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Pachera E, Assassi S, Salazar GA, Stellato M, Renoux F, Wunderlin A, Blyszczuk P, Lafyatis R, Kurreeman F, de Vries-Bouwstra J, Messemaker T, Feghali-Bostwick CA, Rogler G, van Haaften WT, Dijkstra G, Oakley F, Calcagni M, Schniering J, Maurer B, Distler JH, Kania G, Frank-Bertoncelj M, Distler O. Long noncoding RNA H19X is a key mediator of TGF-β-driven fibrosis. J Clin Invest 2021; 130:4888-4905. [PMID: 32603313 DOI: 10.1172/jci135439] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 06/17/2020] [Indexed: 12/22/2022] Open
Abstract
TGF-β is a master regulator of fibrosis, driving the differentiation of fibroblasts into apoptosis-resistant myofibroblasts and sustaining the production of extracellular matrix (ECM) components. Here, we identified the nuclear long noncoding RNA (lncRNA) H19X as a master regulator of TGF-β-driven tissue fibrosis. H19X was consistently upregulated in a wide variety of human fibrotic tissues and diseases and was strongly induced by TGF-β, particularly in fibroblasts and fibroblast-related cells. Functional experiments following H19X silencing revealed that H19X was an obligatory factor for TGF-β-induced ECM synthesis as well as differentiation and survival of ECM-producing myofibroblasts. We showed that H19X regulates DDIT4L gene expression, specifically interacting with a region upstream of the DDIT4L gene and changing the chromatin accessibility of a DDIT4L enhancer. These events resulted in transcriptional repression of DDIT4L and, in turn, in increased collagen expression and fibrosis. Our results shed light on key effectors of TGF-β-induced ECM remodeling and fibrosis.
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Affiliation(s)
- Elena Pachera
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Shervin Assassi
- Division of Rheumatology, Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Gloria A Salazar
- Division of Rheumatology, Department of Internal Medicine, University of Texas Health Science Center at Houston, McGovern Medical School, Houston, Texas, USA
| | - Mara Stellato
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Florian Renoux
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Adam Wunderlin
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Przemyslaw Blyszczuk
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Tobias Messemaker
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Gerhard Rogler
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Wouter T van Haaften
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, Netherlands
| | - Gerard Dijkstra
- Department of Gastroenterology and Hepatology, University Medical Center Groningen, Groningen, Netherlands
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Maurizio Calcagni
- Department of Plastic Surgery and Hand Surgery, University Hospital Zurich, Zurich, Switzerland
| | - Janine Schniering
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Britta Maurer
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Jörg Hw Distler
- Department of Internal Medicine 3, University of Erlangen, Erlangen, Germany
| | - Gabriela Kania
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Oliver Distler
- Center of Experimental Rheumatology, Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
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Zaidi F, Narang RK, Phipps-Green A, Gamble GG, Tausche AK, So A, Riches P, Andres M, Perez-Ruiz F, Doherty M, Janssen M, Joosten LAB, Jansen TL, Kurreeman F, Torres RJ, McCarthy GM, Miner JN, Stamp LK, Merriman TR, Dalbeth N. Systematic genetic analysis of early-onset gout: ABCG2 is the only associated locus. Rheumatology (Oxford) 2021; 59:2544-2549. [PMID: 31998961 DOI: 10.1093/rheumatology/kez685] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/12/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE The aim of this study was to examine whether serum urate-associated genetic variants are associated with early-onset gout. METHODS Participants with gout in the Genetics of Gout in Aotearoa study with available genotyping were included (n = 1648). Early-onset gout was defined as the first presentation of gout <40 years of age. Single nucleotide polymorphisms (SNPs) for the 10 loci most strongly associated with serum urate were genotyped. Allelic association of the SNPs with early-onset gout was tested using logistic regression in an unadjusted model and in a model adjusted for sex, body mass index, tophus presence, flare frequency, serum creatinine and highest serum urate. The analysis was also done in two replication cohorts: Eurogout (n = 704) and Ardea (n = 755), and data were meta-analysed. RESULTS In the Genetics of Gout in Aotearoa study, there were 638 (42.4%) participants with early-onset gout. The ABCG2 rs2231142 gout risk T-allele was present more frequently in participants with early-onset gout compared with the later-onset group. For the other SNPs tested, no differences in risk allele number were observed. In the allelic association analysis, the ABCG2 rs2231142 T-allele was associated with early-onset gout in unadjusted and adjusted models. Analysis of the replication cohorts confirmed the association of early-onset gout with the ABCG2 rs2231142 T-allele, but not with other serum urate-associated SNPs. In the meta-analysis, the odds ratio (95% CI) for early-onset gout for the ABCG2 rs2231142 T-allele was 1.60 (1.41, 1.83). CONCLUSION In contrast to other serum urate-raising variants, the ABCG2 rs2231142 T-allele is strongly associated with early-onset gout.
