1
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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; 80:776-790. [PMID: 38652555 DOI: 10.1097/hep.0000000000000894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [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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Stewart AP, Loudon KW, Routledge M, Lee CYC, Trotter P, Richoz N, Gillman E, Antrobus R, Mccaffrey J, Posner D, Conway Morris A, Karet Frankl FE, Clatworthy MR. Neutrophil extracellular traps protect the kidney from ascending infection and are required for a positive leukocyte dipstick test. Sci Transl Med 2024; 16:eadh5090. [PMID: 39321268 DOI: 10.1126/scitranslmed.adh5090] [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: 03/08/2023] [Revised: 12/10/2023] [Accepted: 09/05/2024] [Indexed: 09/27/2024]
Abstract
Lower urinary tract infection (UTI) is common but only rarely complicated by pyelonephritis. However, the mechanisms preventing extension to the kidney are unclear. Here, we identified neutrophil extracellular traps (NETs) in healthy human urine that provide an antibacterial defense strategy within the urinary tract. In both in vivo murine models of UTI where uropathogenic E. coli are inoculated into the bladder and ex vivo human urine models, NETs interacted with uromodulin to form large webs that entrapped the bacteria. Peptidyl arginine deiminase 4 (PADI4) inhibition in mice blocked NETosis and resulted in progression of cystitis into pyelonephritis, suggesting that NETosis of urinary neutrophils acts to prevent bacterial ascent into the kidney. Analysis of UK Biobank data revealed that genetic variants in PADI4 that associated with increased risk of rheumatoid arthritis in multiple genome-wide association studies were consistently associated with reduced susceptibility to UTI. Last, we showed that urine dipstick testing for leukocyte esterase was negative in the presence of intact blood neutrophils but became positive when neutrophils were stimulated to NET, and this could be prevented by selective PADI4 inhibition, demonstrating that this test does not detect absolute neutrophil count, as has long been assumed, but specifically detects neutrophils that have undergone NETosis. These findings highlight the role of NETosis in preventing ascending infections in the urinary tract and improve our understanding of one of the most common clinical tests in medicine.
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Affiliation(s)
- Andrew P Stewart
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Kevin W Loudon
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Matthew Routledge
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Colin Y C Lee
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Patrick Trotter
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Eleanor Gillman
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Robin Antrobus
- Department of Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - James Mccaffrey
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - David Posner
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
| | - Andrew Conway Morris
- Division of Anaesthesia, Department of Medicine, University of Cambridge, Level 4, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
- Division of Immunology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
- JVF Intensive Care Unit, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Fiona E Karet Frankl
- Department of Medical Genetics and Division of Renal Medicine, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XY, UK
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, CB2 0QH, UK
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3
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Levescot A, Cerf-Bensussan N. Loss of tolerance to dietary proteins: From mouse models to human model diseases. Immunol Rev 2024; 326:173-190. [PMID: 39295093 DOI: 10.1111/imr.13395] [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: 09/21/2024]
Abstract
The critical importance of the immunoregulatory mechanisms, which prevent adverse responses to dietary proteins is demonstrated by the consequences of their failure in two common but distinct human pathological conditions, food allergy and celiac disease. The mechanisms of tolerance to dietary proteins have been extensively studied in mouse models but the extent to which the results in mice can be extrapolated to humans remains unclear. Here, after summarizing the mechanisms known to control oral tolerance in mouse models, we discuss how the monogenic immune disorders associated with food allergy on the one hand, and celiac disease, on the other hand, represent model diseases to gain insight into the key immunoregulatory pathways that control immune responses to food antigens in humans. The spectrum of monogenic disorders, in which the dysfunction of a single gene, is strongly associated with TH2-mediated food allergy suggests an important overlap between the mechanisms that regulate TH2 and IgE responses to food antigens in humans and mice. In contrast, celiac disease provides a unique example of the link between autoimmunity and loss of tolerance to a food antigen.
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Affiliation(s)
- Anais Levescot
- Laboratory of Intestinal Immunity, INSERM UMR 1163 and Imagine Institute, Université Paris Cité, Paris, France
| | - Nadine Cerf-Bensussan
- Laboratory of Intestinal Immunity, INSERM UMR 1163 and Imagine Institute, Université Paris Cité, Paris, France
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4
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Murphy MB, Yang Z, Subati T, Farber-Eger E, Kim K, Blackwell DJ, Fleming MR, Stark JM, Van Amburg JC, Woodall KK, Van Beusecum JP, Agrawal V, Smart CD, Pitzer A, Atkinson JB, Fogo AB, Bastarache JA, Kirabo A, Wells QS, Madhur MS, Barnett JV, Murray KT. LNK/SH2B3 loss of function increases susceptibility to murine and human atrial fibrillation. Cardiovasc Res 2024; 120:899-913. [PMID: 38377486 PMCID: PMC11218690 DOI: 10.1093/cvr/cvae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/31/2023] [Accepted: 10/07/2023] [Indexed: 02/22/2024] Open
Abstract
AIMS The lymphocyte adaptor protein (LNK) is a negative regulator of cytokine and growth factor signalling. The rs3184504 variant in SH2B3 reduces LNK function and is linked to cardiovascular, inflammatory, and haematologic disorders, including stroke. In mice, deletion of Lnk causes inflammation and oxidative stress. We hypothesized that Lnk-/- mice are susceptible to atrial fibrillation (AF) and that rs3184504 is associated with AF and AF-related stroke in humans. During inflammation, reactive lipid dicarbonyls are the major components of oxidative injury, and we further hypothesized that these mediators are critical drivers of the AF substrate in Lnk-/- mice. METHODS AND RESULTS Lnk-/- or wild-type (WT) mice were treated with vehicle or 2-hydroxybenzylamine (2-HOBA), a dicarbonyl scavenger, for 3 months. Compared with WT, Lnk-/- mice displayed increased AF duration that was prevented by 2-HOBA. In the Lnk-/- atria, action potentials were prolonged with reduced transient outward K+ current, increased late Na+ current, and reduced peak Na+ current, pro-arrhythmic effects that were inhibited by 2-HOBA. Mitochondrial dysfunction, especially for Complex I, was evident in Lnk-/- atria, while scavenging lipid dicarbonyls prevented this abnormality. Tumour necrosis factor-α (TNF-α) and interleukin-1 beta (IL-1β) were elevated in Lnk-/- plasma and atrial tissue, respectively, both of which caused electrical and bioenergetic remodelling in vitro. Inhibition of soluble TNF-α prevented electrical remodelling and AF susceptibility, while IL-1β inhibition improved mitochondrial respiration but had no effect on AF susceptibility. In a large database of genotyped patients, rs3184504 was associated with AF, as well as AF-related stroke. CONCLUSION These findings identify a novel role for LNK in the pathophysiology of AF in both experimental mice and humans. Moreover, reactive lipid dicarbonyls are critical to the inflammatory AF substrate in Lnk-/- mice and mediate the pro-arrhythmic effects of pro-inflammatory cytokines, primarily through electrical remodelling.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Action Potentials/drug effects
- Adaptor Proteins, Signal Transducing/genetics
- Adaptor Proteins, Signal Transducing/metabolism
- Atrial Fibrillation/metabolism
- Atrial Fibrillation/physiopathology
- Atrial Fibrillation/genetics
- Benzylamines/pharmacology
- Disease Models, Animal
- Genetic Predisposition to Disease
- Heart Rate/drug effects
- Inflammation Mediators/metabolism
- Interleukin-1beta/metabolism
- Interleukin-1beta/genetics
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Mitochondria, Heart/metabolism
- Mitochondria, Heart/pathology
- Mitochondria, Heart/drug effects
- Myocytes, Cardiac/metabolism
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/pathology
- Oxidative Stress/drug effects
- Phenotype
- Signal Transduction
