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Hitomi Y, Ueno K, Aiba Y, Nishida N, Kono M, Sugihara M, Kawai Y, Kawashima M, Khor SS, Sugi K, Kouno H, Kohno H, Naganuma A, Iwamoto S, Katsushima S, Furuta K, Nikami T, Mannami T, Yamashita T, Ario K, Komatsu T, Makita F, Shimada M, Hirashima N, Yokohama S, Nishimura H, Sugimoto R, Komura T, Ota H, Kojima M, Nakamuta M, Fujimori N, Yoshizawa K, Mano Y, Takahashi H, Hirooka K, Tsuruta S, Sato T, Yamasaki K, Kugiyama Y, Motoyoshi Y, Suehiro T, Saeki A, Matsumoto K, Nagaoka S, Abiru S, Yatsuhashi H, Ito M, Kawata K, Takaki A, Arai K, Arinaga-Hino T, Abe M, Harada M, Taniai M, Zeniya M, Ohira H, Shimoda S, Komori A, Tanaka A, Ishigaki K, Nagasaki M, Tokunaga K, Nakamura M. A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis. Hepatology 2024:01515467-990000000-00853. [PMID: 38652555 DOI: 10.1097/hep.0000000000000894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/22/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND AND AIMS Previous genome-wide association studies (GWAS) have indicated the involvement of shared (population-nonspecific) and nonshared (population-specific) susceptibility genes in the pathogenesis of primary biliary cholangitis (PBC) among European and East-Asian populations. Although a meta-analysis of these distinct populations has recently identified more than 20 novel PBC susceptibility loci, analyses of population-specific genetic architecture are still needed for a more comprehensive search for genetic factors in PBC. APPROACH AND RESULTS Protein tyrosine phosphatase nonreceptor type 2 ( PTPN2) was identified as a novel PBC susceptibility gene locus through GWAS and subsequent genome-wide meta-analysis involving 2181 cases and 2699 controls from the Japanese population (GWAS-lead variant: rs8098858, p = 2.6 × 10 -8 ). In silico and in vitro functional analyses indicated that the risk allele of rs2292758, which is a primary functional variant, decreases PTPN2 expression by disrupting Sp1 binding to the PTPN2 promoter in T follicular helper cells and plasmacytoid dendritic cells. Infiltration of PTPN2-positive T-cells and plasmacytoid dendritic cells was confirmed in the portal area of the PBC liver by immunohistochemistry. Furthermore, transcriptomic analysis of PBC-liver samples indicated the presence of a compromised negative feedback loop in vivo between PTPN2 and IFNG in patients carrying the risk allele of rs2292758. CONCLUSIONS PTPN2 , a novel susceptibility gene for PBC in the Japanese population, may be involved in the pathogenesis of PBC through an insufficient negative feedback loop caused by the risk allele of rs2292758 in IFN-γ signaling. This suggests that PTPN2 could be a potential molecular target for PBC treatment.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Nao Nishida
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Michihiro Kono
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mitsuki Sugihara
- Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | | | - Seik-Soon Khor
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kazuhiro Sugi
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hirotaka Kouno
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Kohno
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Atsushi Naganuma
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Satoru Iwamoto
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Shinji Katsushima
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kiyoshi Furuta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Toshiki Nikami
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tomohiko Mannami
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tsutomu Yamashita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Keisuke Ario
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tatsuji Komatsu
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Fujio Makita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Masaaki Shimada
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Noboru Hirashima
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Shiro Yokohama
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hideo Nishimura
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Rie Sugimoto
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Takuya Komura
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hajime Ota
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Motoyuki Kojima
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Makoto Nakamuta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Naoyuki Fujimori
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kaname Yoshizawa
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yutaka Mano
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hironao Takahashi
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kana Hirooka
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Satoru Tsuruta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Takeaki Sato
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazumi Yamasaki
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yuki Kugiyama
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | | | - Tomoyuki Suehiro
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Akira Saeki
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kosuke Matsumoto
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Shinya Nagaoka
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Seigo Abiru
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | | | - Masahiro Ito
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazuhito Kawata
- Hepatology Division, Department of Internal Medicine II, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Akinobu Takaki
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kuniaki Arai
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Teruko Arinaga-Hino
- Division of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, Japan
| | - Masanori Abe
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, Japan
| | - Masaru Harada
- The Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Makiko Taniai
- Department of Medicine and Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Mikio Zeniya
- Department of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, Japan
| | - Hiromasa Ohira
- Department of Gastroenterology, Fukushima Medical University, Fukushima, Japan
| | - Shinji Shimoda
- Division of Gastroenterology and Hepatology, Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Atsumasa Komori
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masao Nagasaki
- Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
- Division of Biomedical Information Analysis, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
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2
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Tsygankov AY. Role of Tula-Family Proteins in Cell Signaling and Activation: Advances and Challenges. Int J Mol Sci 2024; 25:4434. [PMID: 38674019 PMCID: PMC11050124 DOI: 10.3390/ijms25084434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
This Special Issue entitled "Role of Tula-Family Proteins in Cell Signaling and Activation: Advances and Challenges" is focused on a relatively novel vertebrate gene/protein family termed alternatively TULA, UBASH3, or STS [...].
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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3
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Naito S, Tanaka H, Jiang JJ, Tarumi M, Hashimoto A, Tanaka Y, Murakami K, Kubota SI, Hojyo S, Hashimoto S, Murakami M. DDX6 is involved in the pathogenesis of inflammatory diseases via NF-κB activation. Biochem Biophys Res Commun 2024; 703:149666. [PMID: 38377944 DOI: 10.1016/j.bbrc.2024.149666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024]
Abstract
The IL-6 amplifier was originally discovered as a mechanism for the enhanced activation of NF-κB in non-immune cells. In the IL-6 amplifier, IL-6-STAT3 and NF-κB stimulation is followed by an excessive production of IL-6, chemokines, and growth factors to develop chronic inflammation preceding the development of inflammatory diseases. Previously, using a shRNA-mediated genome-wide screening, we found that DEAD-Box Helicase 6 (DDX6) is a candidate positive regulator of the amplifier. Here, we investigate whether DDX6 is involved in the pathogenesis of inflammatory diseases via the IL-6 amplifier. We found that DDX6-silencing in non-immune cells suppressed the NF-κB pathway and inhibited activation of the IL-6 amplifier, while the forced expression of DDX6 enhanced NF-κB promoter activity independent of the RNA helicase activity of DDX6. The imiquimod-mediated dermatitis model was suppressed by the siRNA-mediated gene downregulation of DDX6. Furthermore, silencing DDX6 significantly reduced the TNF-α-induced phosphorylation of p65/RelA and IκBα, nuclear localization of p65, and the protein levels of IκBα. Mechanistically, DDX6 is strongly associated with p65 and IκBα, but not TRADD, RIP, or TRAF2, suggesting a novel function of DDX6 as an adaptor protein in the NF-κB pathway. Thus, our findings demonstrate a possible role of DDX6 beyond RNA metabolism and suggest DDX6 is a therapeutic target for inflammatory diseases.
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Affiliation(s)
- Seiichiro Naito
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Department of Cardiovascular Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroki Tanaka
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Jing-Jing Jiang
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Masato Tarumi
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Ari Hashimoto
- Department of Molecular Biology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Yuki Tanaka
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Group of Quantum Immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba, Japan
| | - Kaoru Murakami
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shimpei I Kubota
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shintaro Hojyo
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Shigeru Hashimoto
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan.
| | - Masaaki Murakami
- Division of Molecular Psychoimmunology, Institute for Genetic Medicine, Graduate School of Medicine, Hokkaido University, Sapporo, Japan; Group of Quantum Immunology, Institute for Quantum Life Science, National Institute for Quantum and Radiological Science and Technology (QST), Chiba, Japan; Division of Molecular Neuroimmunology, Department of Homeostatic Regulation, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Aichi, Japan; Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan.
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4
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Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Johnson WC, Van Den Berg D, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Barr RG, Lappalainen T. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. Am J Hum Genet 2024; 111:133-149. [PMID: 38181730 PMCID: PMC10806864 DOI: 10.1016/j.ajhg.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 11/29/2023] [Accepted: 11/29/2023] [Indexed: 01/07/2024] Open
Abstract
Bulk-tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, and context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from the blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell-type proportions, we demonstrate that cell-type iQTLs could be considered as proxies for cell-type-specific QTL effects, particularly for the most abundant cell type in the tissue. The interpretation of age iQTLs, however, warrants caution because the moderation effect of age on the genotype and molecular phenotype association could be mediated by changes in cell-type composition. Finally, we show that cell-type iQTLs contribute to cell-type-specific enrichment of diseases that, in combination with additional functional data, could guide future functional studies. Overall, this study highlights the use of iQTLs to gain insights into the context specificity of regulatory effects.
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Affiliation(s)
- Silva Kasela
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA.
| | | | - Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, USA; Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital LMU Munich, Munich, Germany; Computational Health Center, Institute of Translational Genomics, Helmholtz Munich, Neuherberg, Germany
| | - Brielin C Brown
- New York Genome Center, New York, NY, USA; Data Science Institute, Columbia University, New York, NY, USA
| | - Daniel C Nachun
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Russell P Tracy
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Peter Durda
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D Smith
- Northwest Genomics Center, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA; Department of Systems Biology, Columbia University, New York, NY, USA; Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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5
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Gupta A, Weinand K, Nathan A, Sakaue S, Zhang MJ, Donlin L, Wei K, Price AL, Amariuta T, Raychaudhuri S. Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. Nat Genet 2023; 55:2200-2210. [PMID: 38036783 PMCID: PMC10787644 DOI: 10.1038/s41588-023-01577-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 10/18/2023] [Indexed: 12/02/2023]
Abstract
In autoimmune diseases such as rheumatoid arthritis, the immune system attacks the body's own cells. Developing a precise understanding of the cell states where noncoding autoimmune risk variants impart causal mechanisms is critical to developing curative therapies. Here, to identify noncoding regions with accessible chromatin that associate with cell-state-defining gene expression patterns, we leveraged multimodal single-nucleus RNA and assay for transposase-accessible chromatin (ATAC) sequencing data across 28,674 cells from the inflamed synovial tissue of 12 donors. Specifically, we used a multivariate Poisson model to predict peak accessibility from single-nucleus RNA sequencing principal components. For 14 autoimmune diseases, we discovered that cell-state-dependent ('dynamic') chromatin accessibility peaks in immune cell types were enriched for heritability, compared with cell-state-invariant ('cs-invariant') peaks. These dynamic peaks marked regulatory elements associated with T peripheral helper, regulatory T, dendritic and STAT1+CXCL10+ myeloid cell states. We argue that dynamic regulatory elements can help identify precise cell states enriched for disease-critical genetic variation.
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Affiliation(s)
- Anika Gupta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kathryn Weinand
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Aparna Nathan
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Martin Jinye Zhang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Laura Donlin
- Weill Cornell Medicine, New York, NY, USA
- Hospital for Special Surgery, New York, NY, USA
| | - Kevin Wei
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Alkes L Price
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Tiffany Amariuta
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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6
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Garrett-Sinha LA. An update on the roles of transcription factor Ets1 in autoimmune diseases. WIREs Mech Dis 2023; 15:e1627. [PMID: 37565573 PMCID: PMC10842644 DOI: 10.1002/wsbm.1627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023]
Abstract
Transcription factors are crucial to regulate gene expression in immune cells and in other cell types. In lymphocytes, there are a large number of different transcription factors that are known to contribute to cell differentiation and the balance between quiescence and activation. One such transcription factor is E26 oncogene homolog 1 (Ets1). Ets1 expression is high in quiescent B and T lymphocytes and its levels are decreased upon activation. The human ETS1 gene has been identified as a susceptibility locus for many autoimmune and inflammatory diseases. In accord with this, gene knockout of Ets1 in mice leads to development of a lupus-like autoimmune disease, with enhanced activation and differentiation of both B cells and T cells. Prior reviews have summarized functional roles for Ets1 based on studies of Ets1 knockout mice. In recent years, numerous additional studies have been published that further validate ETS1 as a susceptibility locus for human diseases where immune dysregulation plays a causative role. In this update, new information that further links Ets1 to human autoimmune diseases is organized and collated to serve as a resource. This update also describes recent studies that seek to understand molecularly how Ets1 regulates immune cell activation, either using human cells and tissues or mouse models. This resource is expected to be useful to investigators seeking to understand how Ets1 may regulate the human immune response, particularly in terms of its roles in autoimmunity and inflammation. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Lee Ann Garrett-Sinha
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York, Buffalo, New York, USA
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7
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Zhang S, Yao HF, Li H, Su T, Jiang SH, Wang H, Zhang ZG, Dong FY, Yang Q, Yang XM. Transglutaminases are oncogenic biomarkers in human cancers and therapeutic targeting of TGM2 blocks chemoresistance and macrophage infiltration in pancreatic cancer. Cell Oncol (Dordr) 2023; 46:1473-1492. [PMID: 37246171 DOI: 10.1007/s13402-023-00824-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 05/30/2023] Open
Abstract
PURPOSE Transglutaminases (TGs) are multifunctional enzymes exhibiting transglutaminase crosslinking, as well as atypical GTPase/ATPase and kinase activities. Here, we used an integrated comprehensive analysis to assess the genomic, transcriptomic and immunological landscapes of TGs across cancers. METHODS Gene expression and immune cell infiltration patterns across cancers were obtained from The Cancer Genome Atlas (TCGA) database and Gene Set Enrichment Analysis (GSEA) datasets. Western blotting, immunofluorescence staining, enzyme-linked immunosorbent assays, and orthotopic xenograft models were used to validate our database-derived results. RESULTS We found that the overall expression of TGs (designated as the TG score) is significantly upregulated in multiple cancers and related to a worse patient survival. The expression of TG family members can be regulated through multiple mechanisms at the genetic, epigenetic and transcriptional levels. The expression of transcription factors crucial for epithelial-to-mesenchymal transition (EMT) is commonly correlated with the TG score in many cancer types. Importantly, TGM2 expression displays a close connection with chemoresistance to a wide range of chemotherapeutic drugs. We found that TGM2 expression, F13A1 expression and the overall TG score were positively correlated with the infiltration of immune cells in all cancer types tested. Functional and clinical verification revealed that a higher TGM2 expression is linked with a worse patient survival, an increased IC50 value of gemcitabine, and a higher abundance of tumor-infiltrating macrophages in pancreatic cancer. Mechanistically, we found that increased C-C motif chemokine ligand 2 (CCL2) release mediated by TGM2 contributes to macrophage infiltration into the tumor microenvironment. CONCLUSIONS Our results reveal the relevance and molecular networks of TG genes in human cancers and highlight the importance of TGM2 in pancreatic cancer, which may provide promising directions for immunotherapy and for addressing chemoresistance.
