, CA 94143-0435, USA
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36
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Juran BD, Hirschfield GM, Invernizzi P, Atkinson EJ, Li Y, Xie G, Kosoy R, Ransom M, Sun Y, Bianchi I, Schlicht EM, Lleo A, Coltescu C, Bernuzzi F, Podda M, Lammert C, Shigeta R, Chan LL, Balschun T, Marconi M, Cusi D, Heathcote EJ, Mason AL, Myers RP, Milkiewicz P, Odin JA, Luketic VA, Bacon BR, Bodenheimer HC, Liakina V, Vincent C, Levy C, Franke A, Gregersen PK, Bossa F, Gershwin ME, deAndrade M, Amos CI, Lazaridis KN, Seldin MF, Siminovitch KA. Immunochip analyses identify a novel risk locus for primary biliary cirrhosis at 13q14, multiple independent associations at four established risk loci and epistasis between 1p31 and 7q32 risk variants. Hum Mol Genet 2012; 21:5209-21. [PMID: 22936693 DOI: 10.1093/hmg/dds359] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To further characterize the genetic basis of primary biliary cirrhosis (PBC), we genotyped 2426 PBC patients and 5731 unaffected controls from three independent cohorts using a single nucleotide polymorphism (SNP) array (Immunochip) enriched for autoimmune disease risk loci. Meta-analysis of the genotype data sets identified a novel disease-associated locus near the TNFSF11 gene at 13q14, provided evidence for association at six additional immune-related loci not previously implicated in PBC and confirmed associations at 19 of 22 established risk loci. Results of conditional analyses also provided evidence for multiple independent association signals at four risk loci, with haplotype analyses suggesting independent SNP effects at the 2q32 and 16p13 loci, but complex haplotype driven effects at the 3q25 and 6p21 loci. By imputing classical HLA alleles from this data set, four class II alleles independently contributing to the association signal from this region were identified. Imputation of genotypes at the non-HLA loci also provided additional associations, but none with stronger effects than the genotyped variants. An epistatic interaction between the IL12RB2 risk locus at 1p31and the IRF5 risk locus at 7q32 was also identified and suggests a complementary effect of these loci in predisposing to disease. These data expand the repertoire of genes with potential roles in PBC pathogenesis that need to be explored by follow-up biological studies.
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Affiliation(s)
- Brian D Juran
- Center for Basic Research in Digestive Diseases, Mayo Clinic, Rochester, MN, USA
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37
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Abstract
Multiple sclerosis (MS) is a prevalent inflammatory disease of the central nervous system that often leads to disability in young adults. Treatment options are limited and often only partly effective. The disease is likely caused by a complex interaction between multiple genes and environmental factors, leading to inflammatory-mediated central nervous system deterioration. A series of genomic studies have confirmed a central role for the immune system in the development of MS, including genetic association studies that have now dramatically expanded the roster of MS susceptibility genes beyond the longstanding human leukocyte antigen (HLA) association in MS first identified nearly 40 years ago. Advances in technology together with novel models for collaboration across research groups have enabled the discovery of more than 50 non-HLA genetic risk factors associated with MS. However, with a large proportion of the disease heritability still unaccounted for, current studies are now geared towards identification of causal alleles, associated pathways, epigenetic mechanisms, and gene-environment interactions. This article reviews recent efforts in addressing the genetics of MS and the challenges posed by an ever increasing amount of analyzable data, which is spearheading development of novel statistical methods necessary to cope with such complexity.
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Affiliation(s)
- Pierre-Antoine Gourraud
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
| | - Hanne F. Harbo
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
- Department of Neurology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Stephen L. Hauser
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
| | - Sergio E. Baranzini
- Department of Neurology, University of California San Francisco. 513 Parnassus Ave. Room S-256. San Francisco, CA. 94143-0435’
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39
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Ronninger M, Seddighzadeh M, Eike MC, Plant D, Daha NA, Skinningsrud B, Worthington J, Kvien TK, Toes REM, Lie BA, Alfredsson L, Padyukov L. Interaction analysis between HLA-DRB1 shared epitope alleles and MHC class II transactivator CIITA gene with regard to risk of rheumatoid arthritis. PLoS One 2012; 7:e32861. [PMID: 22461888 PMCID: PMC3312880 DOI: 10.1371/journal.pone.0032861] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 02/01/2012] [Indexed: 12/03/2022] Open
Abstract
HLA-DRB1 shared epitope (SE) alleles are the strongest genetic determinants for autoantibody positive rheumatoid arthritis (RA). One of the key regulators in expression of HLA class II receptors is MHC class II transactivator (CIITA). A variant of the CIITA gene has been found to associate with inflammatory diseases. We wanted to explore whether the risk variant rs3087456 in the CIITA gene interacts with the HLA-DRB1 SE alleles regarding the risk of developing RA. We tested this hypothesis in a case-control study with 11767 individuals from four European Caucasian populations (6649 RA cases and 5118 controls). We found no significant additive interaction for risk alleles among Swedish Caucasians with RA (n = 3869, attributable proportion due to interaction (AP) = 0.2, 95%CI: −0.2–0.5) or when stratifying for anti-citrullinated protein antibodies (ACPA) presence (ACPA positive disease: n = 2945, AP = 0.3, 95%CI: −0.05–0.6, ACPA negative: n = 2268, AP = −0.2, 95%CI: −1.0–0.6). We further found no significant interaction between the main subgroups of SE alleles (DRB1*01, DRB1*04 or DRB1*10) and CIITA. Similar analysis of three independent RA cohorts from British, Dutch and Norwegian populations also indicated an absence of significant interaction between genetic variants in CIITA and SE alleles with regard to RA risk. Our data suggest that risk from the CIITA locus is independent of the major risk for RA from HLA-DRB1 SE alleles, given that no significant interaction between rs3087456 and SE alleles was observed. Since a biological link between products of these genes is evident, the genetic contribution from CIITA and class II antigens in the autoimmune process may involve additional unidentified factors.