- Tumor Necrosis Factor-alpha/metabolism
- Tumor Necrosis Factor-alpha/genetics
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Affiliation(s)
- Matthew B Murphy
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Zhenjiang Yang
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Tuerdi Subati
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Eric Farber-Eger
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
| | - Kyungsoo Kim
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Daniel J Blackwell
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Matthew R Fleming
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
| | - Joshua M Stark
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Joseph C Van Amburg
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Kaylen K Woodall
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Justin P Van Beusecum
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Vineet Agrawal
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
| | - Charles D Smart
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Ashley Pitzer
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - James B Atkinson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, 1161 21 Avenue South, Nashville, TN 37232, USA
| | - Agnes B Fogo
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, 1161 21 Avenue South, Nashville, TN 37232, USA
| | - Julie A Bastarache
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
| | - Annet Kirabo
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Quinn S Wells
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, 2525 West End Avenue, Nashville, TN 37203, USA
| | - Meena S Madhur
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Joey V Barnett
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
| | - Katherine T Murray
- Department of Medicine, Division of Clinical Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, 559 PRB, Nashville, TN 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, 2220 Pierce Avenue, Nashville, TN 37232, USA
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5
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Stabach PR, Sims D, Gomez-Bañuelos E, Zehentmeier S, Dammen-Brower K, Bernhisel A, Kujawski S, Lopez SG, Petri M, Goldman DW, Lester ER, Le Q, Ishaq T, Kim H, Srivastava S, Kumar D, Pereira JP, Yarema KJ, Koumpouras F, Andrade F, Braddock DT. A dual-acting DNASE1/DNASE1L3 biologic prevents autoimmunity and death in genetic and induced lupus models. JCI Insight 2024; 9:e177003. [PMID: 38888971 PMCID: PMC11383374 DOI: 10.1172/jci.insight.177003] [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: 10/26/2023] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
A defining feature of systemic lupus erythematosus (SLE) is loss of tolerance to self-DNA, and deficiency of DNASE1L3, the main enzyme responsible for chromatin degradation in blood, is also associated with SLE. This association can be found in an ultrarare population of pediatric patients with DNASE1L3 deficiency who develop SLE, adult patients with loss-of-function variants of DNASE1L3 who are at a higher risk for SLE, and patients with sporadic SLE who have neutralizing autoantibodies against DNASE1L3. To mitigate the pathogenic effects of inherited and acquired DNASE1L3 deficiencies, we engineered a long-acting enzyme biologic with dual DNASE1/DNASE1L3 activity that is resistant to DNASE1 and DNASE1L3 inhibitors. Notably, we found that the biologic prevented the development of lupus in Dnase1-/-Dnase1L3-/- double-knockout mice and rescued animals from death in pristane-induced lupus. Finally, we confirmed that the human isoform of the enzyme biologic was not recognized by autoantibodies in SLE and efficiently degraded genomic and mitochondrial cell-free DNA, as well as microparticle DNA, in SLE plasma. Our findings suggest that autoimmune diseases characterized by aberrant DNA accumulation, such as SLE, can be effectively treated with a replacement DNASE tailored to bypass pathogenic mechanisms, both genetic and acquired, that restrict DNASE1L3 activity.
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Affiliation(s)
- Paul R Stabach
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Dominique Sims
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eduardo Gomez-Bañuelos
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Sandra Zehentmeier
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kris Dammen-Brower
- Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew Bernhisel
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sophia Kujawski
- Department of Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sam G Lopez
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Michelle Petri
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Daniel W Goldman
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ethan R Lester
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Quan Le
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Tayyaba Ishaq
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hana Kim
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Shivani Srivastava
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Deepika Kumar
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joao P Pereira
- Department of Immunobiology and Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kevin J Yarema
- Translational Tissue Engineering Center and Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Fotios Koumpouras
- Department of Rheumatology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Felipe Andrade
- Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Demetrios T Braddock
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively parallel reporter assay confirms regulatory potential of hQTLs and reveals important variants in lupus and other autoimmune diseases. HGG ADVANCES 2024; 5:100279. [PMID: 38389303 PMCID: PMC10943488 DOI: 10.1016/j.xhgg.2024.100279] [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: 09/08/2023] [Revised: 02/15/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024] Open
Abstract
We designed a massively parallel reporter assay (MPRA) in an Epstein-Barr virus transformed B cell line to directly characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate regulatory activity in an allele-dependent manner. Our study demonstrates that hQTLs, as a group, are more likely to modulate regulatory activity in an MPRA compared with other variant classes tested, including a set of eQTLs previously shown to interact with hQTLs and tested AI risk variants. In addition, we nominate 17 variants (including 11 previously unreported) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies in primary and immortalized B cells. Thus, we uncover important insights into the mechanistic relationships among genotype, epigenetics, and gene expression in SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
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7
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Størdal K, Tapia G, Lund-Blix NA, Stene LC. Genotypes predisposing for celiac disease and autoimmune diabetes and risk of infections in early childhood. J Pediatr Gastroenterol Nutr 2024; 78:295-303. [PMID: 38374560 DOI: 10.1002/jpn3.12078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 02/21/2024]
Abstract
OBJECTIVES Infections in early childhood have been associated with risk of celiac disease (CD) and type 1 diabetes (T1D). We investigated whether this is driven by susceptibility genes for autoimmune disease by comparing infection frequency by genetic susceptibility variants for CD or T1D. METHODS We genotyped 373 controls and 384 children who developed CD or T1D in the population-based Norwegian Mother, Father and Child Cohort study (MoBa) study for human leukocyte antigen (HLA)-DQ, FUT2, SH2B3, and PTPN22, and calculated a weighted non-HLA genetic risk score (GRS) for CD and T1D based on over 40 SNPs. Parents reported infections in questionnaires when children were 6 and 18 months old. We used negative binomial regression to estimate incidence rate ratio (IRR) for infections by genotype. RESULTS HLA genotypes for CD and T1D or non-HLA GRS for T1D were not associated with infections. The non-HLA GRS for CD was associated with a nonsignificantly lower frequency of infections (aIRR: 0.95, 95% CI: 0.87-1.03 per weighted allele score), and significantly so when restricting to healthy controls (aIRR: 0.89, 0.81-0.99). Participants homozygous for rs601338(A;A) at FUT2, often referred to as nonsecretors, had a nonsignificantly lower risk of infections (aIRR: 0.91, 95% CI: 0.83-1.01). SH2B3 and PTPN22 genotypes were not associated with infections. The association between infections and risk of CD (OR: 1.15 per five infections) was strengthened after adjustment for HLA genotype and non-HLA GRS (OR: 1.24). CONCLUSIONS HLA variants and non-HLA GRS conferring susceptibility for CD were not associated with increased risk of infections in early childhood and is unlikely to drive the observed association between infections and risk of CD or T1D in many studies.