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Affiliation(s)
- Faseeh Zaidi
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, AucklandNew Zealand
| | - Ravi K Narang
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, AucklandNew Zealand
| | | | - Greg G Gamble
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, AucklandNew Zealand
| | | | - Alexander So
- Department of Medicine, Service of Rheumatology, Centre Hospitalier Universitaire Vaudois and University of Lausanne, Lausanne, Switzerland
| | - Philip Riches
- Rheumatology and Bone Disease Unit, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Mariano Andres
- Department of Medicine, Sección de Reumatología, Hospital General Universitario de Alicante, Alicante, Spain
| | - Fernando Perez-Ruiz
- Rheumatology Division, Hospital Universitario Cruces, Baracaldo, Biscay, Spain
| | - Michael Doherty
- Division of Rheumatology, Orthopaedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, UK
| | - Matthijs Janssen
- Department of Rheumatology, VieCuri Medical Center, Venlo, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Tim L Jansen
- Department of Rheumatology, VieCuri Medical Center, Venlo, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rosa J Torres
- Department of Biochemistry, La Paz University Hospital Health Research Institute (FIBHULP), IdiPaz, Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Geraldine M McCarthy
- Department of Rheumatology, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | | | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, Faculty of Medical and Health Sciences, University of Auckland, AucklandNew Zealand
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3
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Takata M, Pachera E, Frank-Bertoncelj M, Kozlova A, Jüngel A, Whitfield ML, Assassi S, Calcagni M, de Vries-Bouwstra J, Huizinga TW, Kurreeman F, Kania G, Distler O. OTUD6B-AS1 Might Be a Novel Regulator of Apoptosis in Systemic Sclerosis. Front Immunol 2019; 10:1100. [PMID: 31156645 PMCID: PMC6533854 DOI: 10.3389/fimmu.2019.01100] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/30/2019] [Indexed: 12/19/2022] Open
Abstract
Antisense long non-coding RNAs (AS lncRNAs) have increasingly been recognized as important regulators of gene expression and they have been found to play key roles in several diseases. However, very little is known about the role of AS lncRNAs in fibrotic diseases such as systemic sclerosis (SSc). Our recent screening experiments by RNA sequencing showed that ovarian tumor domain containing 6B antisense RNA1 (OTUD6B-AS1) and its sense gene OTUD6B were significantly downregulated in SSc skin biopsies. Therefore, we aimed to identify key regulators of OTUD6B-AS1 and to analyze the functional relevance of OTUD6B-AS1 in SSc. OTUD6B-AS1 and OTUD6B expression in SSc and healthy control (HC) dermal fibroblasts (Fb) after stimulation with transforming growth factor-β (TGFβ), Interleukin (IL)-4, IL-13, and platelet-derived growth factor (PDGF) was analyzed by qPCR. To identify the functional role of OTUD6B-AS1, dermal Fb or human pulmonary artery smooth muscle cells (HPASMC) were transfected with a locked nucleic acid antisense oligonucleotide (ASO) targeting OTUD6B-AS1. Proliferation was measured by BrdU and real-time proliferation assay. Apoptosis was measured by Caspase 3/7 assay and Western blot for cleaved caspase 3. While no difference was recorded at the basal level between HC and SSc dermal Fb, the expression of OTUD6B-AS1 and OTUD6B was significantly downregulated in both SSc and HC dermal Fb after PDGF stimulation in a time-dependent manner. Only mild and inconsistent effects were observed with TGFβ, IL-4, and IL-13. OTUD6B-AS1 knockdown in Fb and HPASMC did not affect extracellular matrix or pro-fibrotic/proinflammatory cytokine production. However, OTUD6B-AS1 knockdown significantly increased Cyclin D1 expression at the mRNA and protein level. Moreover, silencing of OTUD6B-AS1 significantly reduced proliferation and suppressed apoptosis in both dermal Fb and HPASMC. OTUD6B-AS1 knockdown did not affect OTUD6B expression at the mRNA level and protein level. Our data suggest that OTUD6B-AS1 regulates proliferation and apoptosis via cyclin D1 expression in a sense gene independent manner. This is the first report investigating the function of OTUD6B-AS1. Our data shed light on a novel apoptosis resistance mechanism in Fb and vascular smooth muscle cells that might be relevant for pathogenesis of SSc.
