1
|
Bridges SL, Shapira R, Aksentijevich I, Mack SJ, Merriman TR, Klein CJ, Bowen BM, Klein TE. Curating Genetic Associations With Rheumatologic Autoimmune Diseases to Improve Patient Outcomes. Arthritis Rheumatol 2024. [PMID: 38965695 DOI: 10.1002/art.42943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/21/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024]
Affiliation(s)
- S Louis Bridges
- Hospital for Special Surgery and Weill Cornell Medical Center, New York, New York
| | | | | | | | - Tony R Merriman
- University of Alabama at Birmingham School of Medicine, Birmingham, Alabama
| | | | | | | |
Collapse
|
2
|
González‐Serna D, Shi C, Kerick M, Hankinson J, Ding J, McGovern A, Tutino M, Villanueva‐Martin G, Ortego‐Centeno N, Callejas JL, Martin J, Orozco G. Identification of Mechanisms by Which Genetic Susceptibility Loci Influence Systemic Sclerosis Risk Using Functional Genomics in Primary T Cells and Monocytes. Arthritis Rheumatol 2023; 75:1007-1020. [PMID: 36281738 PMCID: PMC10953390 DOI: 10.1002/art.42396] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 09/08/2022] [Accepted: 10/18/2022] [Indexed: 11/08/2022]
Abstract
OBJECTIVE Systemic sclerosis (SSc) is a complex autoimmune disease with a strong genetic component. However, most of the genes associated with the disease are still unknown because associated variants affect mostly noncoding intergenic elements of the genome. We used functional genomics to translate the genetic findings into a better understanding of the disease. METHODS Promoter capture Hi-C and RNA-sequencing experiments were performed in CD4+ T cells and CD14+ monocytes from 10 SSc patients and 5 healthy controls to link SSc-associated variants with their target genes, followed by differential expression and differential interaction analyses between cell types. RESULTS We linked SSc-associated loci to 39 new potential target genes and confirmed 7 previously known SSc-associated genes. We highlight novel causal genes, such as CXCR5, as the most probable candidate gene for the DDX6 locus. Some previously known SSc-associated genes, such as IRF8, STAT4, and CD247, showed cell type-specific interactions. We also identified 15 potential drug targets already in use in other similar immune-mediated diseases that could be repurposed for SSc treatment. Furthermore, we observed that interactions were directly correlated with the expression of important genes implicated in cell type-specific pathways and found evidence that chromatin conformation is associated with genotype. CONCLUSION Our study revealed potential causal genes for SSc-associated loci, some of them acting in a cell type-specific manner, suggesting novel biologic mechanisms that might mediate SSc pathogenesis.
Collapse
Affiliation(s)
- David González‐Serna
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Chenfu Shi
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Martin Kerick
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Jenny Hankinson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - James Ding
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Amanda McGovern
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Mauro Tutino
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and HealthThe University of ManchesterManchesterUK
| | - Gonzalo Villanueva‐Martin
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Norberto Ortego‐Centeno
- Department of Internal Medicine, Hospital Universitario San CecilioInstitute for Biosanitary Research of Granada (ibs.GRANADA)GranadaSpain
| | - José Luis Callejas
- Department of Internal Medicine, Hospital Universitario San CecilioInstitute for Biosanitary Research of Granada (ibs.GRANADA)GranadaSpain
| | - Javier Martin
- Institute of Parasitology and Biomedicine López‐Neyra, Consejo Superior de Investigaciones Científicas (IPBLN‐CSIC)GranadaSpain
| | - Gisela Orozco
- Division of Musculoskeletal and Dermatological Sciences, Centre for Genetics and Genomics Versus Arthritis, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, and NIHR Manchester Biomedical Research CentreManchester University NHS Foundation Trust, Manchester Academic Health Science CentreManchesterUK
| |
Collapse
|
3
|
Acosta-Herrera M, Kerick M, Lopéz-Isac E, Assassi S, Beretta L, Simeón-Aznar CP, Ortego-Centeno N, Proudman SM, Hunzelmann N, Moroncini G, de Vries-Bouwstra JK, Orozco G, Barton A, Herrick AL, Terao C, Allanore Y, Brown MA, Radstake TR, Fonseca C, Denton CP, Mayes MD, Martin J. Comprehensive analysis of the major histocompatibility complex in systemic sclerosis identifies differential HLA associations by clinical and serological subtypes. Ann Rheum Dis 2021; 80:1040-1047. [PMID: 34096881 PMCID: PMC8292594 DOI: 10.1136/annrheumdis-2021-219884] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/19/2022]
Abstract
OBJECTIVE The greatest genetic effect reported for systemic sclerosis (SSc) lies in the major histocompatibility complex (MHC) locus. Leveraging the largest SSc genome-wide association study, we aimed to fine-map this region to identify novel human leucocyte antigen (HLA) genetic variants associated with SSc susceptibility and its main clinical and serological subtypes. METHODS 9095 patients with SSc and 17 584 controls genome-wide genotyped were used to impute and test single-nucleotide polymorphisms (SNPs) across the MHC, classical HLA alleles and their composite amino acid residues. Additionally, patients were stratified according to their clinical and serological status, namely, limited cutaneous systemic sclerosis (lcSSc), diffuse cutaneous systemic sclerosis (dcSSc), anticentromere (ACA), antitopoisomerase (ATA) and anti-RNApolIII autoantibodies (ARA). RESULTS Sequential conditional analyses showed nine SNPs, nine classical alleles and seven amino acids that modelled the observed associations with SSc. This confirmed previously reported associations with HLA-DRB1*11:04 and HLA-DPB1*13:01, and revealed a novel association of HLA-B*08:01. Stratified analyses showed specific associations of HLA-DQA1*02:01 with lcSSc, and an exclusive association of HLA-DQA1*05:01 with dcSSc. Similarly, private associations were detected in HLA-DRB1*08:01 and confirmed the previously reported association of HLA-DRB1*07:01 with ACA-positive patients, as opposed to the HLA-DPA1*02:01 and HLA-DQB1*03:01 alleles associated with ATA presentation. CONCLUSIONS This study confirms the contribution of HLA class II and reveals a novel association of HLA class I with SSc, suggesting novel pathways of disease pathogenesis. Furthermore, we describe specific HLA associations with SSc clinical and serological subtypes that could serve as biomarkers of disease severity and progression.