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Affiliation(s)
- Shan Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hong-Fei Yao
- Department of Biliary-Pancreatic Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200217, People's Republic of China
| | - Hui Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Tong Su
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, 200011, China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
| | - Hao Wang
- Department of Oncology, Shanghai East Hospital, School of Medicine, Tongji University, 1800 Yuntai Road, Pudong District, Shanghai, 200123, China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
| | - Fang-Yuan Dong
- Department of Gastroenterology, Huadong Hospital, Shanghai Medical College, Fudan University, Shanghai, 200040, People's Republic of China.
| | - Qin Yang
- Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
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Kasela S, Aguet F, Kim-Hellmuth S, Brown BC, Nachun DC, Tracy RP, Durda P, Liu Y, Taylor KD, Craig Johnson W, Berg DVD, Gabriel S, Gupta N, Smith JD, Blackwell TW, Rotter JI, Ardlie KG, Manichaikul A, Rich SS, Graham Barr R, Lappalainen T. Interaction molecular QTL mapping discovers cellular and environmental modifiers of genetic regulatory effects. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546528. [PMID: 37425716 PMCID: PMC10326995 DOI: 10.1101/2023.06.26.546528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Bulk tissue molecular quantitative trait loci (QTLs) have been the starting point for interpreting disease-associated variants, while context-specific QTLs show particular relevance for disease. Here, we present the results of mapping interaction QTLs (iQTLs) for cell type, age, and other phenotypic variables in multi-omic, longitudinal data from blood of individuals of diverse ancestries. By modeling the interaction between genotype and estimated cell type proportions, we demonstrate that cell type iQTLs could be considered as proxies for cell type-specific QTL effects. The interpretation of age iQTLs, however, warrants caution as the moderation effect of age on the genotype and molecular phenotype association may be mediated by changes in cell type composition. Finally, we show that cell type iQTLs contribute to cell type-specific enrichment of diseases that, in combination with additional functional data, may guide future functional studies. Overall, this study highlights iQTLs to gain insights into the context-specificity of regulatory effects.
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Affiliation(s)
- Silva Kasela
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | | | - Sarah Kim-Hellmuth
- New York Genome Center, New York, NY, USA
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital LMU Munich, Munich, Germany
- Computational Health Center, Institute of Translational Genomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Brielin C. Brown
- New York Genome Center, New York, NY, USA
- Data Science Institute, Columbia University, New York, NY, USA
| | | | - Russell P. Tracy
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Peter Durda
- Pathology and Laboratory Medicine, The University of Vermont, Larner College of Medicine, Burlington, VT, USA
| | - Yongmei Liu
- Department of Medicine, Duke University, Durham, NC, USA
| | - Kent D. Taylor
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - W. Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David Van Den Berg
- Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joshua D. Smith
- Northwest Genomic Center, University of Washington, Seattle, WA, USA
| | - Thomas W. Blackwell
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jerome I. Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | - Ani Manichaikul
- Center for Public health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen S. Rich
- Center for Public health Genomics, University of Virginia, Charlottesville, VA, USA
| | - R. Graham Barr
- Epidemiology and Medicine, Columbia University Medical Center, New York, NY, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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Tsygankov AY. TULA Proteins in Men, Mice, Hens, and Lice: Welcome to the Family. Int J Mol Sci 2023; 24:ijms24119126. [PMID: 37298079 DOI: 10.3390/ijms24119126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The two members of the UBASH3/STS/TULA protein family have been shown to critically regulate key biological functions, including immunity and hemostasis, in mammalian biological systems. Negative regulation of signaling through immune receptor tyrosine-based activation motif (ITAM)- and hemITAM-bearing receptors mediated by Syk-family protein tyrosine kinases appears to be a major molecular mechanism of the down-regulatory effect of TULA-family proteins, which possess protein tyrosine phosphatase (PTP) activity. However, these proteins are likely to carry out some PTP-independent functions as well. Whereas the effects of TULA-family proteins overlap, their characteristics and their individual contributions to cellular regulation also demonstrate clearly distinct features. Protein structure, enzymatic activity, molecular mechanisms of regulation, and biological functions of TULA-family proteins are discussed in this review. In particular, the usefulness of the comparative analysis of TULA proteins in various metazoan taxa, for identifying potential roles of TULA-family proteins outside of their functions already established in mammalian systems, is examined.
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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Wang NN, Zhang Y, Jiang F, Zhu DL, Di CX, Hu SY, Chen XF, Zhi LQ, Rong Y, Ke X, Duan YY, Dong SS, Yang TL, Yang Z, Guo Y. Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis. Am J Hum Genet 2023; 110:625-637. [PMID: 36924774 PMCID: PMC10119143 DOI: 10.1016/j.ajhg.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/24/2023] [Indexed: 03/17/2023] Open
Abstract
Genome-wide association studies (GWASs) have repeatedly reported multiple non-coding single-nucleotide polymorphisms (SNPs) at 2p14 associated with rheumatoid arthritis (RA), but their functional roles in the pathological mechanisms of RA remain to be explored. In this study, we integrated a series of bioinformatics and functional experiments and identified three intronic RA SNPs (rs1876518, rs268131, and rs2576923) within active enhancers that can regulate the expression of SPRED2 directly. At the same time, SPRED2 and ACTR2 influence each other as a positive feedback signal amplifier to strengthen the protective role in RA by inhibiting the migration and invasion of rheumatoid fibroblast-like synoviocytes (FLSs). In particular, the transcription factor CEBPB preferentially binds to the rs1876518-T allele to increase the expression of SPRED2 in FLSs. Our findings decipher the molecular mechanisms behind the GWAS signals at 2p14 for RA and emphasize SPRED2 as a potential candidate gene for RA, providing a potential target and direction for precise treatment of RA.
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Affiliation(s)
- Nai-Ning Wang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yan Zhang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Feng Jiang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Dong-Li Zhu
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Chen-Xi Di
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shou-Ye Hu
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xiao-Feng Chen
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Li-Qiang Zhi
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yu Rong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Xin Ke
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Yuan-Yuan Duan
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Shan-Shan Dong
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Tie-Lin Yang
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China
| | - Zhi Yang
- Department of Joint Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an, P.R. China.
| | - Yan Guo
- Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Biomedical Informatics & Genomics Center, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, P.R. China.
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11
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Nam B, Jo S, Bang SY, Park Y, Shin JH, Park YS, Lee S, Joo KB, Kim TH. Clinical and genetic factors associated with radiographic damage in patients with ankylosing spondylitis. Ann Rheum Dis 2023; 82:527-532. [PMID: 36543524 PMCID: PMC10086301 DOI: 10.1136/ard-2022-222796] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVES To identify clinical and genetic factors associated with severe radiographic damage in patients with ankylosing spondylitis (AS). METHODS We newly generated genome-wide single nucleotide polymorphism data (833K) for 444 patients with AS. The severity of radiographic damage was assessed using the modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS). To identify clinical and genetic factors associated with severe radiographic damage, multiple linear regression analyses were performed. Human AS-osteoprogenitor and control-osteoprogenitor cells were used for functional validation. RESULTS The significant clinical factors of final mSASSS were baseline mSASSS (β=0.796, p=3.22×10-75), peripheral joint arthritis (β=-0.246, p=6.85×10-6), uveitis (β=0.157, p=1.95×10-3), and smoking (β=0.130, p=2.72×10-2) after adjusting for sex, age and disease duration. After adjusting significant clinical factors, the Ryanodine receptor 3 (RYR3) gene was associated with severe radiographic damage (p=1.00×10-6). For pathway analysis, the PI3K-Akt signalling pathway was associated with severe radiographic damage in AS (p=2.21×10-4, false discovery rate=0.040). Treatment with rhodamine B, a ligand of RYR3, dose-dependently induced matrix mineralisation of AS osteoprogenitors. However, the rhodamine B-induced accelerated matrix mineralisation was not definitive in control osteoprogenitors. Knockdown of RYR3 inhibited matrix mineralisation in SaOS2 cell lines. CONCLUSIONS This study identified clinical and genetic factors that contributed to better understanding of the pathogenesis and biology associated with radiographic damage in AS.
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Affiliation(s)
- Bora Nam
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research (HYIRR), Seoul, South Korea
| | - Sungsin Jo
- Hanyang University Institute for Rheumatology Research (HYIRR), Seoul, South Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research (HYIRR), Seoul, South Korea
| | - Youngho Park
- Department of Big Data Application College of Smart Convergence, Hannam University, Daejeon, South Korea
| | - Ji Hui Shin
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Ye-Soo Park
- Department of Orthopaedic Surgery, Hanyang University College of Medicine, Guri Hospital, Guri, South Korea
| | - Seunghun Lee
- Department of Radiology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
| | - Kyung Bin Joo
- Hanyang University Institute for Rheumatology Research (HYIRR), Seoul, South Korea
| | - Tae-Hwan Kim
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, South Korea
- Hanyang University Institute for Rheumatology Research (HYIRR), Seoul, South Korea
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12
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Stankey CT, Lee JC. Translating non-coding genetic associations into a better understanding of immune-mediated disease. Dis Model Mech 2023; 16:297044. [PMID: 36897113 PMCID: PMC10040244 DOI: 10.1242/dmm.049790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Genome-wide association studies have identified hundreds of genetic loci that are associated with immune-mediated diseases. Most disease-associated variants are non-coding, and a large proportion of these variants lie within enhancers. As a result, there is a pressing need to understand how common genetic variation might affect enhancer function and thereby contribute to immune-mediated (and other) diseases. In this Review, we first describe statistical and experimental methods to identify causal genetic variants that modulate gene expression, including statistical fine-mapping and massively parallel reporter assays. We then discuss approaches to characterise the mechanisms by which these variants modulate immune function, such as clustered regularly interspaced short palindromic repeats (CRISPR)-based screens. We highlight examples of studies that, by elucidating the effects of disease variants within enhancers, have provided important insights into immune function and uncovered key pathways of disease.
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Affiliation(s)
- Christina T Stankey
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College London, London W12 0NN, UK
| | - James C Lee
- Genetic Mechanisms of Disease Laboratory, The Francis Crick Institute, London NW1 1AT, UK
- Institute of Liver and Digestive Health, Royal Free Hospital, University College London, London NW3 2PF, UK
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13
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Khunsriraksakul C, Li Q, Markus H, Patrick MT, Sauteraud R, McGuire D, Wang X, Wang C, Wang L, Chen S, Shenoy G, Li B, Zhong X, Olsen NJ, Carrel L, Tsoi LC, Jiang B, Liu DJ. Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus. Nat Commun 2023; 14:668. [PMID: 36750564 PMCID: PMC9905560 DOI: 10.1038/s41467-023-36306-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 01/25/2023] [Indexed: 02/09/2023] Open
Abstract
Systemic lupus erythematosus is a heritable autoimmune disease that predominantly affects young women. To improve our understanding of genetic etiology, we conduct multi-ancestry and multi-trait meta-analysis of genome-wide association studies, encompassing 12 systemic lupus erythematosus cohorts from 3 different ancestries and 10 genetically correlated autoimmune diseases, and identify 16 novel loci. We also perform transcriptome-wide association studies, computational drug repurposing analysis, and cell type enrichment analysis. We discover putative drug classes, including a histone deacetylase inhibitor that could be repurposed to treat lupus. We also identify multiple cell types enriched with putative target genes, such as non-classical monocytes and B cells, which may be targeted for future therapeutics. Using this newly assembled result, we further construct polygenic risk score models and demonstrate that integrating polygenic risk score with clinical lab biomarkers improves the diagnostic accuracy of systemic lupus erythematosus using the Vanderbilt BioVU and Michigan Genomics Initiative biobanks.