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Affiliation(s)
- Miki Takata
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Elena Pachera
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Mojca Frank-Bertoncelj
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Anastasiia Kozlova
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Astrid Jüngel
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Shervin Assassi
- Department of Internal Medicine, Division of Rheumatology, The University of Texas Health Science Center at Houston, McGovern Medical School, Houston, TX, United States
| | - Maurizio Calcagni
- Department of Plastic Surgery and Hand Surgery, University Hospital Zürich, Zurich, Switzerland
| | | | - Tom W Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, Netherlands
| | - Gabriela Kania
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
| | - Oliver Distler
- Department of Rheumatology, Center of Experimental Rheumatology, University Hospital Zürich, Zurich, Switzerland
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Messemaker TC, Mikkers HMM, Huizinga TW, Toes REM, van der Helm- van Mil AHM, Kurreeman F. Inflammatory genes TNFα and IL6 display no signs of increased H3K4me3 in circulating monocytes from untreated rheumatoid arthritis patients. Genes Immun 2017; 18:191-196. [DOI: 10.1038/gene.2017.20] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 12/11/2022]
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5
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Knevel R, Huizinga TW, Kurreeman F. Genomic Influences on Susceptibility and Severity of Rheumatoid Arthritis. Rheum Dis Clin North Am 2017; 43:347-361. [DOI: 10.1016/j.rdc.2017.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Cui J, Diogo D, Stahl EA, Canhao H, Mariette X, Greenberg JD, Okada Y, Pappas DA, Fulton RS, Tak PP, Nurmohamed MT, Lee A, Larson DE, Kurreeman F, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Mardis ER, van der Horst-Bruinsma IE, Wolbink GJ, Gregersen PK, Kremer JM, Crusius JBA, de Vries N, Huizinga TWJ, Fonseca JE, Miceli-Richard C, Karlson EW, Coenen MJH, Barton A, Plenge RM, Raychaudhuri S. Brief Report: The Role of Rare Protein-Coding Variants in Anti-Tumor Necrosis Factor Treatment Response in Rheumatoid Arthritis. Arthritis Rheumatol 2017; 69:735-741. [PMID: 27788309 DOI: 10.1002/art.39966] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Abstract
OBJECTIVE In many rheumatoid arthritis (RA) patients, disease is controlled with anti-tumor necrosis factor (anti-TNF) biologic therapies. However, in a significant number of patients, the disease fails to respond to anti-TNF therapy. We undertook the present study to examine the hypothesis that rare and low-frequency genetic variants might influence response to anti-TNF treatment. METHODS We sequenced the coding region of 750 genes in 1,094 RA patients of European ancestry who were treated with anti-TNF. After quality control, 690 genes were included in the analysis. We applied single-variant association and gene-based association tests to identify variants associated with anti-TNF treatment response. In addition, given the key mechanistic role of TNF, we performed gene set analyses of 27 TNF pathway genes. RESULTS We identified 14,420 functional variants, of which 6,934 were predicted as nonsynonymous 2,136 of which were further predicted to be "damaging." Despite the fact that the study was well powered, no single variant or gene showed study-wide significant association with change in the outcome measures disease activity or European League Against Rheumatism response. Intriguingly, we observed 3 genes, of 27 with nominal signals of association (P < 0.05), that were involved in the TNF signaling pathway. However, when we performed a rigorous gene set enrichment analysis based on association P value ranking, we observed no evidence of enrichment of association at genes involved in the TNF pathway (Penrichment = 0.15, based on phenotype permutations). CONCLUSION Our findings suggest that rare and low-frequency protein-coding variants in TNF signaling pathway genes or other genes do not contribute substantially to anti-TNF treatment response in patients with RA.
