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Chen Y, Wu Y, Fang L, Zhao H, Xu S, Shuai Z, Yu H, Cai G, Zhan HQ, Pan F. METTL14-m6A-FOXO3a axis regulates autophagy and inflammation in ankylosing spondylitis. Clin Immunol 2023; 257:109838. [PMID: 37935312 DOI: 10.1016/j.clim.2023.109838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The role of m6A in ankylosing spondylitis (AS) remains largely obscure. In this study, we found that m6A modification was decreased in T cells of AS, and the abnormal m6A modification was attributed to the downregulation of methyltransferase-like 14 (METTL14). METTL14 exerted a critical role in regulating autophagy activity and inflammation via targeting Forkhead box O3a (FOXO3a). Mechanistically, the loss of METTL14 decreased the expression of FOXO3a, leading to the damage of autophagic flux and the aggravation of inflammation. Inversely, the forced expression of METTL14 upregulated the expression of FOXO3a, thereby activating autophagy and alleviating inflammation. Furthermore, our results revealed that METTL14 targeted FOXO3a mRNA and regulated its expression and stability in a m6A-dependent manner. These findings uncovered the functional importance of m6A methylation mechanisms in the regulation of autophagy and inflammation, which expanded our understanding of this interaction and was critical for the development of therapeutic strategies for AS.
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Affiliation(s)
- Yuting Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Ye Wu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Lanlan Fang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Hui Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - Shenqian Xu
- Department of Rheumatism and Immunity, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Zongwen Shuai
- Department of Rheumatism and Immunity, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Haiyang Yu
- Department of Orthopedics, Fuyang People's Hospital, 501 Sanqing Road, Fuyang, Anhui 236000, China
| | - Guoqi Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China
| | - He-Qin Zhan
- Department of Pathology, School of Basic Medical Sciences, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China.
| | - Faming Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China; The Key Laboratory of Major Autoimmune Diseases, Anhui Medical University, 81 Meishan Road, Hefei, Anhui 230032, China.
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2
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Brown AC, Cohen CJ, Mielczarek O, Migliorini G, Costantino F, Allcock A, Davidson C, Elliott KS, Fang H, Lledó Lara A, Martin AC, Osgood JA, Sanniti A, Scozzafava G, Vecellio M, Zhang P, Black MH, Li S, Truong D, Molineros J, Howe T, Wordsworth BP, Bowness P, Knight JC. Comprehensive epigenomic profiling reveals the extent of disease-specific chromatin states and informs target discovery in ankylosing spondylitis. CELL GENOMICS 2023; 3:100306. [PMID: 37388915 PMCID: PMC10300554 DOI: 10.1016/j.xgen.2023.100306] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 01/30/2023] [Accepted: 03/27/2023] [Indexed: 07/01/2023]
Abstract
Ankylosing spondylitis (AS) is a common, highly heritable inflammatory arthritis characterized by enthesitis of the spine and sacroiliac joints. Genome-wide association studies (GWASs) have revealed more than 100 genetic associations whose functional effects remain largely unresolved. Here, we present a comprehensive transcriptomic and epigenomic map of disease-relevant blood immune cell subsets from AS patients and healthy controls. We find that, while CD14+ monocytes and CD4+ and CD8+ T cells show disease-specific differences at the RNA level, epigenomic differences are only apparent upon multi-omics integration. The latter reveals enrichment at disease-associated loci in monocytes. We link putative functional SNPs to genes using high-resolution Capture-C at 10 loci, including PTGER4 and ETS1, and show how disease-specific functional genomic data can be integrated with GWASs to enhance therapeutic target discovery. This study combines epigenetic and transcriptional analysis with GWASs to identify disease-relevant cell types and gene regulation of likely pathogenic relevance and prioritize drug targets.