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Affiliation(s)
- Chachrit Khunsriraksakul
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Qinmengge Li
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Havell Markus
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Matthew T Patrick
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Renan Sauteraud
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Daniel McGuire
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Xingyan Wang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Chen Wang
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Lida Wang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Siyuan Chen
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ganesh Shenoy
- Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt University, Nashville, TN, 37235, USA
| | - Xue Zhong
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Nancy J Olsen
- Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Lam C Tsoi
- Department of Dermatology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bibo Jiang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Dajiang J Liu
- Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA. .,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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14
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Innate and adaptive immune abnormalities underlying autoimmune diseases: the genetic connections. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-021-2187-3. [PMID: 36738430 PMCID: PMC9898710 DOI: 10.1007/s11427-021-2187-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 10/10/2022] [Indexed: 02/05/2023]
Abstract
With the exception of an extremely small number of cases caused by single gene mutations, most autoimmune diseases result from the complex interplay between environmental and genetic factors. In a nutshell, etiology of the common autoimmune disorders is unknown in spite of progress elucidating certain effector cells and molecules responsible for pathologies associated with inflammatory and tissue damage. In recent years, population genetics approaches have greatly enriched our knowledge regarding genetic susceptibility of autoimmunity, providing us with a window of opportunities to comprehensively re-examine autoimmunity-associated genes and possible pathways. In this review, we aim to discuss etiology and pathogenesis of common autoimmune disorders from the perspective of human genetics. An overview of the genetic basis of autoimmunity is followed by 3 chapters detailing susceptibility genes involved in innate immunity, adaptive immunity and inflammatory cell death processes respectively. With such attempts, we hope to expand the scope of thinking and bring attention to lesser appreciated molecules and pathways as important contributors of autoimmunity beyond the 'usual suspects' of a limited subset of validated therapeutic targets.
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15
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Arleevskaya M, Takha E, Petrov S, Kazarian G, Renaudineau Y, Brooks W, Larionova R, Korovina M, Valeeva A, Shuralev E, Mukminov M, Kravtsova O, Novikov A. Interplay of Environmental, Individual and Genetic Factors in Rheumatoid Arthritis Provocation. Int J Mol Sci 2022; 23:ijms23158140. [PMID: 35897715 PMCID: PMC9329780 DOI: 10.3390/ijms23158140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 02/05/2023] Open
Abstract
In this review, we explore systemization of knowledge about the triggering effects of non-genetic factors in pathogenic mechanisms that contribute to the development of rheumatoid arthritis (RA). Possible mechanisms involving environmental and individual factors in RA pathogenesis were analyzed, namely, infections, mental stress, sleep deprivation ecology, age, perinatal and gender factors, eating habits, obesity and smoking. The non-genetic factors modulate basic processes in the body with the impact of these factors being non-specific, but these common challenges may be decisive for advancement of the disease in the predisposed body at risk for RA. The provocation of this particular disease is associated with the presence of congenital loci minoris resistentia. The more frequent non-genetic factors form tangles of interdependent relationships and, thereby, several interdependent external factors hit one vulnerable basic process at once, either provoking or reinforcing each other. Understanding the specific mechanisms by which environmental and individual factors impact an individual under RA risk in the preclinical stages can contribute to early disease diagnosis and, if the factor is modifiable, might be useful for the prevention or delay of its development.
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Affiliation(s)
- Marina Arleevskaya
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia;
- Correspondence: ; Tel.: +7-89172-886-679; Fax: +7-843-238-5413
| | - Elena Takha
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
| | - Sergey Petrov
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Gevorg Kazarian
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
| | - Yves Renaudineau
- Department of Immunology, CHU Toulouse, INSERM U1291, CNRS U5051, University Toulouse IIII, 31000 Toulouse, France;
| | - Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA;
| | - Regina Larionova
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
| | - Marina Korovina
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia;
| | - Anna Valeeva
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
| | - Eduard Shuralev
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Malik Mukminov
- Central Research Laboratory, Kazan State Medical Academy, 420012 Kazan, Russia; (E.T.); (S.P.); (G.K.); (R.L.); (M.K.); (A.V.); (E.S.); (M.M.)
- Institute of Environmental Sciences, Kazan (Volga Region) Federal University, 420008 Kazan, Russia
| | - Olga Kravtsova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 420008 Kazan, Russia;
| | - Andrey Novikov
- Mathematical Center, Sobolev Instiute of Mathematics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia;
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16
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Ramírez-Bello J, Jiménez-Morales S, Barbosa-Cobos RE, Sánchez-Zauco N, Hernández-Molina G, Luria-Pérez R, Fragoso JM, Cabello-Gutiérrez C, Montúfar-Robles I. TNFSF4 is a risk factor for rheumatoid arthritis but not for primary Sjögren's syndrome in the Mexican population. Immunobiology 2022; 227:152244. [PMID: 35835012 DOI: 10.1016/j.imbio.2022.152244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/04/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Rheumatoid arthritis (RA) and primary Sjögren's syndrome (pSS) are autoimmune diseases (ADs) characterized by joint damage and involvement of the salivary glands, respectively. ADs share some susceptibility loci, such as TNFSF4, which is a classical susceptibility gene associated with systemic lupus erythematosus, but its role in RA and pSS is not yet clear. Thus, the aim of this study was to determine whether three TNFSFS4 polymorphisms are associated with RA and pSS. METHODS Our case-control study included 500 controls, 459 patients with RA, and 210 patients with pSS from Mexico. TNFSF4 single nucleotide polymorphisms (SNPs) rs1234315C/T, rs2205960G/T, and rs704840T/G were genotyped using TaqMan probes and discrimination allelic assay. RESULTS The three TNFSF4 SNPs were associated with susceptibility to RA (rs1234315C/T: odds ratio [OR] 1.4, p = 0.01; rs2205960G/T: OR 1.23, p = 0.03; rs704840T/G: OR 1.24, p = 0.02). An association between TNFSF4 rs1234315C/T and pSS was also observed (OR 1.28, p = 0.04), however, after Bonferroni correction, this association was lost. CONCLUSION Our data suggest that TNFSF4 could be a risk factor in RA but not pSS in a Mexican population.
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Affiliation(s)
- Julian Ramírez-Bello
- Departamento de Endocrinología, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico.
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, 14610 Mexico City, Mexico.
| | | | - Norma Sánchez-Zauco
- División de Auxiliares de Diagnóstico y Tratamiento, UMAE Hospital de Especialidades, Centro Médico Nacional Siglo XXI, 06720 IMSS, Mexico.
| | - Gabriela Hernández-Molina
- Departamento de Inmunología y Reumatología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080 Mexico City, Mexico.
| | - Rosendo Luria-Pérez
- Unidad de Investigación en Enfermedades Hemato-Oncológicas, Hospital Infantil de México Federico Gómez, 06720, Mexico.
| | - José M Fragoso
- Departamento de Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, 14080 Mexico City, Mexico.
| | - Carlos Cabello-Gutiérrez
- Departamento de Investigación en Virología y Micología, Instituto Nacional de Enfermedades Respiratorias, 14080 Mexico City, Mexico.
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17
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Ortíz-Fernández L, Martín J, Alarcón-Riquelme ME. A Summary on the Genetics of Systemic Lupus Erythematosus, Rheumatoid Arthritis, Systemic Sclerosis, and Sjögren's Syndrome. Clin Rev Allergy Immunol 2022; 64:392-411. [PMID: 35749015 DOI: 10.1007/s12016-022-08951-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Systemic lupus erythematosus, systemic sclerosis, rheumatoid arthritis, and Sjögren's syndrome are four major autoimmune rheumatic diseases characterized by the presence of autoantibodies, caused by a dysregulation of the immune system that leads to a wide variety of clinical manifestations. These conditions present complex etiologies strongly influenced by multiple environmental and genetic factors. The human leukocyte antigen (HLA) region was the first locus identified to be associated and still represents the strongest susceptibility factor for each of these conditions, particularly the HLA class II genes, including DQA1, DQB1, and DRB1, but class I genes have also been associated. Over the last two decades, the genetic component of these disorders has been extensively investigated and hundreds of non-HLA risk genetic variants have been uncovered. Furthermore, it is widely accepted that autoimmune rheumatic diseases share molecular disease pathways, such as the interferon (IFN) type I pathways, which are reflected in a common genetic background. Some examples of well-known pleiotropic loci for autoimmune rheumatic diseases are the HLA region, DNASEL13, TNIP1, and IRF5, among others. The identification of the causal molecular mechanisms behind the genetic associations is still a challenge. However, recent advances have been achieved through mouse models and functional studies of the loci. Here, we provide an updated overview of the genetic architecture underlying these four autoimmune rheumatic diseases, with a special focus on the HLA region.
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Affiliation(s)
- Lourdes Ortíz-Fernández
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, CSIC, Parque Tecnológico de La Salud, 18016, Granada, Spain
| | - Marta E Alarcón-Riquelme
- GENYO. Center for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Av de la Ilustración 114, Parque Tecnológico de La Salud, 18016, Granada, Spain. .,Institute for Environmental Medicine, Karolinska Institutet, 171 77, Solna, Sweden.
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18
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Jaiswal A, Verma A, Dannenfelser R, Melssen M, Tirosh I, Izar B, Kim TG, Nirschl CJ, Devi KSP, Olson WC, Slingluff CL, Engelhard VH, Garraway L, Regev A, Minkis K, Yoon CH, Troyanskaya O, Elemento O, Suárez-Fariñas M, Anandasabapathy N. An activation to memory differentiation trajectory of tumor-infiltrating lymphocytes informs metastatic melanoma outcomes. Cancer Cell 2022; 40:524-544.e5. [PMID: 35537413 PMCID: PMC9122099 DOI: 10.1016/j.ccell.2022.04.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/07/2021] [Accepted: 04/11/2022] [Indexed: 12/11/2022]
Abstract
There is a need for better classification and understanding of tumor-infiltrating lymphocytes (TILs). Here, we applied advanced functional genomics to interrogate 9,000 human tumors and multiple single-cell sequencing sets using benchmarked T cell states, comprehensive T cell differentiation trajectories, human and mouse vaccine responses, and other human TILs. Compared with other T cell states, enrichment of T memory/resident memory programs was observed across solid tumors. Trajectory analysis of single-cell melanoma CD8+ TILs also identified a high fraction of memory/resident memory-scoring TILs in anti-PD-1 responders, which expanded post therapy. In contrast, TILs scoring highly for early T cell activation, but not exhaustion, associated with non-response. Late/persistent, but not early activation signatures, prognosticate melanoma survival, and co-express with dendritic cell and IFN-γ response programs. These data identify an activation-like state associated to poor response and suggest successful memory conversion, above resuscitation of exhaustion, is an under-appreciated aspect of successful anti-tumoral immunity.
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Affiliation(s)
- Abhinav Jaiswal
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10026, USA
| | - Akanksha Verma
- Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ruth Dannenfelser
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Marit Melssen
- Division of Surgical Oncology - Breast and Melanoma Surgery, Department of Surgery, Human Immune Therapy Center, Cancer Center, University of Virginia, Charlottesville, VA 22908, USA; Carter Immunology Center, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Benjamin Izar
- Department of Medicine, Division of Hematology/Oncology, Herbert Irving Comprehensive Cancer Center, Columbia Center for Translational Immunology and Program for Mathematical Genomics, Columbia University, New York, NY 10032, USA
| | - Tae-Gyun Kim
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul, South Korea
| | - Christopher J Nirschl
- Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - K Sanjana P Devi
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA
| | - Walter C Olson
- Division of Surgical Oncology - Breast and Melanoma Surgery, Department of Surgery, Human Immune Therapy Center, Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Craig L Slingluff
- Division of Surgical Oncology - Breast and Melanoma Surgery, Department of Surgery, Human Immune Therapy Center, Cancer Center, University of Virginia, Charlottesville, VA 22908, USA; Carter Immunology Center, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Victor H Engelhard
- Carter Immunology Center, Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Levi Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02115, USA; Center for Cancer for Cancer Precision Medicine, Boston, MA 02115, USA; Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Aviv Regev
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kira Minkis
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA
| | - Charles H Yoon
- Brigham and Women's Hospital, Department of Surgical Oncology Harvard Medical School, Boston, MA 02115, USA
| | - Olga Troyanskaya
- Department of Computer Science and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA; Simons Center for Data Analysis, Simons Foundation, New York, NY 10010, USA
| | - Olivier Elemento
- Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Mayte Suárez-Fariñas
- Department of Genetics and Genomic Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Niroshana Anandasabapathy
- Department of Dermatology, Weill Cornell Medicine, New York, NY 10026, USA; Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, NY 10026, USA; Institute for Computational Biomedicine, Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA; Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10026, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10026, USA.