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Affiliation(s)
- Jing Cui
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dorothee Diogo
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts
| | - Eli A Stahl
- Mount Sinai School of Medicine, New York, New York
| | | | - Xavier Mariette
- Université Paris Sud, INSERM U1184, Center for Immunology of Viral Infections and Autoimmune Diseases, Bicêtre Hospital, AP-HP, Paris, France
| | | | - Yukinori Okada
- Osaka University Graduate School of Medicine, Osaka, Japan
| | | | - Robert S Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Paul P Tak
- University of Amsterdam, Amsterdam, The Netherlands
| | | | - Annette Lee
- Feinstein Institute for Medical Research, Manhasset, New York
| | - David E Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Fina Kurreeman
- Leiden University Medical Centre, Leiden, The Netherlands
| | - Tracie L Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Catrina C Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Lucinda L Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Elaine R Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | | | - Gert-Jan Wolbink
- Amsterdam Rheumatology and Immunology Center, Reade, Amsterdam, The Netherlands
| | | | - Joel M Kremer
- Albany Medical College and the Center for Rheumatology, Albany, New York
| | | | | | | | | | | | | | | | - Anne Barton
- Centre for Musculoskeletal Research, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Robert M Plenge
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, and Broad Institute, Cambridge, Massachusetts
| | - Soumya Raychaudhuri
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, Broad Institute, Cambridge, Massachusetts, and Centre for Musculoskeletal Research, University of Manchester and Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
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7
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Pachera E, Assassi S, Salazar G, Frank-Bertoncelj M, Dobrota R, Brock M, Kurreeman F, de Vries-Bouwstra J, Messemaker T, Feghali-Bostwick C, Distler J, Kania G, Distler O. FRI0247 The Involvement of The Long Noncoding H19x in tGFβ Signaling and Its Profibrotic Effects in Systemic Sclerosis and Other Fibrotic Diseases. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-eular.3237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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8
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Suurmond J, Habets KLL, Tatum Z, Schonkeren JJ, Hoen PAC', Huizinga TWJ, Laros JFJ, Toes REM, Kurreeman F. Repeated FcεRI triggering reveals modified mast cell function related to chronic allergic responses in tissue. J Allergy Clin Immunol 2016; 138:869-880. [PMID: 27033170 DOI: 10.1016/j.jaci.2016.01.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Revised: 12/18/2015] [Accepted: 01/07/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND Activation of mast cells through FcεRI plays an important role in acute allergic reactions. However, little is known about the function of mast cells in patients with chronic allergic inflammation or the effect of repeated FcεRI triggering occurring in such responses. OBJECTIVE We aimed to identify changes in mast cell function after repeated FcεRI triggering and to correlate these changes to chronic allergic responses in tissue. METHODS Human cord blood-derived mast cells were treated for 2 weeks with anti-IgE. The function of naive or treated mast cells was analyzed by means of RNA sequencing, quantitative RT-PCR, flow cytometry, and functional assays. Protein secretion was measured with ELISAs and multiplex assays. RESULTS We observed several changes in mast cell function after repeated anti-IgE triggering. Although the acute response was dampened, we identified 289 genes significantly upregulated after repeated anti-IgE. Most of these genes (84%) were not upregulated after a single anti-IgE stimulus, indicating a significantly different response mode characterized by increased antigen presentation, response to bacteria, and chemotaxis. Changes in mast cell function were related to changes in expression of the transcription factors RXRA and BATF and others. Importantly, we found a substantial overlap between genes upregulated after repeated anti-IgE triggering and genes upregulated in tissue from patients with chronic allergy, in particular those of patients with chronic rhinosinusitis. CONCLUSION Our study provides evidence for intrinsic modulation of mast cell function on repeated FcεRI-mediated activation. The overlap with gene expression in tissues is suggestive of a direct link between repeated IgE-mediated activation of mast cells and chronic allergy.
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Affiliation(s)
- Jolien Suurmond
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kim L L Habets
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Zuotian Tatum
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Joris J Schonkeren
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom W J Huizinga
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - René E M Toes
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands.
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Messemaker TC, Mikkers HMM, Huizinga TW, Toes REM, van der Helm- van Mil AHM, Kurreeman F. A8.09 Trained immunity in monocytes from rheumatoid arthritis patients and healthy individuals. Ann Rheum Dis 2016. [DOI: 10.1136/annrheumdis-2016-209124.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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10
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11
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Messemaker T, Toes REM, Mikkers HMM, Kurreeman F. Comment on "Functional Analysis of a Complement Polymorphism (rs17611) Associated with Rheumatoid Arthritis". J Immunol 2015; 195:3-4. [PMID: 26092809 DOI: 10.4049/jimmunol.1500822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Tobias Messemaker
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; and