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Affiliation(s)
- Andrew C. Brown
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carla J. Cohen
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- MRC WIMM Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | - Olga Mielczarek
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Horizon Discovery (PerkinElmer) Cambridge Research Park, 8100 Beach Dr., Waterbeach, Cambridge CB25 9TL, UK
| | - Gabriele Migliorini
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Félicie Costantino
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- UVSQ, INSERM UMR1173, Infection et Inflammation, Laboratory of Excellence INFLAMEX, Université Paris-Saclay, Paris, France
- Rheumatology Department, AP-HP, Ambroise Paré Hospital, Paris, France
| | - Alice Allcock
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
| | | | - Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Alicia Lledó Lara
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alice C. Martin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Julie A. Osgood
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Anna Sanniti
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Giuseppe Scozzafava
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- Centro Ricerche Fondazione Italiana Ricerca sull’Artrite (FIRA), Fondazione Pisana per la Scienza ONLUS, Via Ferruccio Giovannini 13, 56017 San Giuliano Terme (Pisa), Italy
| | - Ping Zhang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
| | - Mary Helen Black
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Shuwei Li
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Dongnhu Truong
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Julio Molineros
- Data Science, Population Analytics, Janssen R&D, Spring House, PA 19002, USA
| | - Trevor Howe
- Data Science, External Innovation, Janssen R&D, London W1G 0BG, UK
| | - B. Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7LD, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
| | - Julian C. Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Chinese Academy of Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7BN, UK
- National Institute for Health Research, Comprehensive Biomedical Research Centre, Oxford OX4 2PG, UK
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3
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Bhuyan ZA, Rahman MA, Maradana MR, Mehdi AM, Bergot AS, Simone D, El-Kurdi M, Garrido-Mesa J, Cai CBB, Cameron AJ, Hanson AL, Nel HJ, Kenna T, Leo P, Rehaume L, Brown MA, Ciccia F, Thomas R. Genetically encoded Runx3 and CD4 + intestinal epithelial lymphocyte deficiencies link SKG mouse and human predisposition to spondyloarthropathy. Clin Immunol 2023; 247:109220. [PMID: 36596403 DOI: 10.1016/j.clim.2022.109220] [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: 09/26/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 01/02/2023]
Abstract
Disturbances in immune regulation, intestinal dysbiosis and inflammation characterize ankylosing spondylitis (AS), which is associated with RUNX3 loss-of-function variants. ZAP70W163C mutant (SKG) mice have reduced ZAP70 signaling, spondyloarthritis and ileitis. In small intestine, Foxp3+ regulatory T cells (Treg) and CD4+CD8αα+TCRαβ+ intraepithelial lymphocytes (CD4-IEL) control inflammation. TGF-β and retinoic acid (RA)-producing dendritic cells and MHC-class II+ intestinal epithelial cells (IEC) are required for Treg and CD4-IEL differentiation from CD4+ conventional or Treg precursors, with upregulation of Runx3 and suppression of ThPOK. We show in SKG mouse ileum, that ZAP70W163C or ZAP70 inhibition prevented CD4-IEL but not Treg differentiation, dysregulating Runx3 and ThPOK. TGF-β/RA-mediated CD4-IEL development, T-cell IFN-γ production, MHC class-II+ IEC, tissue-resident memory T-cell and Runx3-regulated genes were reduced. In AS intestine, CD4-IEL were decreased, while in AS blood CD4+CD8+ T cells were reduced and Treg increased. Thus, genetically-encoded TCR signaling dysfunction links intestinal T-cell immunodeficiency in mouse and human spondyloarthropathy.
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Affiliation(s)
- Zaied Ahmed Bhuyan
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - M Arifur Rahman
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Muralidhara Rao Maradana
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Ahmed M Mehdi
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Anne-Sophie Bergot
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Davide Simone
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Marya El-Kurdi
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Jose Garrido-Mesa
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Cheng Bang Benjamin Cai
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Amy J Cameron
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Aimee L Hanson
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Hendrik J Nel
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Tony Kenna
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Paul Leo
- Queensland University of Technology, Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland 4006, Australia
| | - Linda Rehaume
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia
| | - Matthew A Brown
- Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Genomics England Ltd, Charterhouse Square, London, United Kingdom
| | - Francesco Ciccia
- Dipartimento di Medicina di Precisione, Section of Rheumatology, Università degli Studi della Campania L. Vanvitelli, Naples, Italy
| | - Ranjeny Thomas
- Frazer Institute, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland 4102, Australia.
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4
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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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5
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Jia M, Zou X, Yin S, Tian W, Zhao Y, Wang H, Xu G, Cai W, Shao Q. CHD4 orchestrates the symphony of T and B lymphocytes development and a good mediator in preventing from autoimmune disease. Immun Inflamm Dis 2022; 10:e644. [PMID: 35759243 PMCID: PMC9168550 DOI: 10.1002/iid3.644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 12/02/2022] Open
Abstract
Chromodomain helicase DNA binding protein 4 (CHD4) is an ATPase subunit of the nucleosome remodeling and deacetylation complex. It has been implicated in gene transcription, DNA damage repair, maintenance of genome stability, and chromatin assembly. Meanwhile, it is highly related to cell cycle progression and the proceeding of malignancy. Most of the previous studies were focused on the function of CHD4 with tumor cells, cancer stem cells, and cancer cells multidrug resistance. Recently, some researchers have explored the CHD4 functions on the development and differentiation of adaptive immune cells, such as T and B lymphocytes. In this review, we will discuss details of CHD4 in lymphocyte differentiation and development, as well as the critical role of CHD4 in the pathogenesis of the autoimmune disease.