Collapse
Affiliation(s)
- Marialbert Acosta-Herrera
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| | - Martin Kerick
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| | - Elena Lopéz-Isac
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| | - Shervin Assassi
- Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Lorenzo Beretta
- Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | | | | | - Susanna M Proudman
- Department of Rheumatology, Royal Adelaide Hospital, Adelaide, Victoria, Australia
| | | | - Gianluca Moroncini
- Department of Clinical and Molecular Science, Università Politecnica delle Marche and Ospedali Riuniti, Ancona, Italy
| | | | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Ariane L Herrick
- Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Salford Royal NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yannick Allanore
- Department of Rheumatology A, Hospital Cochin, Paris, Île-de-France, France
| | - Matthew A Brown
- NIHR Biomedical Research Centre, Guy's and Saint Thomas' NHS Foundation Trust and King's College, London, UK
| | - Timothy Rdj Radstake
- Department of Rheumatology and Clinical Immunology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carmen Fonseca
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Christopher P Denton
- Centre for Rheumatology, Royal Free and University College Medical School, London, UK
| | - Maureen D Mayes
- Rheumatology and Clinical Immunogenetics, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Javier Martin
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine López-Neyra, CSIC, Granada, Andalucía, Spain
| |
Collapse
|
4
|
Li T, Ortiz-Fernández L, Andrés-León E, Ciudad L, Javierre BM, López-Isac E, Guillén-Del-Castillo A, Simeón-Aznar CP, Ballestar E, Martin J. Epigenomics and transcriptomics of systemic sclerosis CD4+ T cells reveal long-range dysregulation of key inflammatory pathways mediated by disease-associated susceptibility loci. Genome Med 2020; 12:81. [PMID: 32977850 PMCID: PMC7519528 DOI: 10.1186/s13073-020-00779-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Systemic sclerosis (SSc) is a genetically complex autoimmune disease mediated by the interplay between genetic and epigenetic factors in a multitude of immune cells, with CD4+ T lymphocytes as one of the principle drivers of pathogenesis. METHODS DNA samples exacted from CD4+ T cells of 48 SSc patients and 16 healthy controls were hybridized on MethylationEPIC BeadChip array. In parallel, gene expression was interrogated by hybridizing total RNA on Clariom™ S array. Downstream bioinformatics analyses were performed to identify correlating differentially methylated CpG positions (DMPs) and differentially expressed genes (DEGs), which were then confirmed utilizing previously published promoter capture Hi-C (PCHi-C) data. RESULTS We identified 9112 and 3929 DMPs and DEGs, respectively. These DMPs and DEGs are enriched in functional categories related to inflammation and T cell biology. Furthermore, correlation analysis identified 17,500 possible DMP-DEG interaction pairs within a window of 5 Mb, and utilizing PCHi-C data, we observed that 212 CD4+ T cell-specific pairs of DMP-DEG also formed part of three-dimensional promoter-enhancer networks, potentially involving CTCF. Finally, combining PCHi-C data with SSc GWAS data, we identified four important SSc-associated susceptibility loci, TNIP1 (rs3792783), GSDMB (rs9303277), IL12RB1 (rs2305743), and CSK (rs1378942), that could potentially interact with DMP-DEG pairs cg17239269-ANXA6, cg19458020-CCR7, cg10808810-JUND, and cg11062629-ULK3, respectively. CONCLUSION Our study unveils a potential link between genetic, epigenetic, and transcriptional deregulation in CD4+ T cells of SSc patients, providing a novel integrated view of molecular components driving SSc pathogenesis.