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Affiliation(s)
- Ketil Størdal
- Department of Pediatric Research, Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - German Tapia
- Norwegian Institute of Public Health, Oslo, Norway
| | | | - Lars C Stene
- Norwegian Institute of Public Health, Oslo, Norway
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8
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de Groen PC. A new, all-encompassing aetiology of type 1 diabetes. Immunology 2024; 171:77-91. [PMID: 37772700 DOI: 10.1111/imm.13700] [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: 04/26/2023] [Accepted: 09/10/2023] [Indexed: 09/30/2023] Open
Abstract
The aetiology of type 1 diabetes (T1D) is considered multifactorial with the contribution of the MHC on chromosome 6 being most important. Multiple factors also contribute to the aetiology of colorectal neoplasia, but the final event causing the change from normal mucosa to polyp and from polyp to cancer is due to a single somatic mutation event. Repeated formation of colorectal neoplasia within an at-risk population results in a predictable, tapering, exponential neoplasia distribution. Critical mutations driving colorectal neoplasia formation occur in mutation-prone DNA. These observations led to three hypotheses related to T1D. First, a single somatic mutation within the MHC of antigen presenting cells results in a change in phenotype from normal to T1D. Second, the distribution of additional autoimmune diseases (AAIDs) among persons with T1D adheres to a predictable, tapering, exponential distribution. And third, critical mutations driving development of T1D occur in mutation-prone DNA. To address the hypotheses in an orderly fashion, a new analytical method called genome-wide aetiology analysis (GWEA) consisting of nine steps is presented. All data required for GWEA of T1D are obtained from peer-reviewed publications or publicly available genome and proteome databases. Critical GWEA steps include AAID distribution among persons with T1D, analysis of at-risk HLA loci for mutation-prone DNA, determination of the role of non-MHC genes on GWAS, and verification of human data by cell culture or animal experiments. GWEA results show that distribution of AAID among persons with T1D adheres to a predictable, tapering, exponential distribution. A single, critical, somatic mutation within the epitope-binding groove of at-risk HLA loci alters HLA-insulin-peptide-T-cell-receptor (TCR) complex binding affinity and creates a new pathway that leads to loss of self-tolerance. The at-risk HLA loci, in particular binding pockets P1, P4 and P9, are encoded by mutation-prone DNA: GC-rich DNA sequence and somatic hypermutation hotspots. All other genes on GWAS can but do not have to amplify the new autoimmune pathway by facilitating DNA mutations, changing peptide binding affinity, reducing signal inhibition or augmenting signal intensity. Animal experiments agree with human studies. In conclusion, T1D is caused by a somatic mutation within the epitope-binding groove of an at-risk HLA gene that affects HLA-insulin-peptide-TCR complex binding affinity and initiates an autoimmune pathway. The nature of the peptide that binds to a mutated epitope-binding groove of an at-risk HLA gene determines the type of autoimmune disease that develops, that is, one at-risk HLA locus, multiple autoimmune diseases. Thus, T1D and AAIDs, and therefore common autoimmune diseases, share a similar somatic mutation-based aetiology.
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Affiliation(s)
- Piet C de Groen
- Division of Gastroenterology, Hepatology & Nutrition, University of Minnesota, Minneapolis, Minnesota, USA
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9
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Joseph J, Mathew J, Alexander J. Scaffold Proteins in Autoimmune Disorders. Curr Rheumatol Rev 2024; 20:14-26. [PMID: 37670692 DOI: 10.2174/1573397119666230904151024] [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: 04/03/2023] [Revised: 06/26/2023] [Accepted: 08/10/2023] [Indexed: 09/07/2023]
Abstract
Cells transmit information to the external environment and within themselves through signaling molecules that modulate cellular activities. Aberrant cell signaling disturbs cellular homeostasis causing a number of different diseases, including autoimmunity. Scaffold proteins, as the name suggests, serve as the anchor for binding and stabilizing signaling proteins at a particular locale, allowing both intra and intercellular signal amplification and effective signal transmission. Scaffold proteins play a critical role in the functioning of tight junctions present at the intersection of two cells. In addition, they also participate in cleavage formation during cytokinesis, and in the organization of neural synapses, and modulate receptor management outcomes. In autoimmune settings such as lupus, scaffold proteins can lower the cell activation threshold resulting in uncontrolled signaling and hyperactivity. Scaffold proteins, through their binding domains, mediate protein- protein interaction and play numerous roles in cellular communication and homeostasis. This review presents an overview of scaffold proteins, their influence on the different signaling pathways, and their role in the pathogenesis of autoimmune and auto inflammatory diseases. Since these proteins participate in many roles and interact with several other signaling pathways, it is necessary to gain a thorough understanding of these proteins and their nuances to facilitate effective target identification and therapeutic design for the treatment of autoimmune disorders.
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Affiliation(s)
- Josna Joseph
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - John Mathew
- Department of Clinical Immunology & Rheumatology, CMC Vellore, Tamil Nadu, India
| | - Jessy Alexander
- Department of Medicine, Jacobs School of Medicine & Biomedical Sciences, University of Buffalo, New York, USA
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Topaloudi A, Jain P, Martinez MB, Bryant JK, Reynolds G, Zagoriti Z, Lagoumintzis G, Zamba-Papanicolaou E, Tzartos J, Poulas K, Kleopa KA, Tzartos S, Georgitsi M, Drineas P, Paschou P. PheWAS and cross-disorder analysis reveal genetic architecture, pleiotropic loci and phenotypic correlations across 11 autoimmune disorders. Front Immunol 2023; 14:1147573. [PMID: 37809097 PMCID: PMC10552152 DOI: 10.3389/fimmu.2023.1147573] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Autoimmune disorders (ADs) are a group of about 80 disorders that occur when self-attacking autoantibodies are produced due to failure in the self-tolerance mechanisms. ADs are polygenic disorders and associations with genes both in the human leukocyte antigen (HLA) region and outside of it have been described. Previous studies have shown that they are highly comorbid with shared genetic risk factors, while epidemiological studies revealed associations between various lifestyle and health-related phenotypes and ADs. Methods Here, for the first time, we performed a comparative polygenic risk score (PRS) - Phenome Wide Association Study (PheWAS) for 11 different ADs (Juvenile Idiopathic Arthritis, Primary Sclerosing Cholangitis, Celiac Disease, Multiple Sclerosis, Rheumatoid Arthritis, Psoriasis, Myasthenia Gravis, Type 1 Diabetes, Systemic Lupus Erythematosus, Vitiligo Late Onset, Vitiligo Early Onset) and 3,254 phenotypes available in the UK Biobank that include a wide range of socio-demographic, lifestyle and health-related outcomes. Additionally, we investigated the genetic relationships of the studied ADs, calculating their genetic correlation and conducting cross-disorder GWAS meta-analyses for the observed AD clusters. Results In total, we identified 508 phenotypes significantly associated with at least one AD PRS. 272 phenotypes were significantly associated after excluding variants in the HLA region from the PRS estimation. Through genetic correlation and genetic factor analyses, we identified four genetic factors that run across studied ADs. Cross-trait meta-analyses within each factor revealed pleiotropic genome-wide significant loci. Discussion Overall, our study confirms the association of different factors with genetic susceptibility for ADs and reveals novel observations that need to be further explored.