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19
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Yazar S, Alquicira-Hernandez J, Wing K, Senabouth A, Gordon MG, Andersen S, Lu Q, Rowson A, Taylor TRP, Clarke L, Maccora K, Chen C, Cook AL, Ye CJ, Fairfax KA, Hewitt AW, Powell JE. Single-cell eQTL mapping identifies cell type-specific genetic control of autoimmune disease. Science 2022; 376:eabf3041. [PMID: 35389779 DOI: 10.1126/science.abf3041] [Citation(s) in RCA: 155] [Impact Index Per Article: 77.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The human immune system displays substantial variation between individuals, leading to differences in susceptibility to autoimmune disease. We present single-cell RNA sequencing (scRNA-seq) data from 1,267,758 peripheral blood mononuclear cells from 982 healthy human subjects. For 14 cell types, we identified 26,597 independent cis-expression quantitative trait loci (eQTLs) and 990 trans-eQTLs, with most showing cell type-specific effects on gene expression. We subsequently show how eQTLs have dynamic allelic effects in B cells that are transitioning from naïve to memory states and demonstrate how commonly segregating alleles lead to interindividual variation in immune function. Finally, using a Mendelian randomization approach, we identify the causal route by which 305 risk loci contribute to autoimmune disease at the cellular level. This work brings together genetic epidemiology with scRNA-seq to uncover drivers of interindividual variation in the immune system.
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Affiliation(s)
- Seyhan Yazar
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Jose Alquicira-Hernandez
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Kristof Wing
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Ophthalmology, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Anne Senabouth
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - M Grace Gordon
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Stacey Andersen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Qinyi Lu
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Antonia Rowson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Surgery, School of Clinical Science at Monash Health, Monash University, VIC, Australia
| | - Thomas R P Taylor
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, University of Melbourne, East Melbourne, VIC, Australia
| | - Katia Maccora
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Surgery, School of Clinical Science at Monash Health, Monash University, VIC, Australia
| | - Christine Chen
- Department of Surgery, School of Clinical Science at Monash Health, Monash University, VIC, Australia
| | - Anthony L Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS, Australia
| | - Chun Jimmie Ye
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Kirsten A Fairfax
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Alex W Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.,Department of Ophthalmology, Royal Hobart Hospital, Hobart, TAS, Australia.,Centre for Eye Research Australia, University of Melbourne, East Melbourne, VIC, Australia
| | - Joseph E Powell
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia.,UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia
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20
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Abstract
Rheumatoid arthritis (RA) is an inflammatory autoimmune disease involving symmetric joints and is generally characterized by persistent pain, tenderness, and destruction of joints. The vast majority of RA patients produce autoantibodies, and immune cell involvement in disease development is well recognized, as is the contribution of other types of cells in synovial tissue, like fibroblasts. It is known that there are major genetic associations with the HLA locus, while multiple non-HLA genetic variants display relatively low risk of RA. Both HLA and non-HLA associations suggest that the profiles of genetic associations for autoantibody-positive vs. autoantibody-negative RA are different. Several alleles of HLA-DRB1 are associated with high risk for autoantibody-positive RA, with the strongest risk characterized by valine at position 11 of the protein sequence (HLA-DRB1*04 and *10 alleles). There is a strong protective effect for the risk of autoantibody-positive RA associated with HLA-DRB1*13 alleles. Although major genetic associations have been known for several years, understanding of the specific mechanisms in the development of increased risk of RA for these variations is work in progress. Current studies focus on the binding of immune receptors involved in recognition of putative peptides in activation of T cells, as well as investigation of cell signaling mechanisms. At least a part of RA risk could be explained by gene-gene and gene-environment interactions. There are currently more than 150 candidate loci with polymorphisms that associate with RA, mainly related to seropositive disease, and new discoveries are anticipated in the future from investigation of diverse human populations. This new research will help create a strong foundation for the continuing process of integrating genetic, epigenetic, transcriptomic, and proteomic data in studies of RA.
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Affiliation(s)
- Leonid Padyukov
- Department of Medicine Solna, Division of Rheumatology, Karolinska Institutet and Karolinska Hospital, Stockholm, Sweden.
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21
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Mena J, Alloza I, Tulloch Navarro R, Aldekoa A, Díez García J, Villanueva Etxebarria A, Lindskog C, Antigüedad A, Boyero S, Mendibe-Bilbao MDM, Álvarez de Arcaya A, Sánchez Menoyo JL, Midaglia L, Villarrubia N, Malhotra S, Montalban X, Villar LM, Comabella M, Vandenbroeck K. Genomic Multiple Sclerosis Risk Variants Modulate the Expression of the ANKRD55- IL6ST Gene Region in Immature Dendritic Cells. Front Immunol 2022; 12:816930. [PMID: 35111166 PMCID: PMC8801523 DOI: 10.3389/fimmu.2021.816930] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/22/2021] [Indexed: 12/25/2022] Open
Abstract
Intronic single-nucleotide polymorphisms (SNPs) in the ANKRD55 gene are associated with the risk for multiple sclerosis (MS) and rheumatoid arthritis by genome-wide association studies (GWAS). The risk alleles have been linked to higher expression levels of ANKRD55 and the neighboring IL6ST (gp130) gene in CD4+ T lymphocytes of healthy controls. The biological function of ANKRD55, its role in the immune system, and cellular sources of expression other than lymphocytes remain uncharacterized. Here, we show that monocytes gain capacity to express ANKRD55 during differentiation in immature monocyte-derived dendritic cells (moDCs) in the presence of interleukin (IL)-4/granulocyte-macrophage colony-stimulating factor (GM-CSF). ANKRD55 expression levels are further enhanced by retinoic acid agonist AM580 but downregulated following maturation with interferon (IFN)-γ and lipopolysaccharide (LPS). ANKRD55 was detected in the nucleus of moDC in nuclear speckles. We also analyzed the adjacent IL6ST, IL31RA, and SLC38A9 genes. Of note, in healthy controls, MS risk SNP genotype influenced ANKRD55 and IL6ST expression in immature moDC in opposite directions to that in CD4+ T cells. This effect was stronger for a partially correlated SNP, rs13186299, that is located, similar to the main MS risk SNPs, in an ANKRD55 intron. Upon analysis in MS patients, the main GWAS MS risk SNP rs7731626 was associated with ANKRD55 expression levels in CD4+ T cells. MoDC-specific ANKRD55 and IL6ST mRNA levels showed significant differences according to the clinical form of the disease, but, in contrast to healthy controls, were not influenced by genotype. We also measured serum sgp130 levels, which were found to be higher in homozygotes of the protective allele of rs7731626. Our study characterizes ANKRD55 expression in moDC and indicates monocyte-to-dendritic cell (Mo-DC) differentiation as a process potentially influenced by MS risk SNPs.
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Affiliation(s)
- Jorge Mena
- Inflammation & Biomarkers Group, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Iraide Alloza
- Inflammation & Biomarkers Group, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Raquel Tulloch Navarro
- Inflammation & Biomarkers Group, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Aldekoa
- Inflammation & Biomarkers Group, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Javier Díez García
- Microscopy Facility, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Ane Villanueva Etxebarria
- Kronikgune Institute for Health Services Research, Barakaldo, Spain
- Health Service Research Network on Chronic Diseases Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Bizkaia, Spain
- Osakidetza-Basque Health Service, Research Unit, Galdakao University Hospital, Galdakao, Spain
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Alfredo Antigüedad
- Department of Neurology, Cruces University Hospital, Osakidetza-Basque Health Service, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Sabas Boyero
- Department of Neurology, Cruces University Hospital, Osakidetza-Basque Health Service, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - María del Mar Mendibe-Bilbao
- Department of Neurology, Cruces University Hospital, Osakidetza-Basque Health Service, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
| | - Amaya Álvarez de Arcaya
- Department of Neurology, Txagorritxu University Hospital, Osakidetza-Basque Health Service, Bioaraba Health Research Institute, Vitoria-Gasteiz, Spain
| | - José Luis Sánchez Menoyo
- Department of Neurology, Galdakao-Usansolo University Hospital, Osakidetza-Basque Health Service, Biocruces-Bizkaia Health Research Institute, Galdakao, Spain
| | - Luciana Midaglia
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Noelia Villarrubia
- Department of Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
| | - Sunny Malhotra
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Xavier Montalban
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Luisa María Villar
- Department of Immunology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Red Española de Esclerosis Múltiple (REEM), Madrid, Spain
| | - Manuel Comabella
- Servei de Neurologia-Neuroimmunologia, Centre d’Esclerosi Múltiple de Catalunya (Cemcat), Institut de Recerca Vall d’Hebron (VHIR), Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Koen Vandenbroeck
- Inflammation & Biomarkers Group, Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
- Department of Biochemistry and Molecular Biology, Universidad del País Vasco (UPV/EHU), Barrio Sarriena, Leioa, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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22
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Guderud K, Sunde LH, Flåm ST, Mæhlen MT, Mjaavatten MD, Norli ES, Evenrød IM, Andreassen BK, Franzenburg S, Franke A, Rayner S, Gervin K, Lie BA. Methotrexate Treatment of Newly Diagnosed RA Patients Is Associated With DNA Methylation Differences at Genes Relevant for Disease Pathogenesis and Pharmacological Action. Front Immunol 2021; 12:713611. [PMID: 34867944 PMCID: PMC8637827 DOI: 10.3389/fimmu.2021.713611] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/27/2021] [Indexed: 12/20/2022] Open
Abstract
Background Methotrexate (MTX) is the first line treatment of rheumatoid arthritis (RA), and methylation changes in bulk T cells have been reported after treatment with MTX. We have investigated cell-type specific DNA methylation changes across the genome in naïve and memory CD4+ T cells before and after MTX treatment of RA patients. DNA methylation profiles of newly diagnosed RA patients (N=9) were assessed by reduced representation bisulfite sequencing. Results We found that MTX treatment significantly influenced DNA methylation levels at multiple CpG sites in both cell populations. Interestingly, we identified differentially methylated sites annotated to two genes; TRIM15 and SORC2, previously reported to predict treatment outcome in RA patients when measured in bulk T cells. Furthermore, several of the genes, including STAT3, annotated to the significant CpG sites are relevant for RA susceptibility or the action of MTX. Conclusion We detected CpG sites that were associated with MTX treatment in CD4+ naïve and memory T cells isolated from RA patients. Several of these sites overlap genetic regions previously associated with RA risk and MTX treatment outcome.
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Affiliation(s)
- Kari Guderud
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Line H Sunde
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Siri T Flåm
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
| | - Marthe T Mæhlen
- Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
| | | | - Ellen S Norli
- Department of Rheumatology, Martina Hansens Hospital, Bærum, Norway
| | - Ida M Evenrød
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Bettina K Andreassen
- Department of Research, Cancer Registry of Norway, Institute for Population-Based Research, Oslo, Norway
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Simon Rayner
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway
| | - Benedicte A Lie
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Inflammation Research Centre, University of Oslo, Oslo, Norway
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23
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Zhao J, Guo S, Schrodi SJ, He D. Molecular and Cellular Heterogeneity in Rheumatoid Arthritis: Mechanisms and Clinical Implications. Front Immunol 2021; 12:790122. [PMID: 34899757 PMCID: PMC8660630 DOI: 10.3389/fimmu.2021.790122] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/08/2021] [Indexed: 12/20/2022] Open
Abstract
Rheumatoid arthritis is an autoimmune disease that exhibits significant clinical heterogeneity. There are various treatments for rheumatoid arthritis, including disease-modifying anti-rheumatic drugs (DMARDs), glucocorticoids, non-steroidal anti-inflammatory drugs (NSAIDs), and inflammatory cytokine inhibitors (ICI), typically associated with differentiated clinical effects and characteristics. Personalized responsiveness is observed to the standard treatment due to the pathophysiological heterogeneity in rheumatoid arthritis, resulting in an overall poor prognosis. Understanding the role of individual variation in cellular and molecular mechanisms related to rheumatoid arthritis will considerably improve clinical care and patient outcomes. In this review, we discuss the source of pathophysiological heterogeneity derived from genetic, molecular, and cellular heterogeneity and their possible impact on precision medicine and personalized treatment of rheumatoid arthritis. We provide emphasized description of the heterogeneity derived from mast cells, monocyte cell, macrophage fibroblast-like synoviocytes and, interactions within immune cells and with inflammatory cytokines, as well as the potential as a new therapeutic target to develop a novel treatment approach. Finally, we summarize the latest clinical trials of treatment options for rheumatoid arthritis and provide a suggestive framework for implementing preclinical and clinical experimental results into clinical practice.