| | - Rene E M Toes
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Harald M M Mikkers
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; and
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, the Netherlands; Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
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12
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Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, Eyre S, Bowes J, Cui J, Lee A, Pappas DA, Kremer JM, Barton A, Coenen MJH, Franke B, Kiemeney LA, Mariette X, Richard-Miceli C, Canhão H, Fonseca JE, de Vries N, Tak PP, Crusius JBA, Nurmohamed MT, Kurreeman F, Mikuls TR, Okada Y, Stahl EA, Larson DE, Deluca TL, O'Laughlin M, Fronick CC, Fulton LL, Kosoy R, Ransom M, Bhangale TR, Ortmann W, Cagan A, Gainer V, Karlson EW, Kohane I, Murphy SN, Martin J, Zhernakova A, Klareskog L, Padyukov L, Worthington J, Mardis ER, Seldin MF, Gregersen PK, Behrens T, Raychaudhuri S, Denny JC, Plenge RM. TYK2 protein-coding variants protect against rheumatoid arthritis and autoimmunity, with no evidence of major pleiotropic effects on non-autoimmune complex traits. PLoS One 2015; 10:e0122271. [PMID: 25849893 PMCID: PMC4388675 DOI: 10.1371/journal.pone.0122271] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/17/2015] [Indexed: 02/06/2023] Open
Abstract
Despite the success of genome-wide association studies (GWAS) in detecting a large number of loci for complex phenotypes such as rheumatoid arthritis (RA) susceptibility, the lack of information on the causal genes leaves important challenges to interpret GWAS results in the context of the disease biology. Here, we genetically fine-map the RA risk locus at 19p13 to define causal variants, and explore the pleiotropic effects of these same variants in other complex traits. First, we combined Immunochip dense genotyping (n = 23,092 case/control samples), Exomechip genotyping (n = 18,409 case/control samples) and targeted exon-sequencing (n = 2,236 case/controls samples) to demonstrate that three protein-coding variants in TYK2 (tyrosine kinase 2) independently protect against RA: P1104A (rs34536443, OR = 0.66, P = 2.3x10-21), A928V (rs35018800, OR = 0.53, P = 1.2x10-9), and I684S (rs12720356, OR = 0.86, P = 4.6x10-7). Second, we show that the same three TYK2 variants protect against systemic lupus erythematosus (SLE, Pomnibus = 6x10-18), and provide suggestive evidence that two of the TYK2 variants (P1104A and A928V) may also protect against inflammatory bowel disease (IBD; Pomnibus = 0.005). Finally, in a phenome-wide association study (PheWAS) assessing >500 phenotypes using electronic medical records (EMR) in >29,000 subjects, we found no convincing evidence for association of P1104A and A928V with complex phenotypes other than autoimmune diseases such as RA, SLE and IBD. Together, our results demonstrate the role of TYK2 in the pathogenesis of RA, SLE and IBD, and provide supporting evidence for TYK2 as a promising drug target for the treatment of autoimmune diseases.
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Affiliation(s)
- Dorothée Diogo
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- * E-mail:
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Katherine P. Liao
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert R. Graham
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Robert S. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jeffrey D. Greenberg
- New York University Hospital for Joint Diseases, New York, New York, United States of America
| | - Steve Eyre
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - John Bowes
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Jing Cui
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Lee
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Dimitrios A. Pappas
- Columbia University, College of Physicians and Surgeons, New York, New York, United States of America
| | - Joel M. Kremer
- The Albany Medical College and The Center for Rheumatology, Albany, New York, United States of America
| | - Anne Barton
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Marieke J. H. Coenen
- Radboud university medical center, Radboud Institute for Health Sciences, Department of Human Genetics, Nijmegen, The Netherlands
| | - Barbara Franke
- Radboud University Medical Center, Donders Centre for Neurosciences, Department of Psychiatry and Human Genetics, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Radboud University Medical Center, Radboud Institute for Health Sciences, Nijmegen, The Netherlands
| | - Xavier Mariette
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Corrine Richard-Miceli
- Université Paris-Sud, Orsay, France
- APHP–Hôpital Bicêtre, INSERM U1012, Le Kremlin Bicêtre, Paris, France
| | - Helena Canhão
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - João E. Fonseca
- Rheumatology Research Unit, Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
- Rheumatology Department, Santa Maria Hospital–CHLN, Lisbon, Portugal
| | - Niek de Vries
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - Paul P. Tak
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology & Rheumatology, Academic Medical Center /University of Amsterdam, Amsterdam, The Netherlands
| | - J. Bart A. Crusius
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - Michael T. Nurmohamed
- Amsterdam Rheumatology and Immunology Center, Department of Rheumatology, Reade, Amsterdam, The Netherlands
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Ted R. Mikuls
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Yukinori Okada
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eli A. Stahl
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
| | - David E. Larson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Tracie L. Deluca
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michelle O'Laughlin
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Lucinda L. Fulton
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Roman Kosoy
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Michael Ransom