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Affiliation(s)
- Apostolia Topaloudi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Pritesh Jain
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Melanie B. Martinez
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Josephine K. Bryant
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Grace Reynolds
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- West Lafayette High School, West Lafayette, IN, United States
| | - Zoi Zagoriti
- Department of Pharmacy, University of Patras, Rio, Greece
| | | | - Eleni Zamba-Papanicolaou
- Department of Neuroepidemiology and Centre for Neuromuscular Disorders, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - John Tzartos
- B’ Neurology Department, School of Medicine, National & Kapodistrian University of Athens, “Attikon” University Hospital., Athens, Greece
| | | | - Kleopas A. Kleopa
- Department of Neuroscience and Centre for Neuromuscular Disorders, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Socrates Tzartos
- Department of Pharmacy, University of Patras, Rio, Greece
- Tzartos NeuroDiagnostics, Athens, Greece
| | - Marianthi Georgitsi
- Department of Molecular Biology and Genetics, School of Health Sciences, Democritus University of Thrace, Alexandroupoli, Greece
| | - Petros Drineas
- Department of Computer Science, Purdue University, West Lafayette, IN, United States
| | - Peristera Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
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Asgari Y, Sugier PE, Baghfalaki T, Lucotte E, Karimi M, Sedki M, Ngo A, Liquet B, Truong T. GCPBayes pipeline: a tool for exploring pleiotropy at the gene level. NAR Genom Bioinform 2023; 5:lqad065. [PMID: 37416786 PMCID: PMC10320750 DOI: 10.1093/nargab/lqad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/16/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023] Open
Abstract
Cross-phenotype association using gene-set analysis can help to detect pleiotropic genes and inform about common mechanisms between diseases. Although there are an increasing number of statistical methods for exploring pleiotropy, there is a lack of proper pipelines to apply gene-set analysis in this context and using genome-scale data in a reasonable running time. We designed a user-friendly pipeline to perform cross-phenotype gene-set analysis between two traits using GCPBayes, a method developed by our team. All analyses could be performed automatically by calling for different scripts in a simple way (using a Shiny app, Bash or R script). A Shiny application was also developed to create different plots to visualize outputs from GCPBayes. Finally, a comprehensive and step-by-step tutorial on how to use the pipeline is provided in our group's GitHub page. We illustrated the application on publicly available GWAS (genome-wide association studies) summary statistics data to identify breast cancer and ovarian cancer susceptibility genes. We have shown that the GCPBayes pipeline could extract pleiotropic genes previously mentioned in the literature, while it also provided new pleiotropic genes and regions that are worthwhile for further investigation. We have also provided some recommendations about parameter selection for decreasing computational time of GCPBayes on genome-scale data.
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Affiliation(s)
- Yazdan Asgari
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Pierre-Emmanuel Sugier
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
- Laboratoire de Mathématiques et de leurs Applications de Pau, Université de Pau et des Pays de l’Adour, UMR CNRS 5142, E2S-UPPA, 64000 Pau, France
| | | | - Elise Lucotte
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Mojgan Karimi
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Mohammed Sedki
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Psychiatrie du développement et trajectoires, 94807 Villejuif, France
| | - Amélie Ngo
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
| | - Benoit Liquet
- Laboratoire de Mathématiques et de leurs Applications de Pau, Université de Pau et des Pays de l’Adour, UMR CNRS 5142, E2S-UPPA, 64000 Pau, France
- School of Mathematical and Physical Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Thérèse Truong
- Paris-Saclay University, UVSQ, Gustave Roussy, Inserm, CESP, Team Exposome and Heredity, 94807 Villejuif, France
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12
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Fu Y, Kelly JA, Gopalakrishnan J, Pelikan RC, Tessneer KL, Pasula S, Grundahl K, Murphy DA, Gaffney PM. Massively Parallel Reporter Assay Confirms Regulatory Potential of hQTLs and Reveals Important Variants in Lupus and Other Autoimmune Diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553722. [PMID: 37645944 PMCID: PMC10462090 DOI: 10.1101/2023.08.17.553722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Objective To systematically characterize the potential for histone post-translational modifications, i.e., histone quantitative trait loci (hQTLs), expression QTLs (eQTLs), and variants on systemic lupus erythematosus (SLE) and autoimmune (AI) disease risk haplotypes to modulate gene expression in an allele dependent manner. Methods We designed a massively parallel reporter assay (MPRA) containing ~32K variants and transfected it into an Epstein-Barr virus transformed B cell line generated from an SLE case. Results Our study expands our understanding of hQTLs, illustrating that epigenetic QTLs are more likely to contribute to functional mechanisms than eQTLs and other variant types, and a large proportion of hQTLs overlap transcription start sites (TSS) of noncoding RNAs. In addition, we nominate 17 variants (including 11 novel) as putative causal variants for SLE and another 14 for various other AI diseases, prioritizing these variants for future functional studies primary and immortalized B cells. Conclusion We uncover important insights into the mechanistic relationships between genotype, epigenetics, gene expression, and SLE and AI disease phenotypes.
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Affiliation(s)
- Yao Fu
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jennifer A Kelly
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Jaanam Gopalakrishnan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
- Neuro-Immune Regulome Unit, National Eye Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Richard C Pelikan
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kandice L Tessneer
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Satish Pasula
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Kiely Grundahl
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - David A Murphy
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Patrick M Gaffney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
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Wang Y, Zhao J, Gu Y, Wang H, Jiang M, Zhao S, Qing H, Ni J. Cathepsin H: molecular characteristics and clues to function and mechanism. Biochem Pharmacol 2023; 212:115585. [PMID: 37148981 DOI: 10.1016/j.bcp.2023.115585] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/08/2023]
Abstract
Cathepsin H (CatH) is a lysosomal cysteine protease with a unique aminopeptidase activity that is extensively expressed in the lung, pancreas, thymus, kidney, liver, skin, and brain. Owing to its specific enzymatic activity, CatH has critical effects on the regulation of biological behaviours of cancer cells and pathological processes in brain diseases. Moreover, a neutral pH level is optimal for CatH activity, so it is expected to be active in the extra-lysosomal and extracellular space. In the present review, we describe the expression, maturation, and enzymatic properties of CatH, and summarize the available experimental evidence that mechanistically links CatH to various physiological and pathological processes. Finally, we discuss the challenges and potentials of CatH inhibitors in CatH-induced disease therapy.
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Affiliation(s)
- Yanfeng Wang
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Juan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China; Aerospace Medical Center, Aerospace Center Hospital, Beijing, 100081, China
| | - Yebo Gu
- Department of Stomatology, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Haiping Wang
- School of Pharmaceutical Science, Nanjing Tech University, Nanjing, China
| | - Muzhou Jiang
- Department of Periodontics, Liaoning Provincial Key Laboratory of Oral Diseases, School and Hospital of Stomatology, China Medical University, Shenyang, 110002, China
| | - Shuxuan Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Hong Qing
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China.
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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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Ivanova M, Bottiglieri L, Sajjadi E, Venetis K, Fusco N. Malignancies in Patients with Celiac Disease: Diagnostic Challenges and Molecular Advances. Genes (Basel) 2023; 14:376. [PMID: 36833303 PMCID: PMC9956047 DOI: 10.3390/genes14020376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/26/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Celiac disease (CD) is a multiorgan autoimmune disorder of the chronic intestinal disease group characterized by duodenal inflammation in genetically predisposed individuals, precipitated by gluten ingestion. The pathogenesis of celiac disease is now widely studied, overcoming the limits of the purely autoimmune concept and explaining its hereditability. The genomic profiling of this condition has led to the discovery of numerous genes involved in interleukin signaling and immune-related pathways. The spectrum of disease manifestations is not limited to the gastrointestinal tract, and a significant number of studies have considered the possible association between CD and neoplasms. Patients with CD are found to be at increased risk of developing malignancies, with a particular predisposition of certain types of intestinal cancer, lymphomas, and oropharyngeal cancers. This can be partially explained by common cancer hallmarks present in these patients. The study of gut microbiota, microRNAs, and DNA methylation is evolving to find the any possible missing links between CD and cancer incidence in these patients. However, the literature is extremely mixed and, therefore, our understanding of the biological interplay between CD and cancer remains limited, with significant implications in terms of clinical management and screening protocols. In this review article, we seek to provide a comprehensive overview of the genomics, epigenomics, and transcriptomics data on CD and its relation to the most frequent types of neoplasms that may occur in these patients.