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Affiliation(s)
- Jianan Zhao
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Shicheng Guo
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Steven J. Schrodi
- Computation and Informatics in Biology and Medicine, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Dongyi He
- Guanghua Clinical Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Department of Rheumatology, Shanghai Guanghua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Arthritis Institute of Integrated Traditional and Western Medicine, Shanghai Chinese Medicine Research Institute, Shanghai, China
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24
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Sukharani N, Dev K, Rahul F, Bai P, Ali A, Avinash F, Kammawal Y, Kumar N, Rizwan A. Association Between Rheumatoid Arthritis and Serum Vitamin D Levels. Cureus 2021; 13:e18255. [PMID: 34712532 PMCID: PMC8542394 DOI: 10.7759/cureus.18255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction Vitamin D is responsible for regulating innate and adaptive immune responses and for boosting the immune system; hence, a decline in its levels results in autoimmunity. Current studies have linked the deficiency of vitamin D to different autoimmune diseases, including rheumatoid arthritis (RA). In this study, we will determine the association between vitamin D level and RA. Methods This is a case-control study, conducted in a tertiary care hospital in Pakistan from January 2021 to May 2021. Three hundred patients with a confirmed recent diagnosis of RA were enrolled as the study group. Another 300 participants without RA, matched for age and gender, were enrolled in the study as a control group. RA was diagnosed on the basis of clinical symptoms, radiological features on X-ray, and anti-citrullinated protein levels of more than 20 u/mL. Results The mean vitamin D level in participants with RA was significantly lower than in the placebo group (30.18 ± 6.27 vs. 38.29 ± 7.98; p-value: <0.0001). The mean vitamin D level in participants with positive RF patients was significantly lower compared to rheumatoid factor (RF)-negative RA patients (29.21 ± 5.16 vs. 32.26 ± 7.02; p-value: <0.0001). There were more participants with hypovitaminosis D in RF-positive participants as compared to RF negative (88.6% vs. 44.3%; p-value: 0.00001). Conclusion There is a high prevalence of vitamin D deficiency in patients with RA and there is a link with disease severity. Therefore, a high index of suspicion is required while evaluating the at-risk patients, especially women, with complaints of vitamin D deficiency. Vitamin D supplementation may be needed for the prevention or avoidance of the progression of the disease.
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Affiliation(s)
- Naintara Sukharani
- Internal Medicine, Peoples University of Medical & Health Sciences for Women, Nawabshah, PAK
| | - Kapeel Dev
- Internal Medicine, Ghulam Muhammad Mahar Medical College, Sukkur, PAK
| | - Fnu Rahul
- Internal Medicine, Jinnah Sindh Medical University, Karachi, PAK
| | - Pinky Bai
- Internal Medicine, Jinnah Sindh Medical University, Karachi, PAK
| | - Azka Ali
- Internal Medicine, King Edward Medical University, Lahore, PAK
| | - Fnu Avinash
- Internal Medicine, Jinnah Sindh Medical University, Karachi, PAK
| | - Yasir Kammawal
- Anatomical and Clinical Pathology, University of Arizona College of Medicine, Tucson, USA
| | - Narindar Kumar
- Internal Medicine, Bhitai Dental and Medical College, Mirpurkhas, PAK
| | - Amber Rizwan
- Family Medicine, Jinnah Post Graduate Medical Center, Karachi, PAK
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25
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So T. The immunological significance of tumor necrosis factor receptor-associated factors (TRAFs). Int Immunol 2021; 34:7-20. [PMID: 34453532 DOI: 10.1093/intimm/dxab058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 07/27/2021] [Indexed: 01/03/2023] Open
Abstract
The tumor necrosis factor receptor (TNFR)-associated factor (TRAF) family of molecules are intracellular signaling adaptors and control diverse signaling pathways mediated not only by the TNFR superfamily and the Toll-like receptor/interleukin-1 receptor superfamily but also by unconventional cytokine receptors such as IL-6 and IL-17 receptors. There are seven family members, TRAF1 to TRAF7, in mammals. Exaggerated immune responses induced through TRAF signaling downstream of these receptors often lead to inflammatory and autoimmune diseases including rheumatoid arthritis, inflammatory bowel disease, psoriasis and autoinflammatory syndromes, and thus those signals are major targets for therapeutic intervention. For this reason, it has been very important to understand signaling mechanisms regulated by TRAFs that greatly impact on life/death decisions and the activation, differentiation and survival of cells of the innate and adaptive immune systems. Accumulating evidence suggests that dysregulated cellular expression and/or signaling of TRAFs causes overproduction of proinflammatory cytokines, which facilitates aberrant activation of immune cells. In this review, I will explain the structural and functional aspects that are responsible for the cellular activity and disease outcomes of TRAFs, and summarize the findings of recent studies on TRAFs in terms of how individual TRAF family molecules regulates biological and disease processes in the body in both positive and negative ways. This review also discusses how TRAF mutations contribute to human disease.
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Affiliation(s)
- Takanori So
- Laboratory of Molecular Cell Biology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama, Japan
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26
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Korinfskaya S, Parameswaran S, Weirauch MT, Barski A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development? Front Immunol 2021; 12:701924. [PMID: 34421907 PMCID: PMC8377396 DOI: 10.3389/fimmu.2021.701924] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Runx proteins (also known as Runt-domain transcription factors) have been studied for a long time as key regulators of cellular differentiation. RUNX2 has been described as essential for osteogenesis, whereas RUNX1 and RUNX3 are known to control blood cell development during different stages of cell lineage specification. However, recent studies show evidence of complex relationships between RUNX proteins, chromatin-modifying machinery, the cytoskeleton and different transcription factors in various non-embryonic contexts, including mature T cell homeostasis, inflammation and cancer. In this review, we discuss the diversity of Runx functions in mature T helper cells, such as production of cytokines and chemokines by different CD4 T cell populations; apoptosis; and immunologic memory acquisition. We then briefly cover recent findings about the contribution of RUNX1, RUNX2 and RUNX3 to various immunologic diseases. Finally, we discuss areas that require further study to better understand the role that Runx proteins play in inflammation and immunity.
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Affiliation(s)
- Svetlana Korinfskaya
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sreeja Parameswaran
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
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27
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VanEvery H, Yang W, Olsen N, Bao L, Lu B, Wu S, Cui L, Gao X. Alcohol Consumption and Risk of Rheumatoid Arthritis among Chinese Adults: A Prospective Study. Nutrients 2021; 13:nu13072231. [PMID: 34209676 PMCID: PMC8308382 DOI: 10.3390/nu13072231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/08/2021] [Accepted: 06/25/2021] [Indexed: 12/27/2022] Open
Abstract
Alcohol consumption may be associated with the risk of rheumatoid arthritis (RA), but potential sex-related differences in this association have not been explored. Thus, we utilized 87,118 participants in the Kailuan Study, a prospective cohort initiated in 2006 to study the risk factors of cardiovascular disease in a Chinese population. We included those that did not have RA at baseline (2006), and performed cox proportional hazard modeling to calculate the hazard ratio (HR) and 95% confidence interval (95% CI) of RA according to the levels of alcohol consumption (never or past, light or moderate (<1 serving/day for women, <2 servings/day for men), and heavy (>1 serving/day for women, >2 servings/day for men), adjusting for age, sex, body mass index, and smoking. Diagnoses of RA were confirmed via medical record review by rheumatologists. From 2006 to 2018, we identified 87 incident RA cases. After adjusting for potential confounders, the HR of RA was 1.26 (95% CI: 0.62, 2.56) for participants with light or moderate alcohol consumption and 1.98 (95% CI: 0.93, 4.22) for participants with heavy alcohol consumption) versus non-drinkers. The HR of each 10 g increase in alcohol consumption was 1.11 (95% CI: 0.98, 1.26) (p-trend = 0.09). A significant association between alcohol consumption and RA risk was observed in women, but not in men (p for interaction = 0.06). Among women, each 10 g increase in alcohol consumption was significantly associated with a high risk of RA (HR: 1.56; 95% CI: 1.06, 2.29). In contrast, each 10 g increase in alcohol consumption was not significantly associated with the risk of RA in men (HR: 1.10; 95% CI: 0.97, 1.25). Excluding past drinkers generated similar results. In this prospective Chinese cohort, increasing alcohol consumption was associated with an elevated risk of RA among women, but not in men. These findings highlight the importance of incorporating analysis of sex differences into future studies of alcohol consumption and RA risk.
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Affiliation(s)
- Hannah VanEvery
- Department of Nutritional Sciences, The Pennsylvania State University, State College, PA 16802, USA;
| | - Wenhao Yang
- Department of Rheumatology and Immunology, Kailuan General Hospital, Tangshan 063000, China; (W.Y.); (L.C.)
| | - Nancy Olsen
- Division of Rheumatology, Department of Medicine, Penn State Milton S. Hershey Medical Center, Hershey, PA 17033, USA;
| | - Le Bao
- Department of Statistics, The Pennsylvania State University, State College, PA 16802, USA;
| | - Bing Lu
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA;
| | - Shouling Wu
- Department of Cardiology, Kailuan General Hospital, Tangshan 063000, China;
| | - Liufu Cui
- Department of Rheumatology and Immunology, Kailuan General Hospital, Tangshan 063000, China; (W.Y.); (L.C.)
| | - Xiang Gao
- Department of Nutritional Sciences, The Pennsylvania State University, State College, PA 16802, USA;
- Correspondence: ; Tel.: +814-867-5959
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28
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Global discovery of lupus genetic risk variant allelic enhancer activity. Nat Commun 2021; 12:1611. [PMID: 33712590 PMCID: PMC7955039 DOI: 10.1038/s41467-021-21854-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we construct a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 reveals 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE. Thousands of genetic variants have been associated with lupus, but causal variants and mechanisms are unknown. Here, the authors combine a massively parallel reporter assay with genome-wide ChIP experiments to identify risk variants with allelic enhancer activity mediated through transcription factor binding.
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29
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Bell S, Rigas AS, Magnusson MK, Ferkingstad E, Allara E, Bjornsdottir G, Ramond A, Sørensen E, Halldorsson GH, Paul DS, Burgdorf KS, Eggertsson HP, Howson JMM, Thørner LW, Kristmundsdottir S, Astle WJ, Erikstrup C, Sigurdsson JK, Vuckovic D, Dinh KM, Tragante V, Surendran P, Pedersen OB, Vidarsson B, Jiang T, Paarup HM, Onundarson PT, Akbari P, Nielsen KR, Lund SH, Juliusson K, Magnusson MI, Frigge ML, Oddsson A, Olafsson I, Kaptoge S, Hjalgrim H, Runarsson G, Wood AM, Jonsdottir I, Hansen TF, Sigurdardottir O, Stefansson H, Rye D, Peters JE, Westergaard D, Holm H, Soranzo N, Banasik K, Thorleifsson G, Ouwehand WH, Thorsteinsdottir U, Roberts DJ, Sulem P, Butterworth AS, Gudbjartsson DF, Danesh J, Brunak S, Di Angelantonio E, Ullum H, Stefansson K. A genome-wide meta-analysis yields 46 new loci associating with biomarkers of iron homeostasis. Commun Biol 2021; 4:156. [PMID: 33536631 PMCID: PMC7859200 DOI: 10.1038/s42003-020-01575-z] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 12/07/2020] [Indexed: 02/07/2023] Open
Abstract
Iron is essential for many biological functions and iron deficiency and overload have major health implications. We performed a meta-analysis of three genome-wide association studies from Iceland, the UK and Denmark of blood levels of ferritin (N = 246,139), total iron binding capacity (N = 135,430), iron (N = 163,511) and transferrin saturation (N = 131,471). We found 62 independent sequence variants associating with iron homeostasis parameters at 56 loci, including 46 novel loci. Variants at DUOX2, F5, SLC11A2 and TMPRSS6 associate with iron deficiency anemia, while variants at TF, HFE, TFR2 and TMPRSS6 associate with iron overload. A HBS1L-MYB intergenic region variant associates both with increased risk of iron overload and reduced risk of iron deficiency anemia. The DUOX2 missense variant is present in 14% of the population, associates with all iron homeostasis biomarkers, and increases the risk of iron deficiency anemia by 29%. The associations implicate proteins contributing to the main physiological processes involved in iron homeostasis: iron sensing and storage, inflammation, absorption of iron from the gut, iron recycling, erythropoiesis and bleeding/menstruation.
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Affiliation(s)
- Steven Bell
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Andreas S Rigas
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Magnus K Magnusson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | | | - Elias Allara
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Anna Ramond
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Dirk S Paul
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kristoffer S Burgdorf
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Joanna M M Howson
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Lise W Thørner
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - William J Astle
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Medical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Dragana Vuckovic
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Khoa M Dinh
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Vinicius Tragante
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Department of Cardiology, Division Heart & Lungs, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Praveen Surendran
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Rutherford Fund Fellow, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ole B Pedersen
- Department of Clinical Immunology, Næstved Hospital, Næstved, Denmark
| | | | - Tao Jiang
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Helene M Paarup
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Pall T Onundarson
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Department of Laboratory Hematology, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Parsa Akbari
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | | | | | | | | | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali, the National University Hospital of Iceland, Reykjavik, Iceland
| | - Stephen Kaptoge
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Henrik Hjalgrim
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Angela M Wood
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Thomas F Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet-Glostrup, Glostrup, Denmark
- Institute of Biological Psychiatry, Copenhagen University Hospital MHC Sct. Hans, Roskilde, Denmark
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | | | | | - David Rye
- Department of Neurology and Program in Sleep, Emory University School of Medicine, Atlanta, GA, USA
| | - James E Peters
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - David Westergaard
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | - Nicole Soranzo
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Karina Banasik
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Willem H Ouwehand
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- UK National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - David J Roberts
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- Radcliffe Department of Medicine and National Health Service Blood and Transplant, John Radcliffe Hospital, Oxford, UK
- UK National Health Service Blood and Transplant, John Radcliffe Hospital, Oxford, OX3 9BQ, UK
| | | | - Adam S Butterworth
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - John Danesh
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Human Genetics, Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Søren Brunak
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Emanuele Di Angelantonio
- The National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- UK National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.
| | - Henrik Ullum
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark.
| | - Kari Stefansson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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He YS, Yang XK, Hu YQ, Xiang K, Pan HF. Emerging role of Fli1 in autoimmune diseases. Int Immunopharmacol 2020; 90:107127. [PMID: 33234418 DOI: 10.1016/j.intimp.2020.107127] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/21/2020] [Accepted: 10/19/2020] [Indexed: 11/25/2022]
Abstract
The Ets transcription factor family exerts crucial role in cell proliferation, apoptosis, differentiation and migration. Friend leukemia integration 1 (Fli1), a member of the Ets family, is expressed in fibroblasts, endothelial cells and immune cells. Fli1 gene is participated in the development, proliferation, activation, migration and other processes of immune cells. Fli1 can also affect the function of immune cells by regulating cytokines and chemokines. Emerging evidence has shown that Fli1 is implicated in the etiology of several autoimmune diseases, including systemic sclerosis (SSc) and systemic lupus erythematosus (SLE). In this review, we mainly discuss the current evidence for the role of Fli1 in these diseases.