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
| | - Tushar R. Bhangale
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Ward Ortmann
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Andrew Cagan
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Vivian Gainer
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Elizabeth W. Karlson
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Isaac Kohane
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Shawn N. Murphy
- Information Systems, Partners Healthcare, Charlestown, Massachusetts, United States of America
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, 18100, Spain
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
- Genetics Department, University Medical Center and Groningen University, Groningen, The Netherlands
| | - Lars Klareskog
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Elaine R. Mardis
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Michael F. Seldin
- Division of Rheumatology and Immunology, Omaha VA and University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore-Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Timothy Behrens
- ITGR Human Genetics Group, Genentech Inc, San Francisco, California, United States of America
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Partners HealthCare Center for Personalized Genetic Medicine, Boston, Massachusetts, United States of America
- Arthritis Research UK Epidemiology Unit, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Joshua C. Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Robert M. Plenge
- Division of Rheumatology, Immunology, and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
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13
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Maehlen MT, Olsen IC, Andreassen BK, Viken MK, Jiang X, Alfredsson L, Källberg H, Brynedal B, Kurreeman F, Daha N, Toes R, Zhernakova A, Gutierrez-Achury J, de Bakker PIW, Martin J, Teruel M, Gonzalez-Gay MA, Rodríguez-Rodríguez L, Balsa A, Uhlig T, Kvien TK, Lie BA. Genetic risk scores and number of autoantibodies in patients with rheumatoid arthritis. Ann Rheum Dis 2013; 74:762-8. [PMID: 24336335 DOI: 10.1136/annrheumdis-2013-204173] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE Certain HLA-DRB1 alleles and single-nucleotide polymorphisms (SNPs) are associated with rheumatoid arthritis (RA). Our objective was to examine the combined effect of these associated variants, calculated as a cumulative genetic risk score (GRS) on RA predisposition, as well as the number of autoantibodies (none, one or two present). METHOD We calculated four GRSs in 4956 patients and 4983 controls from four European countries. All four scores contained data on 22 non-HLA-risk SNPs, and three scores also contained HLA-DRB1 genotypes but had different HLA typing resolution. Most patients had data on both rheumatoid factor (RF) and anti-citrullinated proteins antibodies (ACPA). The GRSs were standardised (std.GRS) to account for population heterogeneity. Discrimination between patients and controls was examined by receiveroperating characteristics curves, and the four std.GRSs were compared across subgroups according to autoantibody status. RESULTS The std.GRS improved its discriminatory ability between patients and controls when HLA-DRB1 data of higher resolution were added to the combined score. Patients had higher mean std.GRS than controls (p=7.9×10(-156)), and this score was significantly higher in patients with autoantibodies (shown for both RF and ACPA). Mean std.GRS was also higher in those with two versus one autoantibody (p=3.7×10(-23)) but was similar in patients without autoantibodies and controls (p=0.12). CONCLUSIONS The GRS was associated with the number of autoantibodies and to both RF and ACPA positivity. ACPA play a more important role than RF with regards to the genetic risk profile, but stratification of patients according to both RF and ACPA may optimise future genetic studies.
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Affiliation(s)
- Marthe T Maehlen
- Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway Department of Medical Genetics, University of Oslo and Oslo University Hospital, Ullevål, Oslo, Norway
| | - Inge C Olsen
- Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
| | - Bettina K Andreassen
- Department of EpiGen, Institute of Clinical Medicine, University of Oslo, Oslo, Norway Department of Biostatistics, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Marte K Viken
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Ullevål, Oslo, Norway
| | - Xia Jiang
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Henrik Källberg
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Boel Brynedal
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Fina Kurreeman
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Nina Daha
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Rene Toes
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Alexandra Zhernakova
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Javier Gutierrez-Achury
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Paul I W de Bakker
- Departments of Medical Genetics and of Epidemiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Javier Martin
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, Spain
| | - María Teruel
- Instituto de Parasitologia y Biomedicina Lopez-Neyra, CSIC, Granada, Spain
| | | | | | | | - Till Uhlig
- Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
| | - Tore K Kvien
- Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Ullevål, Oslo, Norway
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14
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De Rooy D, Zhernakova A, Tsonaka R, Willemze A, Kurreeman F, Trynka G, van Toorn L, Toes R, Huizinga T, Houwing-Duistermaat J, Gregersen P, van der Helm-van Mil A. OP0049 A Genetic Variant in the Region of MMP-9 is Associated with Serum Levels and Progression of Joint Damage in Rheumatoid Arthritis. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2013-eular.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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15