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Affiliation(s)
- Mariia Ivanova
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Luca Bottiglieri
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO, European Institute of Oncology IRCCS, 20141 Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
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16
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Jiang Y, Zhong S, He S, Weng J, Liu L, Ye Y, Chen H. Biomarkers (mRNAs and non-coding RNAs) for the diagnosis and prognosis of rheumatoid arthritis. Front Immunol 2023; 14:1087925. [PMID: 36817438 PMCID: PMC9929281 DOI: 10.3389/fimmu.2023.1087925] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
In recent years, diagnostic and therapeutic approaches for rheumatoid arthritis (RA) have continued to improve. However, in the advanced stages of the disease, patients are unable to achieve long-term clinical remission and often suffer from systemic multi-organ damage and severe complications. Patients with RA usually have no overt clinical manifestations in the early stages, and by the time a definitive diagnosis is made, the disease is already at an advanced stage. RA is diagnosed clinically and with laboratory tests, including the blood markers C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) and the autoantibodies rheumatoid factor (RF) and anticitrullinated protein antibodies (ACPA). However, the presence of RF and ACPA autoantibodies is associated with aggravated disease, joint damage, and increased mortality, and these autoantibodies have low specificity and sensitivity. The etiology of RA is unknown, with the pathogenesis involving multiple factors and clinical heterogeneity. The early diagnosis, subtype classification, and prognosis of RA remain challenging, and studies to develop minimally invasive or non-invasive biomarkers in the form of biofluid biopsies are becoming more common. Non-coding RNA (ncRNA) molecules are composed of long non-coding RNAs, small nucleolar RNAs, microRNAs, and circular RNAs, which play an essential role in disease onset and progression and can be used in the early diagnosis and prognosis of RA. In this review of the diagnostic and prognostic approaches to RA disease, we provide an overview of the current knowledge on the subject, focusing on recent advances in mRNA-ncRNA as diagnostic and prognostic biomarkers from the biofluid to the tissue level.
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Affiliation(s)
- Yong Jiang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shuxin Zhong
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, China
| | - Shenghua He
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Juanling Weng
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Lijin Liu
- The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yufeng Ye
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Hanwei Chen
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Department of Radiology, GuangzhouPanyu Health Management Center (Panyu Rehabilitation Hospital), Guangzhou, China
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17
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Exploring potential shared genetic influences between rheumatoid arthritis and blood lipid levels. Atherosclerosis 2022; 363:48-56. [PMID: 36455308 DOI: 10.1016/j.atherosclerosis.2022.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/11/2022] [Accepted: 11/04/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND AND AIMS The association between rheumatoid arthritis (RA) and blood lipid levels has often been described as paradoxical, despite the strong association between RA and cardiovascular disease (CVD) risk. We aimed to clarify the genetic architecture that would explain the relationship between RA and blood-lipid levels, while considering inflammation as measured by C-reactive protein (CRP). METHODS Genome-wide association study (GWAS) summary statistics were collected from the CHARGE Consortium and Global Lipids Genetics Consortium. Blood-lipid levels includes HDL-C, LDL-C, triglycerides (TG), and total cholesterol (TC). Causality was examined by assessing Mendelian Randomization (MR) analysis. Pleiotropy, the identification of shared causal variants between traits, was assessed by conducting colocalization analyses. RESULTS Using the MR Egger method, RA did not appear to causally predict alterations in lipid factors, rather the MR Egger intercept revealed that the genetic relationship between RA and HDL-C, LDL-C and TC may be explained by horizontal pleiotropy (p=0.003, 0.006, and 0.018, respectively). MR was suggestive of a horizontally pleiotropic relationship between CRP and lipid factors, while a causal relationship could not be ruled out. Recurring genes arising from shared causal genetic variants between RA and varying lipid factors included NAT2/PSD3, FADS2/FADS1, SH2B3, and YDJC. CONCLUSIONS Horizontal pleiotropy appears to explain the genetic relationship between RA and blood-lipid levels. In addition, blood-lipid levels appear to suggest a horizontally pleiotropic relationship to CRP, if not mediated through RA as well. Consideration of the pleiotropic genes between RA and blood lipid levels may aid in enhancing diagnostic means to predict CVD.
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18
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Murata R, Kinoshita S, Matsuda K, Kawaguchi A, Shibuya A, Shibuya K. G307S DNAM-1 Mutation Exacerbates Autoimmune Encephalomyelitis via Enhancing CD4+ T Cell Activation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:ji2200608. [PMID: 36426998 DOI: 10.4049/jimmunol.2200608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/12/2022] [Indexed: 02/17/2024]
Abstract
Although rs763361, which causes a nonsynonymous glycine-to-serine mutation at residue 307 (G307S mutation) of the DNAX accessory molecule-1 (DNAM-1) immunoreceptor, is a single-nucleotide polymorphism associated with autoimmune disease susceptibility, little is known about how the single-nucleotide polymorphism is involved in pathogenesis. In this study, we established human CD4+ T cell transfectants stably expressing wild-type (WT) or G307S DNAM-1 and showed that the costimulatory signal from G307S DNAM-1 induced greater proinflammatory cytokine production and cell proliferation than that from wild-type DNAM-1. The G307S mutation also enhanced the recruitment of the tyrosine kinase Lck and augmented p-Tyr322 of DNAM-1. We also established a mouse myelin Ag-specific CD4+ T cell transfectant stably expressing the chimeric DNAM-1 (chDNAM-1) consisting of the extracellular, transmembrane, and a part of intracellular regions of mouse DNAM-1 (residues 1-285) fused with the part of the intracellular region (residues 286-336) of human WT or G307S chDNAM-1. Adoptive transfer of the mouse T cell transfectant expressing the G307S chDNAM-1 into mice exacerbated experimental autoimmune encephalomyelitis compared with the transfer of cells expressing the WT chDNAM-1. These findings suggest that rs763361 is a gain-of-function mutation that enhances DNAM-1-mediated costimulatory signaling for proinflammatory responses.