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Affiliation(s)
- Yi-Sheng He
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, 81 Meishan Road, Hefei, Anhui, China
| | - Xiao-Ke Yang
- Department of Rheumatology and Immunology, the First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, Anhui, China
| | - Yu-Qian Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, 81 Meishan Road, Hefei, Anhui, China
| | - Kun Xiang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, 81 Meishan Road, Hefei, Anhui, China
| | - Hai-Feng Pan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, 81 Meishan Road, Hefei, Anhui, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, 81 Meishan Road, Hefei, Anhui, China.
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Genetic analyses identify GSDMB associated with asthma severity, exacerbations, and antiviral pathways. J Allergy Clin Immunol 2020; 147:894-909. [PMID: 32795586 DOI: 10.1016/j.jaci.2020.07.030] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Chr17q12-21.2 region is the strongest and most consistently associated region with asthma susceptibility. The functional genes or single nucleotide polymorphisms (SNPs) are not obvious due to linkage disequilibrium. OBJECTIVES We sought to comprehensively investigate whole-genome sequence and RNA sequence from human bronchial epithelial cells to dissect functional genes/SNPs for asthma severity in the Severe Asthma Research Program. METHODS Expression quantitative trait loci analysis (n = 114), correlation analysis (n = 156) of gene expression and asthma phenotypes, and pathway analysis were performed in bronchial epithelial cells and replicated. Genetic association for asthma severity (426 severe vs 531 nonsevere asthma) and longitudinal asthma exacerbations (n = 273) was performed. RESULTS Multiple SNPs in gasdermin B (GSDMB) associated with asthma severity (odds ratio, >1.25) and longitudinal asthma exacerbations (P < .05). Expression quantitative trait loci analyses identified multiple SNPs associated with expression levels of post-GPI attachment to proteins 3, GSDMB, or gasdermin A (3.1 × 10-9 <P < 1.8 × 10-4). Higher expression levels of GSDMB correlated with asthma and greater number of exacerbations (P < .05). Expression levels of GSDMB correlated with genes involved in IFN signaling, MHC class I antigen presentation, and immune system pathways (false-discovery rate-adjusted P < .05). rs1031458 and rs3902920 in GSDMB colocalized with IFN regulatory factor binding sites and associated with GSDMB expression, asthma severity, and asthma exacerbations (P < .05). CONCLUSIONS By using a unique set of gene expression data from lung cells obtained using bronchoscopy from comprehensively characterized subjects with asthma, we show that SNPs in GSDMB associated with asthma severity, exacerbations, and GSDMB expression levels. Furthermore, its expression levels correlated with asthma exacerbations and antiviral pathways. Thus, GSDMB is a functional gene for both asthma susceptibility and severity.
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Investigating the GWAS-Implicated Loci for Rheumatoid Arthritis in the Pakistani Population. DISEASE MARKERS 2020; 2020:1910215. [PMID: 32831971 PMCID: PMC7422001 DOI: 10.1155/2020/1910215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022]
Abstract
Rheumatoid arthritis (RA) is a complex and multifactorial autoimmune disorder with the involvement of multiple genetic and environmental factors. Genome-wide association studies (GWAS) have identified more than 50 RA genetic loci in European populations. Given the anticipated overlap of RA-relevant genes and pathways across different ethnic groups, we sought to replicate 58 GWAS-implicated SNPs reported in Europeans in Pakistani subjects. 1,959 unrelated subjects comprising 1,222 RA cases and 737 controls were collected from three rheumatology facilities in Pakistan. Genotyping was performed using iPLEX or TaqMan® methods. A total of 50 SNPs were included in the final association analysis after excluding those that failed assay design/run or postrun QC analysis. Fourteen SNPs (LINC00824/rs1516971, PADI4/rs2240336, CEP57/rs4409785, CTLA4/rs3087243, STAT4/rs13426947, HLA-B/MICA/rs2596565, C5orf30/rs26232, CCL21/rs951005, GATA3/rs2275806, VPS37C/rs595158, HLA-DRB1/rs660895, EOMES/rs3806624, SPRED2/rs934734, and RUNX1/rs9979383) were replicated in our Pakistani sample at false discovery rate (FDR) of <0.20 with nominal p values ranging from 4.73E-06 to 3.48E-02. Our results indicate that several RA susceptibility loci are shared between Pakistani and European populations, supporting the role of common genes/pathways.
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Mikhaylenko DS, Nemtsova MV, Bure IV, Kuznetsova EB, Alekseeva EA, Tarasov VV, Lukashev AN, Beloukhova MI, Deviatkin AA, Zamyatnin AA. Genetic Polymorphisms Associated with Rheumatoid Arthritis Development and Antirheumatic Therapy Response. Int J Mol Sci 2020; 21:E4911. [PMID: 32664585 PMCID: PMC7402327 DOI: 10.3390/ijms21144911] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/11/2022] Open
Abstract
Rheumatoid arthritis (RA) is the most common inflammatory arthropathy worldwide. Possible manifestations of RA can be represented by a wide variability of symptoms, clinical forms, and course options. This multifactorial disease is triggered by a genetic predisposition and environmental factors. Both clinical and genealogical studies have demonstrated disease case accumulation in families. Revealing the impact of candidate gene missense variants on the disease course elucidates understanding of RA molecular pathogenesis. A multivariate genomewide association study (GWAS) based analysis identified the genes and signalling pathways involved in the pathogenesis of the disease. However, these identified RA candidate gene variants only explain 30% of familial disease cases. The genetic causes for a significant proportion of familial RA have not been determined until now. Therefore, it is important to identify RA risk groups in different populations, as well as the possible prognostic value of some genetic variants for disease development, progression, and treatment. Our review has two purposes. First, to summarise the data on RA candidate genes and the increased disease risk associated with these alleles in various populations. Second, to describe how the genetic variants can be used in the selection of drugs for the treatment of RA.
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Affiliation(s)
- Dmitry S. Mikhaylenko
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Marina V. Nemtsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Irina V. Bure
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Ekaterina B. Kuznetsova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Ekaterina A. Alekseeva
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Laboratory of Epigenetics, Research Centre for Medical Genetics, 115478 Moscow, Russia
| | - Vadim V. Tarasov
- Department of Pharmacology and Pharmacy, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Alexander N. Lukashev
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Marina I. Beloukhova
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Andrei A. Deviatkin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
| | - Andrey A. Zamyatnin
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University (Sechenov University), 119991 Moscow, Russia; (M.V.N.); (I.V.B.); (E.B.K.); (E.A.A.); (A.N.L.); (M.I.B.); (A.A.D.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
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Tuncel J, Holmberg J, Haag S, Hopkins MH, Wester-Rosenlöf L, Carlsen S, Olofsson P, Holmdahl R. Self-reactive T cells induce and perpetuate chronic relapsing arthritis. Arthritis Res Ther 2020; 22:95. [PMID: 32345366 PMCID: PMC7187533 DOI: 10.1186/s13075-020-2104-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 01/13/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND CD4+ T cells play a central role during the early stages of rheumatoid arthritis (RA), but to which extent they are required for the perpetuation of the disease is still not fully understood. The aim of the current study was to obtain conclusive evidence that T cells drive chronic relapsing arthritis. METHODS We used the rat pristane-induced arthritis model, which accurately portrays the chronic relapsing-remitting disease course of RA, to examine the contribution of T cells to chronic arthritis. RESULTS Rats subjected to whole-body irradiation and injected with CD4+ T cells from lymph nodes of pristane-injected donors developed chronic arthritis that lasted for more than 4 months, whereas T cells from the spleen only induced acute disease. Thymectomy in combination with irradiation enhanced the severity of arthritis, suggesting that sustained lymphopenia promotes T cell-driven chronic inflammation in this model. The ability of T cells to induce chronic arthritis correlated with their expression of Th17-associated transcripts, and while depletion of T cells in rats with chronic PIA led to transient, albeit significant, reduction in disease, neutralization of IL-17 resulted in almost complete and sustained remission. CONCLUSION These findings show that, once activated, self-reactive T cells can sustain inflammatory responses for extended periods of time and suggest that such responses are promoted in the presence of IL-17.
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Affiliation(s)
- Jonatan Tuncel
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jens Holmberg
- Section for Medical Inflammation Research, BMCI11, Lund University, Lund, Sweden
| | - Sabrina Haag
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Lena Wester-Rosenlöf
- Section for Medical Inflammation Research, BMCI11, Lund University, Lund, Sweden
| | - Stefan Carlsen
- Section for Medical Inflammation Research, BMCI11, Lund University, Lund, Sweden
| | - Peter Olofsson
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rikard Holmdahl
- Division of Medical Inflammation Research, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden. .,Section for Medical Inflammation Research, BMCI11, Lund University, Lund, Sweden.
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35
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Mucaki EJ, Shirley BC, Rogan PK. Expression Changes Confirm Genomic Variants Predicted to Result in Allele-Specific, Alternative mRNA Splicing. Front Genet 2020; 11:109. [PMID: 32211018 PMCID: PMC7066660 DOI: 10.3389/fgene.2020.00109] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/30/2020] [Indexed: 12/11/2022] Open
Abstract
Splice isoform structure and abundance can be affected by either noncoding or masquerading coding variants that alter the structure or abundance of transcripts. When these variants are common in the population, these nonconstitutive transcripts are sufficiently frequent so as to resemble naturally occurring, alternative mRNA splicing. Prediction of the effects of such variants has been shown to be accurate using information theory-based methods. Single nucleotide polymorphisms (SNPs) predicted to significantly alter natural and/or cryptic splice site strength were shown to affect gene expression. Splicing changes for known SNP genotypes were confirmed in HapMap lymphoblastoid cell lines with gene expression microarrays and custom designed q-RT-PCR or TaqMan assays. The majority of these SNPs (15 of 22) as well as an independent set of 24 variants were then subjected to RNAseq analysis using the ValidSpliceMut web beacon (http://validsplicemut.cytognomix.com), which is based on data from the Cancer Genome Atlas and International Cancer Genome Consortium. SNPs from different genes analyzed with gene expression microarray and q-RT-PCR exhibited significant changes in affected splice site use. Thirteen SNPs directly affected exon inclusion and 10 altered cryptic site use. Homozygous SNP genotypes resulting in stronger splice sites exhibited higher levels of processed mRNA than alleles associated with weaker sites. Four SNPs exhibited variable expression among individuals with the same genotypes, masking statistically significant expression differences between alleles. Genome-wide information theory and expression analyses (RNAseq) in tumor exomes and genomes confirmed splicing effects for 7 of the HapMap SNP and 14 SNPs identified from tumor genomes. q-RT-PCR resolved rare splice isoforms with read abundance too low for statistical significance in ValidSpliceMut. Nevertheless, the web-beacon provides evidence of unanticipated splicing outcomes, for example, intron retention due to compromised recognition of constitutive splice sites. Thus, ValidSpliceMut and q-RT-PCR represent complementary resources for identification of allele-specific, alternative splicing.
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Affiliation(s)
- Eliseos J Mucaki
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
| | | | - Peter K Rogan
- Department of Biochemistry, University of Western Ontario, London, ON, Canada.,CytoGnomix, London, ON, Canada.,Department of Oncology University of Western Ontario, London, ON, Canada.,Department of Computer Science, University of Western Ontario, London, ON, Canada
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Campos AI, García-Marín LM, Byrne EM, Martin NG, Cuéllar-Partida G, Rentería ME. Insights into the aetiology of snoring from observational and genetic investigations in the UK Biobank. Nat Commun 2020; 11:817. [PMID: 32060260 PMCID: PMC7021827 DOI: 10.1038/s41467-020-14625-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
Although snoring is common in the general population, its aetiology has been largely understudied. Here we report a genetic study on snoring (n ~ 408,000; snorers ~ 152,000) using data from the UK Biobank. We identify 42 genome-wide significant loci, with an SNP-based heritability estimate of ~10% on the liability scale. Genetic correlations with body mass index, alcohol intake, smoking, schizophrenia, anorexia nervosa and neuroticism are observed. Gene-based associations identify 173 genes, including DLEU7, MSRB3 and POC5, highlighting genes expressed in the brain, cerebellum, lungs, blood and oesophagus. We use polygenic scores (PGS) to predict recent snoring and probable obstructive sleep apnoea (OSA) in an independent Australian sample (n ~ 8000). Mendelian randomization analyses suggest a potential causal relationship between high BMI and snoring. Altogether, our results uncover insights into the aetiology of snoring as a complex sleep-related trait and its role in health and disease beyond it being a cardinal symptom of OSA. Snoring is common in the population and tends to be more prevalent in older and/or male individuals. Here, the authors perform GWAS for habitual snoring, identify 41 genomic loci and explore potential causal relationships with anthropometric and cardiometabolic disease traits.