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Affiliation(s)
- Miaomiao Jia
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Xueqin Zou
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Shuying Yin
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Weihong Tian
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Yangjing Zhao
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Hui Wang
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
| | - Guoying Xu
- School of Medical Science and Laboratory Medicine, Institute of Medical Genetics and Reproductive Immunity Jiangsu College of Nursing Huai'an Jiangsu P.R. China
| | - Weili Cai
- School of Medical Science and Laboratory Medicine, Institute of Medical Genetics and Reproductive Immunity Jiangsu College of Nursing Huai'an Jiangsu P.R. China
| | - Qixiang Shao
- Reproductive Sciences Institute Jiangsu University Zhenjiang Jiangsu P.R. China
- Department of Immunology, School of Medicine Jiangsu University Zhenjiang Jiangsu P.R. China
- School of Medical Science and Laboratory Medicine, Institute of Medical Genetics and Reproductive Immunity Jiangsu College of Nursing Huai'an Jiangsu P.R. China
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6
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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7
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Cohen CJ, Davidson C, Selmi C, Bowness P, Knight JC, Wordsworth BP, Vecellio M. Disruption of c-MYC Binding and Chromosomal Looping Involving Genetic Variants Associated With Ankylosing Spondylitis Upstream of the RUNX3 Promoter. Front Genet 2022; 12:741867. [PMID: 35069677 PMCID: PMC8782160 DOI: 10.3389/fgene.2021.741867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Ankylosing Spondylitis (AS) is a common form of inflammatory spinal arthritis with a complex aetiology and high heritability, involving more than 100 genetic associations. These include several AS-associated single nucleotide polymorphisms (SNPs) upstream of RUNX3, which encodes the multifunctional RUNT-related transcription factor (TF) 3. The lead associated SNP rs6600247 (p = 2.6 × 10−15) lies ∼13kb upstream of the RUNX3 promoter adjacent to a c-MYC TF binding-site. The effect of rs6600247 genotype on DNA binding and chromosome looping were investigated by electrophoretic mobility gel shift assays (EMSA), Western blotting-EMSA (WEMSA) and Chromosome Conformation Capture (3C). Results: Interrogation of ENCODE published data showed open chromatin in the region overlapping rs6600247 in primary human CD14+ monocytes, in contrast to the Jurkat T cell line or primary human T-cells. The rs6600247 AS-risk allele is predicted to specifically disrupt a c-MYC binding-site. Using a 50bp DNA probe spanning rs6600247 we consistently observed reduced binding to the AS-risk “C” allele of both purified c-MYC protein and nuclear extracts (NE) from monocyte-like U937 cells. WEMSA on U937 NE and purified c-MYC protein confirmed these differences (n = 3; p < 0.05). 3C experiments demonstrated negligible interaction between the region encompassing rs6600247 and the RUNX3 promoter. A stronger interaction frequency was demonstrated between the RUNX3 promoter and the previously characterised AS-associated SNP rs4648889. Conclusion: The lead SNP rs6600247, located in an enhancer-like region upstream of the RUNX3 promoter, modulates c-MYC binding. However, the region encompassing rs6600247 has rather limited physical interaction with the promoter of RUNX3. In contrast a clear chromatin looping event between the region encompassing rs4648889 and the RUNX3 promoter was observed. These data provide further evidence for complexity in the regulatory elements upstream of the RUNX3 promoter and the involvement of RUNX3 transcriptional regulation in AS.
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Affiliation(s)
- Carla J Cohen
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research Oxford Comprehensive Biomedical Research Centre, Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Connor Davidson
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research Oxford Comprehensive Biomedical Research Centre, Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Carlo Selmi
- Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
| | - Paul Bowness
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research Oxford Comprehensive Biomedical Research Centre, Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - B Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research Oxford Comprehensive Biomedical Research Centre, Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research Oxford Comprehensive Biomedical Research Centre, Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom.,Division of Rheumatology and Clinical Immunology, Humanitas Clinical and Research Center - IRCCS, Rozzano, Italy
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8
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Wordsworth BP, Cohen CJ, Davidson C, Vecellio M. Perspectives on the Genetic Associations of Ankylosing Spondylitis. Front Immunol 2021; 12:603726. [PMID: 33746951 PMCID: PMC7977288 DOI: 10.3389/fimmu.2021.603726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/05/2021] [Indexed: 12/11/2022] Open
Abstract
Ankylosing spondylitis (AS) is a common form of inflammatory spinal arthritis with a complex polygenic aetiology. Genome-wide association studies have identified more than 100 loci, including some involved in antigen presentation (HLA-B27, ERAP1, and ERAP2), some in Th17 responses (IL6R, IL23R, TYK2, and STAT3), and others in macrophages and T-cells (IL7R, CSF2, RUNX3, and GPR65). Such observations have already helped identify potential new therapies targeting IL-17 and GM-CSF. Most AS genetic associations are not in protein-coding sequences but lie in intergenic regions where their direct relationship to particular genes is difficult to assess. They most likely reflect functional polymorphisms concerned with cell type-specific regulation of gene expression. Clarifying the nature of these associations should help to understand the pathogenic pathways involved in AS better and suggest potential cellular and molecular targets for drug therapy. However, even identifying the precise mechanisms behind the extremely strong HLA-B27 association with AS has so far proved elusive. Polygenic risk scores (using all the known genetic associations with AS) can be effective for the diagnosis of AS, particularly where there is a relatively high pre-test probability of AS. Genetic prediction of disease outcomes and response to biologics is not currently practicable.
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Affiliation(s)
- B Paul Wordsworth
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Institute of Musculoskeletal Sciences, Oxford, United Kingdom.,Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Carla J Cohen
- Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Connor Davidson
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Matteo Vecellio
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford Institute of Musculoskeletal Sciences, Oxford, United Kingdom.,Botnar Research Centre, Nuffield Orthopaedic Centre, Oxford, United Kingdom.,Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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