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Affiliation(s)
- Rikito Murata
- Department of Immunology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- PhD Program in Human Biology, University of Tsukuba, Tsukuba, Japan
| | - Shota Kinoshita
- Department of Immunology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- PhD Program in Human Biology, University of Tsukuba, Tsukuba, Japan
| | - Kenshiro Matsuda
- Department of Immunology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Japan
| | - Atsushi Kawaguchi
- Infection Biology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan; and
| | - Akira Shibuya
- Department of Immunology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tsukuba, Japan
- R&D Center for Innovative Drug Discovery, University of Tsukuba, Tsukuba, Japan
| | - Kazuko Shibuya
- Department of Immunology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
- R&D Center for Innovative Drug Discovery, University of Tsukuba, Tsukuba, Japan
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19
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Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC, Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat Genet 2022; 54:1640-1651. [PMID: 36333501 PMCID: PMC10165422 DOI: 10.1038/s41588-022-01213-w] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10-8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, 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
| | - Chun Lai Too
- Immunogenetics Unit, Allergy and Immunology Research Center, Institute for Medical Research, National Institutes of Health Complex, Ministry of Health, Kuala Lumpur, Malaysia
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Vincent A Laufer
- Department of Clinical Immunology and Rheumatology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Ian C Scott
- Haywood Academic Rheumatology Centre, Haywood Hospital, Midlands Partnership NHS Foundation Trust, Burslem, UK
- Primary Care Centre Versus Arthritis, School of Medicine, Keele University, Keele, UK
| | - Sebastien Viatte
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Murasawa
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - Motomu Hashimoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiromu Ito
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kurashiki Central Hospital, Kurashiki, Japan
| | - Mohammed Hammoudeh
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Samar Al Emadi
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Basel K Masri
- Department of Internal Medicine, Jordan Hospital, Amman, Jordan
| | - Hussein Halabi
- Section of Rheumatology, Department of Internal Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Humeira Badsha
- Dr. Humeira Badsha Medical Center, Emirates Hospital, Dubai, United Arab Emirates
| | - Imad W Uthman
- Department of Rheumatology, American University of Beirut, Beirut, Lebanon
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Suzanne M M Verstappen
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | | | - Suguru Honda
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Eiichi Tanaka
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Gang Xie
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Jinyi Zhang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center (ARC), Reade, Amsterdam, the Netherlands
| | - Irene van der Horst-Bruinsma
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Katherine A Siminovitch
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Niek de Vries
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location AMC/University of Amsterdam, Amsterdam, the Netherlands
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Robert P Kimberly
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C Edberg
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, Assistance Pubique - Hôpitaux de Paris, Hôpital Bicêtre, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Tom Huizinga
- Leiden University Medical Center, Leiden, the Netherlands
| | - Philippe Dieudé
- University of Paris Cité, Inserm, PHERE, F-75018, Paris, France
- Department of Rheumatology, Hôpital Bichat, APHP, Paris, France
| | - Matthias Schneider
- Department of Rheumatology & Hiller Research Unit Rheumatology, UKD, Heinrich-Heine University, Düsseldorf, Germany
| | - Martin Kerick
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- All of Us Research Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Matthew Traylor
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Cathryn M Lewis
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
- School of Clinical Medicine Tsinghua University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Thurayya Arayssi
- Department of Internal Medicine, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Orthopedic Surgery, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
- Division of Multidisciplinary Management of Rheumatic Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayoshi Harigai
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Division of Rheumatology, Weill Cornell Medicine, New York, NY, USA
| | - Leonid Padyukov
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Javier Martin
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Lars Klareskog
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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20
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Huang M, Xu H. Genetic susceptibility to autoimmunity-Current status and challenges. Adv Immunol 2022; 156:25-54. [PMID: 36410874 DOI: 10.1016/bs.ai.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Autoimmune diseases (ADs) often arise from a combination of genetic and environmental triggers that disrupt the immune system's capability to properly tolerate body self-antigens. Familial studies provided the earliest insights into the risk loci of such diseases, while genome-wide association studies (GWAS) significantly broadened the horizons. A drug targeting a prominent pathological pathway can be applied to multiple indications sharing overlapping mechanisms. Advances in genomic technologies used in genetic studies provide critical insights into future research on gene-environment interactions in autoimmunity. This Review summarizes the history and recent advances in the understanding of genetic susceptibility to ADs and related immune disorders, including coronavirus disease 2019 (COVID-19), and their indications for the development of diagnostic or prognostic markers for translational applications.
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Affiliation(s)
| | - Huji Xu
- School of Medicine, Tsinghua University, Beijing, China; Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, The Navel Medical University, Shanghai, China; Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China.
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21
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Jin W, Zheng Y, Zhu P. T cell abnormalities in systemic sclerosis. Autoimmun Rev 2022; 21:103185. [PMID: 36031049 DOI: 10.1016/j.autrev.2022.103185] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/18/2022] [Accepted: 08/21/2022] [Indexed: 11/02/2022]
Abstract
Systemic sclerosis (SSc) is an autoimmune disease with a poor prognosis. To date, the pathogenesis of SSc is still unclear; moreover, its pathological conditions include microvascular damage, inflammation, and immune abnormalities. Different types of T cells may cause vasculitis and fibrosis in SSc by means of up- and down-regulation of cell surface molecules, abnormal release of pro-fibrotic or pro-inflammatory cytokines and direct contact with fibroblasts. These T cells, which are mainly CD4 + T cells, include the subtypes, T follicular helper (Tfh) cells, regulatory T Cells (Treg), interleukin-17 (IL-17)-producing Th17 cells, CD4+ cytotoxic T lymphocytes (CTLs), and angiogenic T (Tang) cells. In addition to the Th1/Th2 imbalance, which has long been established, there is also a Th17/Treg imbalance in SSc. This imbalance may be closely related to the abnormal immune status of SSc. There is mounting evidence that suggest T cell abnormalities may be crucial to the pathogenesis of SSc. In terms of treatment, existing therapies that target T cells, such as immunosuppressive therapy (tacrolimus), Janus kinase(JAK) inhibitors, and biologics(abatacept), have had some success. Other non-drug therapies, including Mesenchymal stem cells (MSCs), have extensive and complex mechanisms of action actually including T cell regulation. Based on the current evidence, we believe that the study of T cells will further our understanding of the pathogenesis of SSc, and may lead to more targeted treatment optionsfor patients with SSc.
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Affiliation(s)
- Wei Jin
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China
| | - Yan Zheng
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China; National Translational Science Center for Molecular Medicine, Xi'an, PR China
| | - Ping Zhu
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi'an, PR China; National Translational Science Center for Molecular Medicine, Xi'an, PR China.
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22
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Recent advances in elucidating the genetic basis of systemic sclerosis. Curr Opin Rheumatol 2022; 34:295-301. [PMID: 35979692 DOI: 10.1097/bor.0000000000000897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Systemic sclerosis (SSc) is a complex autoimmune disorder that affects the connective tissue and causes severe vascular damage and fibrosis of the skin and internal organs. There are recent advances in the field that apply novel methods to high throughput genotype information of thousands of patients with SSc and provide promising results towards the use of genomic data to help SSc diagnosis and clinical care. RECENT FINDINGS This review addresses the development of the first SSc genomic risk score, which can contribute to differentiating SSc patients from healthy controls and other immune-mediated diseases. Moreover, we explore the implementation of data mining strategies on the results of genome-wide association studies to highlight subtype-specific HLA class II associations and a strong association of the HLA class I locus with SSc for the first time. Finally, the combination of genomic data with transcriptomics informed drug repurposing and genetic association studies in well characterized SSc patient cohorts identified markers of severe complications of the disease. SUMMARY Early diagnosis and clinical management of SSc and SSc-related complications are still challenging for rheumatologists. The development of predictive models and tools using genotype data may help to finally deliver personalized clinical care and treatment for patients with SSc in the near future.