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Affiliation(s)
- Adrián I Campos
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Luis M García-Marín
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Zapopan, Jalisco, México
| | - Enda M Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nicholas G Martin
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gabriel Cuéllar-Partida
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia. .,University of Queensland Diamantina Institute, Brisbane, QLD, Australia.
| | - Miguel E Rentería
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. .,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
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Harrison SR, Li D, Jeffery LE, Raza K, Hewison M. Vitamin D, Autoimmune Disease and Rheumatoid Arthritis. Calcif Tissue Int 2020; 106:58-75. [PMID: 31286174 PMCID: PMC6960236 DOI: 10.1007/s00223-019-00577-2] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/18/2019] [Indexed: 02/06/2023]
Abstract
Vitamin D has been reported to influence physiological systems that extend far beyond its established functions in calcium and bone homeostasis. Prominent amongst these are the potent immunomodulatory effects of the active form of vitamin D, 1,25-dihydroxyvitamin D3 (1,25-(OH)2D3). The nuclear vitamin D receptor (VDR) for 1,25-(OH)2D3 is expressed by many cells within the immune system and resulting effects include modulation of T cell phenotype to suppress pro-inflammatory Th1 and Th17 CD4+ T cells and promote tolerogenic regulatory T cells. In addition, antigen-presenting cells have been shown to express the enzyme 1α-hydroxylase that converts precursor 25-hydroxyvitamin D3 (25-OHD3) to 1,25-(OH)2D3, so that immune microenvironments are able to both activate and respond to vitamin D. As a consequence of this local, intracrine, system, immune responses may vary according to the availability of 25-OHD3, and vitamin D deficiency has been linked to various autoimmune disorders including rheumatoid arthritis (RA). The aim of this review is to explore the immune activities of vitamin D that impact autoimmune disease, with specific reference to RA. As well as outlining the mechanisms linking vitamin D with autoimmune disease, the review will also describe the different studies that have linked vitamin D status to RA, and the current supplementation studies that have explored the potential benefits of vitamin D for prevention or treatment of RA. The overall aim of the review is to provide a fresh perspective on the potential role of vitamin D in RA pathogenesis and treatment.
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Affiliation(s)
- Stephanie R Harrison
- Institute of Metabolism and Systems Research, The University of Birmingham, Birmingham, B15 2TT, UK
- Department of Rheumatology, Sandwell and West, Birmingham Hospitals NHS Trust, Birmingham, B18 7QH, UK
| | - Danyang Li
- Institute of Metabolism and Systems Research, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Louisa E Jeffery
- Institute of Translation Medicine, The University of Birmingham, Birmingham, B15 2TT, UK
| | - Karim Raza
- Department of Rheumatology, Sandwell and West, Birmingham Hospitals NHS Trust, Birmingham, B18 7QH, UK
- Institute of Inflammation and Ageing, Arthritis Research UK Rheumatoid Arthritis Pathogenesis Centre of Excellence and MRC Arthritis Research UK Centre for Musculoskeletal Ageing Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Martin Hewison
- Institute of Metabolism and Systems Research, The University of Birmingham, Birmingham, B15 2TT, UK.
- Centre for Endocrinology, Diabetes and Metabolism, Birmingham Health Partners, Birmingham, B15 2TT, UK.
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Fang H, Chen L, Knight JC. From genome-wide association studies to rational drug target prioritisation in inflammatory arthritis. THE LANCET. RHEUMATOLOGY 2020; 2:e50-e62. [PMID: 38258277 DOI: 10.1016/s2665-9913(19)30134-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 12/24/2022]
Abstract
Early identification of genetically validated drug targets can increase the chances of successful late-stage drug development. 81 high-quality genome-wide association studies (GWAS) in diseases related to inflammatory arthritis have been curated into the GWAS catalogue; however, translation of genetic findings from GWAS into rational drug target discovery has been poor. No human genetic findings have completely driven drug development for inflammatory arthritis; however, genetic associations have partly driven the development of abatacept (CTLA-4-Ig) in rheumatoid arthritis and secukinumab (anti-IL-23R) in ankylosing spondylitis. Roadblocks to progress exist, including little knowledge of the genetic architecture and regulatory mechanisms underlying associations, and the need to identify gene regulatory networks and assess target tractability. New opportunities are arising that could maximise the informativeness of GWAS for drug target validation. Genetic variants can be linked to core genes by using functional genomics and then to peripheral genes interconnected to core genes using network information. Moreover, identification of crosstalk between biological pathways might highlight key points for therapeutic intervention.
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Affiliation(s)
- Hai Fang
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Liye Chen
- Botnar Research Centre, University of Oxford, Oxford, UK
| | - Julian C Knight
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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39
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Ravel JM, Mignot EJM. [Narcolepsy: From the discovery of a wake promoting peptide to autoimmune T cell biology and molecular mimicry with flu epitopes]. Biol Aujourdhui 2019; 213:87-108. [PMID: 31829930 DOI: 10.1051/jbio/2019026] [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: 10/16/2019] [Indexed: 11/14/2022]
Abstract
Narcolepsy-cataplexy was first described in the late 19th century in Germany and France. Prevalence was established to be 0.05 % and a canine model was discovered in the 1970s. In 1983, a Japanese study found that all patients carried HLA-DR2, suggesting autoimmunity as the cause of the disease. Studies in the canine model established that dopaminergic stimulation underlies anti-narcoleptic action of psychostimulants, while antidepressants were found to suppress cataplexy through adrenergic reuptake inhibition. No HLA association was found in canines. A linkage study initiated in 1988 revealed in hypocretin (orexin) receptor two mutations as the cause of canine narcolepsy in 1999. In 1992, studies on African Americans showed that DQ0602 was a better marker than DR2 across all ethnic groups. In 2000, hypocretin-1/orexin A levels were measured in the cerebrospinal fluid (CSF) and found to be undetectable in most patients, establishing hypocretin deficiency as the cause of narcolepsy. Decreased CSF hypocretin-1 was then found to be secondary to the loss of the 70,000 neurons producing hypocretin in the hypothalamus, suggesting immune destruction of these cells as the cause of the disease. Additional genetic studies, notably genome wide associations (GWAS), found multiple genetic predisposing factors for narcolepsy. These were almost all involved in other autoimmune diseases, although a strong and unique association with T cell receptor (TCR) alpha and beta loci were observed. Nonetheless, all attempts to demonstrate presence of autoantibodies against hypocretin cells in narcolepsy failed, and the presumed autoimmune cause remained unproven. In 2009, association with strep throat infections were found, and narcolepsy onsets were found to occur more frequently in spring and summer, suggesting upper away infections as triggers. Following reports that narcolepsy cases were triggered by vaccinations and infections against influenza A 2009 pH1N1, a new pandemic strain that erupted in 2009, molecular mimicry with influenza A virus was suggested in 2010. This hypothesis was later confirmed by peptide screening showing higher activity of CD4+ T cell reactivity to a specific post-translationally amidated segment of hypocretin (HCRT-NH2) and cross-reactivity of specific TCRs with a pH1N1-specific segment of hemagglutinin that shares homology with HCRT-NH2. Strikingly, the most frequent TCR recognizing these antigens was found to carry sequences containing TRAJ24 or TRVB4-2, segments modulated by narcolepsy-associated genetic polymorphisms. Cross-reactive CD4+ T cells with these cross-reactive TCRs likely subsequently recruit CD8+ T cells that are then involved in hypocretin cell destruction. Additional flu mimics are also likely to be discovered since narcolepsy existed prior to 2009. The work that has been conducted over the years on narcolepsy offers a unique perspective on the conduct of research on the etiopathogeny of a specific disease.
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Affiliation(s)
- Jean-Marie Ravel
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Medicine, Stanford University, 3615 Porter Drive, Palo Alto, CA, USA
| | - Emmanuel J M Mignot
- Stanford Center for Sleep Sciences and Medicine, Department of Psychiatry and Behavioral Medicine, Stanford University, 3615 Porter Drive, Palo Alto, CA, USA
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40
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Abstract
Interleukin (IL)-10 is an essential anti-inflammatory cytokine and functions as a negative regulator of immune responses to microbial antigens. IL-10 is particularly important in maintaining the intestinal microbe-immune homeostasis. Loss of IL-10 promotes the development of inflammatory bowel disease (IBD) as a consequence of an excessive immune response to the gut microbiota. IL-10 also functions more generally to prevent excessive inflammation during the course of infection. Although IL-10 can be produced by virtually all cells of the innate and adaptive immune system, T cells constitute a non-redundant source for IL-10 in many cases. The various roles of T cell-derived IL-10 will be discussed in this review. Given that IL-10 is at the center of maintaining the delicate balance between effective immunity and tissue protection, it is not surprising that IL-10 expression is highly dynamic and tightly regulated. We summarize the environmental signals and molecular pathways that regulate IL-10 expression. While numerous studies have provided us with a deep understanding of IL-10 biology, the majority of findings have been made in murine models, prompting us to highlight gaps in our knowledge about T cell-derived IL-10 in the human system.
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Machaj F, Rosik J, Szostak B, Pawlik A. The evolution in our understanding of the genetics of rheumatoid arthritis and the impact on novel drug discovery. Expert Opin Drug Discov 2019; 15:85-99. [PMID: 31661990 DOI: 10.1080/17460441.2020.1682992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Rheumatoid arthritis (RA) is an autoimmune disease that is characterized by chronic inflammation of the joints and affects 1% of the population. Polymorphisms of genes that encode proteins that primarily participate in inflammation may influence RA occurrence or become useful biomarkers for certain types of anti-rheumatic treatment.Areas covered: The authors summarize the recent progress in our understanding of the genetics of RA. In the last few years, multiple variants of genes that are associated with RA risk have been identified. The development of new technologies and the detection of new potential therapeutic targets that contribute to novel drug discovery are also described.Expert opinion: There is still the need to search for new genes which may be a potential target for RA therapy. The challenge is to develop appropriate strategies for achieving insight into the molecular pathways involved in RA pathogenesis. Understanding the genetics, immunogenetics, epigenetics and immunology of RA could help to identify new targets for RA therapy. The development of new technologies has enabled the detection of a number of new genes, particularly genes associated with proinflammatory cytokines and chemokines, B- and T-cell activation pathways, signal transducers and transcriptional activators, which might be potential therapeutic targets in RA.
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Affiliation(s)
- Filip Machaj
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Jakub Rosik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Bartosz Szostak
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Pawlik
- Department of Physiology, Pomeranian Medical University, Szczecin, Poland
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Motegi T, Kochi Y, Matsuda K, Kubo M, Yamamoto K, Momozawa Y. Identification of rare coding variants in TYK2 protective for rheumatoid arthritis in the Japanese population and their effects on cytokine signalling. Ann Rheum Dis 2019; 78:1062-1069. [PMID: 31118190 DOI: 10.1136/annrheumdis-2019-215062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/19/2019] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE Although genome-wide association studies (GWAS) have identified approximately 100 loci for rheumatoid arthritis (RA), the disease mechanisms are not completely understood. We evaluated the pathogenesis of RA by focusing on rare coding variants. METHODS The coding regions of 98 candidate genes identified by GWAS were sequenced in 2294 patients with RA and 4461 controls in Japan. An association analysis was performed using cases and controls for variants, genes and domains of TYK2. Cytokine responses for two associated variants (R231W, rs201917359; and R703W, rs55882956) in TYK2 as well as a previously reported risk variant (P1004A, rs34536443) for multiple autoimmune diseases were evaluated by reporter assays. RESULTS A variant in TYK2 (R703W) showed a suggestive association (p=5.47×10-8, OR=0.48). We observed more accumulation of rare coding variants in controls in TYK2 (p=3.94×10-12, OR=0.56). The four-point-one, ezrin, radixin, moesin (FERM; 2.14×10-3, OR=0.66) and pseudokinase domains (1.63×10-8, OR=0.52) of TYK2 also showed enrichment of variants in controls. R231W in FERM domain especially reduced interleukin (IL)-6 and interferon (IFN)-γ signalling, whereas P1104A in kinase domain reduced IL-12, IL-23 and IFN-α signalling. R703W in pseudokinase domain reduced cytokine signals similarly to P1104A, but the effects were weaker than those of P1104A. CONCLUSIONS The FERM and pseudokinase domains in TYK2 were associated with the risk of RA in the Japanese population. Variants in TYK2 had different effects on cytokine signalling, suggesting that the regulation of selective cytokine signalling is a target for RA treatment.