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Affiliation(s)
- Marcus Ronninger
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.
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40
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“Omics” and the immunopathogenesis of multiple sclerosis. Neurosci Lett 2012; 508:1-3. [DOI: 10.1016/j.neulet.2011.11.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 11/30/2011] [Indexed: 11/22/2022]
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Association of primary biliary cirrhosis with variants in the CLEC16A, SOCS1, SPIB and SIAE immunomodulatory genes. Genes Immun 2012; 13:328-35. [PMID: 22257840 DOI: 10.1038/gene.2011.89] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We fine mapped two primary biliary cirrhosis (PBC) risk loci, CLEC16A (C-type lectin domain family 16 member A)-suppressor of cytokine signaling 1 (SOCS1) and Spi-B protein (SPIB) and sequenced a locus, sialic acid acetylesterase (SIAE), proposed to harbor autoimmunity-associated mutations. In all, 1450 PBC cases and 2957 healthy controls were genotyped for 84 single-nucleotide polymorphisms (SNPs) across the CLEC16A-SOCS1 and SPIB loci. All 10 exons of the SIAE gene were resequenced in 381 cases and point substitutions of unknown significance assayed for activity and secretion. Fine mapping identified 26 SNPs across the CLEC16A-SOCS1 and 11 SNPs across the SPIB locus with significant association to PBC, the strongest signals at the CLEC16A-SOCS1 locus emanating from a SOCS1 intergenic SNP (rs243325; P=9.91 × 10(-9)) and at the SPIB locus from a SPIB intronic SNP (rs34944112; P=3.65 × 10(-9)). Among the associated SNPs at the CLEC16A-SOCS1 locus, two within the CLEC16A gene as well as one SOCS1 SNP (rs243325) remained significant after conditional logistic regression and contributed independently to risk. Sequencing of the SIAE gene and functional assays of newly identified variants revealed six patients with functional non-synonymous SIAE mutations (Fisher's P=9 × 10(-4) vs controls) We demonstrate independent effects on risk of PBC for CLEC16A, SOCS1 and SPIB variants, while identifying functionally defective SIAE variants as potential factors in risk for PBC.
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Davison LJ, Wallace C, Cooper JD, Cope NF, Wilson NK, Smyth DJ, Howson JM, Saleh N, Al-Jeffery A, Angus KL, Stevens HE, Nutland S, Duley S, Coulson RM, Walker NM, Burren OS, Rice CM, Cambien F, Zeller T, Munzel T, Lackner K, Blankenberg S, Fraser P, Gottgens B, Todd JA. Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. Hum Mol Genet 2012; 21:322-33. [PMID: 21989056 PMCID: PMC3276289 DOI: 10.1093/hmg/ddr468] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Revised: 09/27/2011] [Accepted: 10/06/2011] [Indexed: 01/13/2023] Open
Abstract
The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes.
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Affiliation(s)
- Lucy J. Davison
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Chris Wallace
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Jason D. Cooper
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Nathan F. Cope
- Nuclear Dynamics Laboratory, Babraham Institute, Cambridge, UK
| | - Nicola K. Wilson
- Haematopoetic Stem Cell Lab, Cambridge Institute for Medical Research (CIMR), NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Joanna M.M. Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Nada Saleh
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Abdullah Al-Jeffery
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Karen L. Angus
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Helen E. Stevens
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Sarah Nutland
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Simon Duley
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Richard M.R. Coulson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Neil M. Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Oliver S. Burren
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Catherine M. Rice
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Francois Cambien
- INSERM UMRS 937, Pierre and Marie Curie University and Medical School, Paris, France
| | - Tanja Zeller
- University Heart Center Hamburg, Clinical for General and Interventional Cardiology, 20246 Hamburg, Germany
| | - Thomas Munzel
- Medizinische Klinik und Poliklinik, Johannes-Gutenberg Universität Mainz, Germany and
| | - Karl Lackner
- Department of Clinical Chemistry and Laboratory Medicine, Johannes-Gutenberg Universität Mainz, Germany
| | - Stefan Blankenberg
- University Heart Center Hamburg, Clinical for General and Interventional Cardiology, 20246 Hamburg, Germany
| | | | - Peter Fraser
- Nuclear Dynamics Laboratory, Babraham Institute, Cambridge, UK
| | - Berthold Gottgens
- Haematopoetic Stem Cell Lab, Cambridge Institute for Medical Research (CIMR), NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
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Mortlock DP, Pregizer S. Identifying Functional Annotation for Noncoding Genomic Sequences. ACTA ACUST UNITED AC 2012; Chapter 1:Unit1.10. [DOI: 10.1002/0471142905.hg0110s72] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Douglas P. Mortlock
- Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center Nashville Tennessee
- Center for Human Genetics Research, Vanderbilt University Medical Center Nashville Tennessee
| | - Steven Pregizer
- Department of Molecular Physiology & Biophysics, Vanderbilt University Medical Center Nashville Tennessee
- Center for Human Genetics Research, Vanderbilt University Medical Center Nashville Tennessee
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