Collapse
Affiliation(s)
- Tianlu Li
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Lourdes Ortiz-Fernández
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Biola M Javierre
- 3D Chromatin Organization, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain
| | - Elena López-Isac
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Alfredo Guillén-Del-Castillo
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Carmen Pilar Simeón-Aznar
- Unit of Systemic Autoimmunity Diseases, Department of Internal Medicine, Vall d'Hebron Hospital, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), 08916, Badalona, Barcelona, Spain.
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.
| |
Collapse
|
5
|
Beretta L, Barturen G, Vigone B, Bellocchi C, Hunzelmann N, De Langhe E, Cervera R, Gerosa M, Kovács L, Ortega Castro R, Almeida I, Cornec D, Chizzolini C, Pers JO, Makowska Z, Lesche R, Kerick M, Alarcón-Riquelme ME, Martin J. Genome-wide whole blood transcriptome profiling in a large European cohort of systemic sclerosis patients. Ann Rheum Dis 2020; 79:1218-1226. [PMID: 32561607 PMCID: PMC7456554 DOI: 10.1136/annrheumdis-2020-217116] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023]
Abstract
Objectives The analysis of annotated transcripts from genome-wide expression studies may help to understand the pathogenesis of complex diseases, such as systemic sclerosis (SSc). We performed a whole blood (WB) transcriptome analysis on RNA collected in the context of the European PRECISESADS project, aiming at characterising the pathways that differentiate SSc from controls and that are reproducible in geographically diverse populations. Methods Samples from 162 patients and 252 controls were collected in RNA stabilisers. Cases and controls were divided into a discovery (n=79+163; Southern Europe) and validation cohort (n=83+89; Central-Western Europe). RNA sequencing was performed by an Illumina assay. Functional annotations of Reactome pathways were performed with the Functional Analysis of Individual Microarray Expression (FAIME) algorithm. In parallel, immunophenotyping of 28 circulating cell populations was performed. We tested the presence of differentially expressed genes/pathways and the correlation between absolute cell counts and RNA transcripts/FAIME scores in regression models. Results significant in both populations were considered as replicated. Results Overall, 15 224 genes and 1277 functional pathways were available; of these, 99 and 225 were significant in both sets. Among replicated pathways, we found a deregulation in type-I interferon, Toll-like receptor cascade, tumour suppressor p53 protein function, platelet degranulation and activation. RNA transcripts or FAIME scores were jointly correlated with cell subtypes with strong geographical differences; neutrophils were the major determinant of gene expression in SSc-WB samples. Conclusions We discovered a set of differentially expressed genes/pathways validated in two independent sets of patients with SSc, highlighting a number of deregulated processes that have relevance for the pathogenesis of autoimmunity and SSc.
Collapse
Affiliation(s)
- Lorenzo Beretta
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Guillermo Barturen
- GENYO, Centre for Genomics and Oncological Research Pfizer, University of Granada, Andalusian Regional Government, PTS GRANADA, Granada, Spain
| | - Barbara Vigone
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
| | - Chiara Bellocchi
- Scleroderma Unit, Referral Center for Systemic Autoimmune Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Nicolas Hunzelmann
- Klinik und Poliklinik für Dermatologie und Venerologie, Uniklinik Köln, Köln, Germany
| | - Ellen De Langhe
- Division of Rheumatology, University Hospitals Leuven and Skeletal Biology and Engineering Research Center, KU Leuven, Leuven, Belgium
| | - Ricard Cervera
- Department of Autoimmune Diseases, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Maria Gerosa
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - László Kovács
- Department of Rheumatology and Immunology, University of Szeged, Faculty of Medicine, Szeged, Hungary
| | - Rafaela Ortega Castro
- Servicio de Reumatologia, Hospital Universitario Reina Sofía, Instituto Maimónides de Investigación Biomédica IMIBIC, Córdoba, Spain
| | - Isabel Almeida
- Serviço de Imunologia EX-CICAP, Centro Hospitalar e Universitário do Porto, Porto, Portugal
| | - Divi Cornec
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, Labex IGO, Brest, France
- Rheumatology Department, Cavale Blanche Hospital, Brest, France
| | - Carlo Chizzolini
- Immunology & Allergy, University Hospital and School of Medicine (HCUGE), Geneva, Switzerland
| | - Jacques-Olivier Pers
- UMR1227, Lymphocytes B et Autoimmunité, Université de Brest, Inserm, Labex IGO, Brest, France
| | | | | | - Martin Kerick
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada, Spain
| | - Marta Eugenia Alarcón-Riquelme
- GENYO, Centre for Genomics and Oncological Research Pfizer, University of Granada, Andalusian Regional Government, PTS GRANADA, Granada, Spain
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, Granada, Spain
| |
Collapse
|
6
|
Casares-Marfil D, Martín J, Acosta-Herrera M. Genomic opportunities for drug repositioning in systemic seropositive rheumatic diseases. Expert Rev Clin Immunol 2020; 16:343-346. [DOI: 10.1080/1744666x.2020.1738926] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, IPBLN-CSIC, Granada, Spain
| | | |
Collapse
|