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23
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Levescot A, Malamut G, Cerf-Bensussan N. Immunopathogenesis and environmental triggers in coeliac disease. Gut 2022; 71:gutjnl-2021-326257. [PMID: 35879049 PMCID: PMC9554150 DOI: 10.1136/gutjnl-2021-326257] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/07/2022] [Indexed: 12/21/2022]
Abstract
Coeliac disease (CD) is a frequent immune enteropathy induced by gluten in genetically predisposed individuals. Its pathogenesis has been extensively studied and CD has emerged as a model disease to decipher how the interplay between environmental and genetic factors can predispose to autoimmunity and promote lymphomagenesis. The keystone event is the activation of a gluten-specific immune response that is driven by molecular interactions between gluten, the indispensable environmental factor, HLA-DQ2/8, the main predisposing genetic factor and transglutaminase 2, the CD-specific autoantigen. The antigluten response is however not sufficient to induce epithelial damage which requires the activation of cytotoxic CD8+ intraepithelial lymphocytes (IEL). In a plausible scenario, cooperation between cytokines released by gluten-specific CD4+ T cells and interleukin-15 produced in excess in the coeliac gut, licenses the autoimmune-like attack of the gut epithelium, likely via sustained activation of the Janus kinase-signal transducer and activator of transcription (JAK/STAT) pathway in IEL. Demonstration that lymphomas complicating CD arise from IEL that have acquired gain-of-function JAK1 or STAT3 mutations stresses the key role of this pathway and explains how gluten-driven chronic inflammation may promote this rare but most severe complication. If our understanding of CD pathogenesis has considerably progressed, several questions and challenges remain. One unsolved question concerns the considerable variability in disease penetrance, severity and presentation, pointing to the role of additional genetic and environmental factors that remain however uneasy to untangle and hierarchize. A current challenge is to transfer the considerable mechanistic insight gained into CD pathogenesis into benefits for the patients, notably to alleviate the gluten-free diet, a burden for many patients.
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Affiliation(s)
- Anais Levescot
- Université Paris Cité, Institut Imagine, INSERM UMR1163, Laboratory Intestinal Immunity, Paris, France
| | - Georgia Malamut
- Université Paris Cité, Institut Imagine, INSERM UMR1163, Laboratory Intestinal Immunity, Paris, France
- Université Paris Cité, APHP Centre, Gastroenterology Department, Hôpital Cochin, Paris, France
| | - Nadine Cerf-Bensussan
- Université Paris Cité, Institut Imagine, INSERM UMR1163, Laboratory Intestinal Immunity, Paris, France
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24
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Liu N, Sadlon T, Wong YY, Pederson S, Breen J, Barry SC. 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. Epigenetics Chromatin 2022; 15:24. [PMID: 35773720 PMCID: PMC9244893 DOI: 10.1186/s13072-022-00456-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/06/2022] [Indexed: 11/26/2022] Open
Abstract
Background Genome-wide association studies (GWAS) have enabled the discovery of single nucleotide polymorphisms (SNPs) that are significantly associated with many autoimmune diseases including type 1 diabetes (T1D). However, many of the identified variants lie in non-coding regions, limiting the identification of mechanisms that contribute to autoimmune disease progression. To address this problem, we developed a variant filtering workflow called 3DFAACTS-SNP to link genetic variants to target genes in a cell-specific manner. Here, we use 3DFAACTS-SNP to identify candidate SNPs and target genes associated with the loss of immune tolerance in regulatory T cells (Treg) in T1D. Results Using 3DFAACTS-SNP, we identified from a list of 1228 previously fine-mapped variants, 36 SNPs with plausible Treg-specific mechanisms of action. The integration of cell type-specific chromosome conformation capture data in 3DFAACTS-SNP identified 266 regulatory regions and 47 candidate target genes that interact with these variant-containing regions in Treg cells. We further demonstrated the utility of the workflow by applying it to three other SNP autoimmune datasets, identifying 16 Treg-centric candidate variants and 60 interacting genes. Finally, we demonstrate the broad utility of 3DFAACTS-SNP for functional annotation of all known common (> 10% allele frequency) variants from the Genome Aggregation Database (gnomAD). We identified 9376 candidate variants and 4968 candidate target genes, generating a list of potential sites for future T1D or other autoimmune disease research. Conclusions We demonstrate that it is possible to further prioritise variants that contribute to T1D based on regulatory function, and illustrate the power of using cell type-specific multi-omics datasets to determine disease mechanisms. Our workflow can be customised to any cell type for which the individual datasets for functional annotation have been generated, giving broad applicability and utility. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00456-5.
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Affiliation(s)
- Ning Liu
- South Australian Health and Medical Research Institute, Adelaide, Australia.,Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
| | - Stephen Pederson
- Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia
| | - James Breen
- South Australian Health and Medical Research Institute, Adelaide, Australia. .,Robinson Research Institute, University of Adelaide, Adelaide, Australia. .,Bioinformatics Hub, School of Biological Sciences, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, Australia. .,Black Ochre Data Labs, Indigenous Genomics, Telethon Kids Institute, Adelaide, Australia. .,John Curtin School of Medical Research, Australian National University, Canberra, Australia.
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.,Women's and Children's Health Network, Women's and Children's Hospital, Adelaide, Australia
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25
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Khunsriraksakul C, Markus H, Olsen NJ, Carrel L, Jiang B, Liu DJ. Construction and Application of Polygenic Risk Scores in Autoimmune Diseases. Front Immunol 2022; 13:889296. [PMID: 35833142 PMCID: PMC9271862 DOI: 10.3389/fimmu.2022.889296] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified hundreds of genetic variants associated with autoimmune diseases and provided unique mechanistic insights and informed novel treatments. These individual genetic variants on their own typically confer a small effect of disease risk with limited predictive power; however, when aggregated (e.g., via polygenic risk score method), they could provide meaningful risk predictions for a myriad of diseases. In this review, we describe the recent advances in GWAS for autoimmune diseases and the practical application of this knowledge to predict an individual’s susceptibility/severity for autoimmune diseases such as systemic lupus erythematosus (SLE) via the polygenic risk score method. We provide an overview of methods for deriving different polygenic risk scores and discuss the strategies to integrate additional information from correlated traits and diverse ancestries. We further advocate for the need to integrate clinical features (e.g., anti-nuclear antibody status) with genetic profiling to better identify patients at high risk of disease susceptibility/severity even before clinical signs or symptoms develop. We conclude by discussing future challenges and opportunities of applying polygenic risk score methods in clinical care.
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Affiliation(s)
- Chachrit Khunsriraksakul
- Graduate Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Havell Markus
- Graduate Program in Bioinformatics and Genomics, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Nancy J. Olsen
- Department of Medicine, Division of Rheumatology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Laura Carrel
- Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Bibo Jiang
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Dajiang J. Liu
- Institute for Personalized Medicine, Pennsylvania State University College of Medicine, Hershey, PA, United States
- Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA, United States
- *Correspondence: Dajiang J. Liu,
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26
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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: 15] [Impact Index Per Article: 7.5] [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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27
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Brooks-Warburton J, Modos D, Sudhakar P, Madgwick M, Thomas JP, Bohar B, Fazekas D, Zoufir A, Kapuy O, Szalay-Beko M, Verstockt B, Hall LJ, Watson A, Tremelling M, Parkes M, Vermeire S, Bender A, Carding SR, Korcsmaros T. A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis. Nat Commun 2022; 13:2299. [PMID: 35484353 PMCID: PMC9051123 DOI: 10.1038/s41467-022-29998-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/06/2022] [Indexed: 12/11/2022] Open
Abstract
We describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 378 UC patients we map the regulatory effects of the SNPs to a human signalling network containing protein-protein, miRNA-mRNA and transcription factor binding interactions. With unsupervised clustering algorithms we group these patient-specific networks into four distinct clusters driven by PRKCB, HLA, SNAI1/CEBPB/PTPN1 and VEGFA/XPO5/POLH hubs. The pathway analysis identifies calcium homeostasis, wound healing and cell motility as key processes in UC pathogenesis. Using transcriptomic data from an independent patient cohort, with three complementary validation approaches focusing on the SNP-affected genes, the patient specific modules and affected functions, we confirm the regulatory impact of non-coding SNPs. iSNP identified regulatory effects for disease-associated non-coding SNPs, and by predicting the patient-specific pathogenic processes, we propose a systems-level way to stratify patients.