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Affiliation(s)
- Tomoki Motegi
- Veterinary Medical Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuta Kochi
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Koichi Matsuda
- Laboratory of Clinical Genome Sequencing, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
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Emmer A, Abobarin-Adeagbo A, Posa A, Jordan B, Delank KS, Staege MS, Surov A, Zierz S, Kornhuber ME. Myositis in Lewis rats induced by the superantigen Staphylococcal enterotoxin A. Mol Biol Rep 2019; 46:4085-4094. [DOI: 10.1007/s11033-019-04858-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 05/03/2019] [Indexed: 12/18/2022]
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Xu J, He Y, Wang J, Li X, Huang L, Li S, Qin X. Influence of the TNFSF4 rs1234315 polymorphism in the susceptibility to systemic lupus erythematosus and rheumatoid arthritis. Hum Immunol 2019; 80:270-275. [DOI: 10.1016/j.humimm.2018.11.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 01/09/2023]
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Wells PM, Williams FMK, Matey-Hernandez ML, Menni C, Steves CJ. 'RA and the microbiome: do host genetic factors provide the link? J Autoimmun 2019; 99:104-115. [PMID: 30850234 PMCID: PMC6470121 DOI: 10.1016/j.jaut.2019.02.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 12/29/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic autoimmune disease, characterised by painful synovium inflammation, bony erosions, immune activation and the circulation of autoantibodies. Despite recent advances in therapeutics enabling disease suppression, there is a considerable demand for alternative therapeutic strategies as well as optimising those available at present. The relatively low concordance rate between monozygotic twins, 20–30% contrasts with heritability estimates of ∼65%, indicating a substantive role of other risk factors in RA pathogenesis. There is established evidence that RA has an infective component to its aetiology. More recently, differences in the commensal microbiota in RA compared to controls have been identified. Studies have shown that the gut, oral and lung microbiota is different in new onset treatment naïve, and established RA patients, compared to controls. Key taxonomic associations are an increase in abundance of Porphyromonas gingivalis and Prevotella copri in RA patients, compared to healthy controls. Host genetics may provide the link between disease and the microbiome. Genetic influence may be mediated by the host immune system; a differential response to RA associated taxa is suggested. The gut microbiome contains elements which are as much as 30% heritable. A better understanding of the influence of host genetics will shed light onto the role of the microbiome in RA. Here we review the role of the microbiome in RA through the lens of host genetics, and consider future research areas addressing microbiome study design and bioinformatics approaches. Rheumatoid arthritis (RA) affects 1% of the population and is highly debilitating. RA is ~65% heritable, yet the concordance rate between monozygotic twins is just 20–30%, indicating a substantive role of other risk factors. Studies have shown that the gut, oral and lung microbiome is different in treatment naïve and established RA patients, compared to controls. Current findings suggest an important influence of host genetics on the microbiome, which may contribute to RA via the host immune system. Associations of the microbiome with RA described thus far are confounded by host genetics, and future studies need to take account of this.
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Affiliation(s)
- Philippa M Wells
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK.
| | - Frances M K Williams
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - M L Matey-Hernandez
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Cristina Menni
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK
| | - Claire J Steves
- The Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Hospital, Lambeth Palace Road, London, SE1 7EH, UK; Clinical Age Research Unit, Kings College Hospital Foundation Trust, London, UK
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Yang XK, Liu J, Chen SY, Li M, Zhang MM, Leng RX, Pan HF, Shen Y, Liu WX, Xu SQ, Ye DQ, Shuai ZW. UBASH3A gene polymorphisms and expression profile in rheumatoid arthritis. Autoimmunity 2019; 52:21-26. [PMID: 30822156 DOI: 10.1080/08916934.2019.1581773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVES Recent evidence has demonstrated that UBASH3A play a pivotal role in multiple autoimmune diseases. In this study, we explored the association between UBASH3A gene single-nucleotide polymorphisms (SNPs) and rheumatoid arthritis (RA) in a Chinese Han population. We also comparatively evaluated the UBASH3A expression profile in peripheral blood mononuclear cells (PBMCs) from patients with RA and healthy controls. METHODS Four UBASH3A polymorphisms (rs1893592, rs11203203, rs2277798, and rs3788013) were studied in 553 patients with RA and 587 controls in a Chinese population. Genotyping was performed using the Fluidigm 192.24 Dynamic Array Integrated Fluidic Circuit (IFC). For gene expression study, UBASH3A mRNA levels of 30 RA patients and 31 healthy individuals were assessed by real-time quantitative polymerase chain reaction (RT-qPCR). Data were analyzed by SPSS 19.0 software. RESULTS A significant association between rs1893592 polymorphism and RA was found under all genetic models (all p<.05). We also discovered a significant association between rs3788013 polymorphism and RA in the allele and genotype distributions, as well as the recessive model (all p<.05). Moreover, we found the genotype distribution and allele frequency of rs1893592 were significantly associated with RF phenotype in the RA patients (χ2 = 6.786, p=.034; χ2 = 4.534, p=.033; respectively). We also found the genotype distribution and allele frequency of rs2277798 were significantly associated with anti-CCP phenotype in the RA patients (χ2 = 7.873, p=.020; χ2 = 4.473, p=.034; respectively). However, we did not detect any significant associations between rs11203203 and RA susceptibility and autoantibody profiles (all p>.05). The mRNA expression of UBASH3A was increased in PBMCs of patients with RA when compared to healthy controls (p=.001). CONCLUSIONS Our observations suggested that the dysregulation of UBASH3A might be associated with the pathogenesis of RA, and UBASH3A gene polymorphisms (rs1893592 and rs3788013) might contribute to RA susceptibility in Chinese Han population.
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Affiliation(s)
- Xiao-Ke Yang
- a Department of Rheumatology and Immunology , the First Affiliated Hospital of Anhui Medical University , Hefei , Anhui , China
| | - Juan Liu
- b Wuxi Center for Disease Control and Prevention , Wuxi , Jiangsu , China
| | - Shan-Yu Chen
- a Department of Rheumatology and Immunology , the First Affiliated Hospital of Anhui Medical University , Hefei , Anhui , China
| | - Mu Li
- a Department of Rheumatology and Immunology , the First Affiliated Hospital of Anhui Medical University , Hefei , Anhui , China
| | - Ming-Ming Zhang
- a Department of Rheumatology and Immunology , the First Affiliated Hospital of Anhui Medical University , Hefei , Anhui , China
| | - Rui-Xue Leng
- c Department of Epidemiology and Biostatistics, School of Public Health , Anhui Medical University , Hefei , Anhui , China
| | - Hai-Feng Pan
- c Department of Epidemiology and Biostatistics, School of Public Health , Anhui Medical University , Hefei , Anhui , China
| | - Yuan Shen
- b Wuxi Center for Disease Control and Prevention , Wuxi , Jiangsu , China
| | - Wen-Xue Liu
- d Wuxi Emergency Medical Centre , Wuxi , Jiangsu , China
| | - Sheng-Qian Xu
- a Department of Rheumatology and Immunology , the First Affiliated Hospital of Anhui Medical University , Hefei , Anhui , China
| | - Dong-Qing Ye
- c Department of Epidemiology and Biostatistics, School of Public Health , Anhui Medical University , Hefei , Anhui , China
| | - Zong-Wen Shuai
- a Department of Rheumatology and Immunology , the First Affiliated Hospital of Anhui Medical University , Hefei , Anhui , China
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Yin X, Cheng F, Wang X, Mu J, Ma C, Zhai C, Wang Q. Top 100 cited articles on rheumatoid arthritis: A bibliometric analysis. Medicine (Baltimore) 2019; 98:e14523. [PMID: 30813156 PMCID: PMC6408095 DOI: 10.1097/md.0000000000014523] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is a worldwide health issue; although the prospects for most patients are favorable, many still do not respond to the current therapies. Numerous articles related to RA have been published in the past 3 decades; an analysis of the most cited articles in this field was undertaken to identify important articles regarding RA related to pathogenesis, diagnosis, and treatment. METHODS We searched the Web of Science and collected the general information of the top 100 cited articles. The citation number, publication year, authorship, impact factor (IF) of the journal in the publication year, country origins, article types, and funding source were evaluated. RESULTS The total citations of the top 100 articles varied from 11,922 to 556 and were published between 1985 and 2014. These articles were published in 24 journals, led by Arthritis and Rheumatism (n = 33), followed by the New England Journal of Medicine (n = 15). Most of the articles (n = 80) were produced by ≥5 authors. They were from 34 countries, and the United Stated contributed to most of the articles (n = 58), followed by the United Kingdom (n = 42). The article types were divided into clinical study (n = 55), review (n = 17), meta-analysis (n = 4), clinical guideline (n = 10), and basic science (n = 14). Eighty-seven percent of the articles were supported either by public organizations or medical companies. CONCLUSION This study provided insights into the development of publications and their citations of RA in the past 3 decades. Clinical studies or clinical guidelines published in high-impact journals were more likely to be cited in the field of RA. The latest publications may not be included in the top 100 cited articles, as the more recent studies have not had sufficient time to accumulate the number of citations.
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Abstract
PURPOSE OF REVIEW Aberrant epigenetic changes in DNA methylation, histone marks, and noncoding RNA expression regulate the pathogenesis of many rheumatic diseases. The present article will review the recent advances in the epigenetic profile of inflammatory arthritis and discuss diagnostic biomarkers and potential therapeutic targets. RECENT FINDINGS Methylation signatures of fibroblast-like synoviocytes not only distinguish rheumatoid arthritis (RA) and osteoarthritis (OA), but also early RA from late RA or juvenile idiopathic arthritis. Methylation patterns are also specific to individual joint locations, which might explain the distribution of joint involvement in some rheumatic diseases. Hypomethylation in systemic lupus erythematosus (SLE) T cells is, in part, because of active demethylation and 5-hydroxymethylation. The methylation status of some genes in SLE is associated with disease severity and has potential as a diagnostic marker. An integrative analysis of OA methylome, transcriptome, and proteome in chondrocytes has identified multiple-evidence genes that might be evaluated for therapeutic potential. Class-specific histone deacetylase inhibitors are being evaluated for therapy in inflammatory arthritis. SUMMARY Disease pathogenesis is regulated by the interplay of genetics, environment, and epigenetics. Understanding how these mechanisms regulate cell function in health and disease has implications for individualized therapy.
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49
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Zamanpoor M. The genetic pathogenesis, diagnosis and therapeutic insight of rheumatoid arthritis. Clin Genet 2019; 95:547-557. [PMID: 30578544 DOI: 10.1111/cge.13498] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/18/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022]
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease that causes chronic inflammation of the joints. RA is a heterogeneous disorder caused by an abnormal autoimmune response triggered by the complex interactions of genetic and environmental factors that contribute to RA etiology. However, its underlying pathogenic mechanisms are yet to be fully understood. In this review, I provide an overview of the pathogenesis, diagnosis and therapeutic insight in the clinical management of RA in light of the recent updates to classification criteria and recent discoveries of genetic loci associated with susceptibility for RA.
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Affiliation(s)
- Mansour Zamanpoor
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Wellington Regional Genetics Laboratory, Genetic Health Service New Zealand, Wellington Regional Hospital, Wellington, New Zealand
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50
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Carey HA, Hildreth BE, Samuvel DJ, Thies KA, Rosol TJ, Toribio RE, Charles JF, Ostrowski MC, Sharma SM. Eomes partners with PU.1 and MITF to Regulate Transcription Factors Critical for osteoclast differentiation. iScience 2019; 11:238-245. [PMID: 30634169 PMCID: PMC6327072 DOI: 10.1016/j.isci.2018.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/12/2018] [Accepted: 12/20/2018] [Indexed: 01/08/2023] Open
Abstract
Bone-resorbing osteoclasts (OCs) are derived from myeloid precursors (MPs). Several transcription factors are implicated in OC differentiation and function; however, their hierarchical architecture and interplay are not well known. Analysis for enriched motifs in PU.1 and MITF chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) data from differentiating OCs identified eomesodermin (EOMES) as a potential novel binding partner of PU.1 and MITF at genes critical for OC differentiation and function. We were able to demonstrate using co-immunoprecipitation and sequential ChIP analysis that PU.1, MITF, and EOMES are in the same complex and present as a complex at OC genomic loci. Furthermore, EOMES knockdown in MPs led to osteopetrosis associated with decreased OC differentiation and function both in vitro and in vivo. Although EOMES is associated with embryonic development and other hematopoietic lineages, this is the first study demonstrating the requirement of EOMES in the myeloid compartment.
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Affiliation(s)
- Heather A Carey
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Blake E Hildreth
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Hollings Cancer Center, 86 Jonathan Lucas St, Charleston, SC 29425, USA
| | - Devadoss J Samuvel
- Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Hollings Cancer Center, 86 Jonathan Lucas St, Charleston, SC 29425, USA
| | - Katie A Thies
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Hollings Cancer Center, 86 Jonathan Lucas St, Charleston, SC 29425, USA
| | - Thomas J Rosol
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Ramiro E Toribio
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
| | - Julia F Charles
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael C Ostrowski
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Hollings Cancer Center, 86 Jonathan Lucas St, Charleston, SC 29425, USA.
| | - Sudarshana M Sharma
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA; Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Hollings Cancer Center, 86 Jonathan Lucas St, Charleston, SC 29425, USA.
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