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Li G, Diogo D, Wu D, Spoonamore J, Dancik V, Franke L, Kurreeman F, Rossin EJ, Duclos G, Hartland C, Zhou X, Li K, Liu J, De Jager PL, Siminovitch KA, Zhernakova A, Raychaudhuri S, Bowes J, Eyre S, Padyukov L, Gregersen PK, Worthington J, Gupta N, Clemons PA, Stahl E, Tolliday N, Plenge RM. Human genetics in rheumatoid arthritis guides a high-throughput drug screen of the CD40 signaling pathway. PLoS Genet 2013; 9:e1003487. [PMID: 23696745 PMCID: PMC3656093 DOI: 10.1371/journal.pgen.1003487] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 03/15/2013] [Indexed: 12/21/2022] Open
Abstract
Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis (RA), there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease. Here, we sought to understand the biological consequences of a CD40 risk variant in RA discovered by a previous genome-wide association study (GWAS) and to perform a high-throughput drug screen for modulators of CD40 signaling based on human genetic findings. First, we fine-map the CD40 risk locus in 7,222 seropositive RA patients and 15,870 controls, together with deep sequencing of CD40 coding exons in 500 RA cases and 650 controls, to identify a single SNP that explains the entire signal of association (rs4810485, P = 1.4×10−9). Second, we demonstrate that subjects homozygous for the RA risk allele have ∼33% more CD40 on the surface of primary human CD19+ B lymphocytes than subjects homozygous for the non-risk allele (P = 10−9), a finding corroborated by expression quantitative trait loci (eQTL) analysis in peripheral blood mononuclear cells from 1,469 healthy control individuals. Third, we use retroviral shRNA infection to perturb the amount of CD40 on the surface of a human B lymphocyte cell line (BL2) and observe a direct correlation between amount of CD40 protein and phosphorylation of RelA (p65), a subunit of the NF-κB transcription factor. Finally, we develop a high-throughput NF-κB luciferase reporter assay in BL2 cells activated with trimerized CD40 ligand (tCD40L) and conduct an HTS of 1,982 chemical compounds and FDA–approved drugs. After a series of counter-screens and testing in primary human CD19+ B cells, we identify 2 novel chemical inhibitors not previously implicated in inflammation or CD40-mediated NF-κB signaling. Our study demonstrates proof-of-concept that human genetics can be used to guide the development of phenotype-based, high-throughput small-molecule screens to identify potential novel therapies in complex traits such as RA. A current challenge in human genetics is to follow-up “hits” from genome-wide association studies (GWAS) to guide drug discovery for complex traits. Previously, we identified a common variant in the CD40 locus as associated with risk of rheumatoid arthritis (RA). Here, we fine-map the CD40 signal of association through a combination of dense genotyping and exonic sequencing in large patient collections. Further, we demonstrate that the RA risk allele is a gain-of-function allele that increases the amount of CD40 on the surface of primary human B lymphocyte cells from healthy control individuals. Based on these observations, we develop a high-throughput assay to recapitulate the biology of the RA risk allele in a system suitable for a small molecule drug screen. After a series of primary screens and counter screens, we identify small molecules that inhibit CD40-mediated NF-kB signaling in human B cells. While this is only the first step towards a more comprehensive effort to identify CD40-specific inhibitors that may be used to treat RA, our study demonstrates a successful strategy to progress from a GWAS to a drug screen for complex traits such as RA.
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Affiliation(s)
- Gang Li
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dorothée Diogo
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Di Wu
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Jim Spoonamore
- Chemical Biology Platform, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Vlado Dancik
- Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
| | - Fina Kurreeman
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Elizabeth J. Rossin
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Biological and Biomedical Sciences Program, Health Sciences and Technology Program, Harvard Medical School, Boston, Massachusetts, United States of America
- Analytical and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Grant Duclos
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Cathy Hartland
- Chemical Biology Platform, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Xuezhong Zhou
- School of Computer and Information Technology, Beijing Jiaotong University, Beijing, China
| | - Kejie Li
- Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Jun Liu
- Department of Statistics, Harvard University, Cambridge, Massachusetts, United States of America
| | - Philip L. De Jager
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences Department of Neurology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America
| | - Katherine A. Siminovitch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Samuel Lunenfeld Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen and University of Groningen, Groningen, The Netherlands
- Department of Rheumatology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - John Bowes
- Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Steve Eyre
- Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Leonid Padyukov
- Rheumatology Unit, Department of Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Peter K. Gregersen
- The Feinstein Institute for Medical Research, North Shore–Long Island Jewish Health System, Manhasset, New York, United States of America
| | - Jane Worthington
- Arthritis Research UK Epidemiology Unit, Musculoskeletal Research Group, University of Manchester, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
- NIHR Manchester Musculoskeletal Biomedical Research Unit, Central Manchester NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | | | - Namrata Gupta
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Paul A. Clemons
- Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Eli Stahl
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Nicola Tolliday
- Chemical Biology Platform, Broad Institute, Cambridge, Massachusetts, United States of America
| | - Robert M. Plenge
- Division of Rheumatology, Immunology, and Allergy and Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Medical and Population Genetics Program, Chemical Biology Program, Broad Institute, Cambridge, Massachusetts, United States of America
- * E-mail:
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16
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Liao KP, Kurreeman F, Li G, Duclos G, Murphy S, Guzman R, Cai T, Gupta N, Gainer V, Schur P, Cui J, Denny JC, Szolovits P, Churchill S, Kohane I, Karlson EW, Plenge RM. Associations of autoantibodies, autoimmune risk alleles, and clinical diagnoses from the electronic medical records in rheumatoid arthritis cases and non-rheumatoid arthritis controls. ACTA ACUST UNITED AC 2013; 65:571-81. [PMID: 23233247 DOI: 10.1002/art.37801] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/15/2012] [Indexed: 12/29/2022]
Abstract
OBJECTIVE The significance of non-rheumatoid arthritis (RA) autoantibodies in patients with RA is unclear. The aim of this study was to assess associations of autoantibodies with autoimmune risk alleles and with clinical diagnoses from the electronic medical records (EMRs) among RA cases and non-RA controls. METHODS Data on 1,290 RA cases and 1,236 non-RA controls of European genetic ancestry were obtained from the EMRs of 2 large academic centers. The levels of anti-citrullinated protein antibodies (ACPAs), antinuclear antibodies (ANAs), anti-tissue transglutaminase antibodies (AGTAs), and anti-thyroid peroxidase (anti-TPO) antibodies were measured. All subjects were genotyped for autoimmune risk alleles, and the association between number of autoimmune risk alleles present and number of types of autoantibodies present was studied. A phenome-wide association study (PheWAS) was conducted to study potential associations between autoantibodies and clinical diagnoses among RA cases and non-RA controls. RESULTS The mean ages were 60.7 years in RA cases and 64.6 years in non-RA controls. The proportion of female subjects was 79% in each group. The prevalence of ACPAs and ANAs was higher in RA cases compared to controls (each P < 0.0001); there were no differences in the prevalence of anti-TPO antibodies and AGTAs. Carriage of higher numbers of autoimmune risk alleles was associated with increasing numbers of autoantibody types in RA cases (P = 2.1 × 10(-5)) and non-RA controls (P = 5.0 × 10(-3)). From the PheWAS, the presence of ANAs was significantly associated with a diagnosis of Sjögren's/sicca syndrome in RA cases. CONCLUSION The increased frequency of autoantibodies in RA cases and non-RA controls was associated with the number of autoimmune risk alleles carried by an individual. PheWAS of EMR data, with linkage to laboratory data obtained from blood samples, provide a novel method to test for the clinical significance of biomarkers in disease.
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Affiliation(s)
- Katherine P Liao
- Brigham and Women's Hospital, 75 Francis Street, PBB-B3, Boston, MA 02115, USA.
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17
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Diogo D, Kurreeman F, Stahl E, Liao K, Gupta N, Greenberg J, Rivas M, Hickey B, Flannick J, Thomson B, Guiducci C, Ripke S, Adzhubey I, Barton A, Kremer J, Alfredsson L, Sunyaev S, Martin J, Zhernakova A, Bowes J, Eyre S, Siminovitch K, Gregersen P, Worthington J, Klareskog L, Padyukov L, Raychaudhuri S, Plenge R, Raychaudhuri S, Plenge RM. Rare, low-frequency, and common variants in the protein-coding sequence of biological candidate genes from GWASs contribute to risk of rheumatoid arthritis. Am J Hum Genet 2013; 92:15-27. [PMID: 23261300 DOI: 10.1016/j.ajhg.2012.11.012] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 09/04/2012] [Accepted: 11/26/2012] [Indexed: 01/29/2023] Open
Abstract
The extent to which variants in the protein-coding sequence of genes contribute to risk of rheumatoid arthritis (RA) is unknown. In this study, we addressed this issue by deep exon sequencing and large-scale genotyping of 25 biological candidate genes located within RA risk loci discovered by genome-wide association studies (GWASs). First, we assessed the contribution of rare coding variants in the 25 genes to the risk of RA in a pooled sequencing study of 500 RA cases and 650 controls of European ancestry. We observed an accumulation of rare nonsynonymous variants exclusive to RA cases in IL2RA and IL2RB (burden test: p = 0.007 and p = 0.018, respectively). Next, we assessed the aggregate contribution of low-frequency and common coding variants to the risk of RA by dense genotyping of the 25 gene loci in 10,609 RA cases and 35,605 controls. We observed a strong enrichment of coding variants with a nominal signal of association with RA (p < 0.05) after adjusting for the best signal of association at the loci (p(enrichment) = 6.4 × 10(-4)). For one locus containing CD2, we found that a missense variant, rs699738 (c.798C>A [p.His266Gln]), and a noncoding variant, rs624988, reside on distinct haplotypes and independently contribute to the risk of RA (p = 4.6 × 10(-6)). Overall, our results indicate that variants (distributed across the allele-frequency spectrum) within the protein-coding portion of a subset of biological candidate genes identified by GWASs contribute to the risk of RA. Further, we have demonstrated that very large sample sizes will be required for comprehensively identifying the independent alleles contributing to the missing heritability of RA.
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