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Affiliation(s)
- Johanne Brooks-Warburton
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hertford, UK
- Gastroenterology Department, Lister Hospital, Stevenage, UK
| | - Dezso Modos
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Padhmanand Sudhakar
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- KU Leuven, Department of Chronic diseases, Metabolism and Ageing, Leuven, Belgium
| | - Matthew Madgwick
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - John P Thomas
- Earlham Institute, Norwich Research Park, Norwich, UK
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Department of Gastroenterology, Norfolk and Norwich University Hospitals, Norwich, UK
| | - Balazs Bohar
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - David Fazekas
- Earlham Institute, Norwich Research Park, Norwich, UK
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Azedine Zoufir
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Orsolya Kapuy
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary
| | | | - Bram Verstockt
- KU Leuven, Department of Chronic diseases, Metabolism and Ageing, Leuven, Belgium
- University Hospitals Leuven, Department of Gastroenterology and Hepatology, KU Leuven, Leuven, Belgium
| | - Lindsay J Hall
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- School of Life Sciences, ZIEL - Institute for Food & Health, Technical University of Munich, 80333, Freising, Germany
| | - Alastair Watson
- Department of Gastroenterology, Norfolk and Norwich University Hospitals, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Mark Tremelling
- Department of Gastroenterology, Norfolk and Norwich University Hospitals, Norwich, UK
| | - Miles Parkes
- Inflammatory Bowel Disease Research Group, Addenbrooke's Hospital, University of Cambridge, Cambridge, UK
| | - Severine Vermeire
- KU Leuven, Department of Chronic diseases, Metabolism and Ageing, Leuven, Belgium
- University Hospitals Leuven, Department of Gastroenterology and Hepatology, KU Leuven, Leuven, Belgium
| | - Andreas Bender
- Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Simon R Carding
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
- Norwich Medical School, University of East Anglia, Norwich, UK.
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Gut Microbes and Health Programme, The Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
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28
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Construction of disease-specific cytokine profiles by associating disease genes with immune responses. PLoS Comput Biol 2022; 18:e1009497. [PMID: 35404985 PMCID: PMC9022887 DOI: 10.1371/journal.pcbi.1009497] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 04/21/2022] [Accepted: 03/17/2022] [Indexed: 12/29/2022] Open
Abstract
The pathogenesis of many inflammatory diseases is a coordinated process involving metabolic dysfunctions and immune response—usually modulated by the production of cytokines and associated inflammatory molecules. In this work, we seek to understand how genes involved in pathogenesis which are often not associated with the immune system in an obvious way communicate with the immune system. We have embedded a network of human protein-protein interactions (PPI) from the STRING database with 14,707 human genes using feature learning that captures high confidence edges. We have found that our predicted Association Scores derived from the features extracted from STRING’s high confidence edges are useful for predicting novel connections between genes, thus enabling the construction of a full map of predicted associations for all possible pairs between 14,707 human genes. In particular, we analyzed the pattern of associations for 126 cytokines and found that the six patterns of cytokine interaction with human genes are consistent with their functional classifications. To define the disease-specific roles of cytokines we have collected gene sets for 11,944 diseases from DisGeNET. We used these gene sets to predict disease-specific gene associations with cytokines by calculating the normalized average Association Scores between disease-associated gene sets and the 126 cytokines; this creates a unique profile of inflammatory genes (both known and predicted) for each disease. We validated our predicted cytokine associations by comparing them to known associations for 171 diseases. The predicted cytokine profiles correlate (p-value<0.0003) with the known ones in 95 diseases. We further characterized the profiles of each disease by calculating an “Inflammation Score” that summarizes different modes of immune responses. Finally, by analyzing subnetworks formed between disease-specific pathogenesis genes, hormones, receptors, and cytokines, we identified the key genes responsible for interactions between pathogenesis and inflammatory responses. These genes and the corresponding cytokines used by different immune disorders suggest unique targets for drug discovery. The success of anti-TNF treatment in multiple inflammatory diseases suggest that there is a shared cytokine framework that defines highly conserved mechanisms of inflammation. However, clinical trials testing the efficacy of new cytokine inhibitors suggest a more complex set of interacting cytokine mechanisms that are associated with different diseases. In this work, we aim to define the disease-specific role of cytokines that mediate pathogenesis and inflammatory processes, focusing on autoimmune diseases. We hypothesize that specific clinical phenotypes result from the interactions between disease-specific cytokines and disease-related genes (identified through genetics, transcriptomics, and analysis of metabolic dysfunctions), even though they also may share a common cytokine elements and conserved mechanisms of inflammation. We have developed novel network methods that show a robust ability to identify differential associations between characteristic cytokines and genetics factors contributing to pathogenesis. We have validated our methods on 171 well-studied diseases; the predicted associations between cytokines and disease modules correlate with the published data. Our predictions provide the underlying difference of molecular mechanisms that may be responsible for clinical phenotypes.
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29
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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: 179] [Impact Index Per Article: 89.5] [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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30
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Scofield RH, Lewis VM, Cavitt J, Kurien BT, Assassi S, Martin J, Gorlova O, Gregersen P, Lee A, Rider LG, O'Hanlon T, Rothwell S, Lilleker J, Kochi Y, Terao C, Igoe A, Stevens W, Sahhar J, Roddy J, Rischmueller M, Lester S, Proudman S, Chen S, Brown MA, Mayes MD, Lamb JA, Miller FW. 47XXY and 47XXX in Scleroderma and Myositis. ACR Open Rheumatol 2022; 4:528-533. [PMID: 35352506 PMCID: PMC9190224 DOI: 10.1002/acr2.11413] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 01/05/2023] Open
Abstract
Objective We undertook this study to examine the X chromosome complement in participants with systemic sclerosis (SSc) as well as idiopathic inflammatory myopathies. Methods The participants met classification criteria for the diseases. All participants underwent single‐nucleotide polymorphism typing. We examined X and Y single‐nucleotide polymorphism heterogeneity to determine the number of X chromosomes. For statistical comparisons, we used χ2 analyses with calculation of 95% confidence intervals. Results Three of seventy men with SSc had 47,XXY (P = 0.0001 compared with control men). Among the 435 women with SSc, none had 47,XXX. Among 709 men with polymyositis or dermatomyositis (PM/DM), seven had 47,XXY (P = 0.0016), whereas among the 1783 women with PM/DM, two had 47,XXX. Of 147 men with inclusion body myositis (IBM), six had 47,XXY, and 1 of the 114 women with IBM had 47,XXX. For each of these myositis disease groups, the excess 47,XXY and/or 47,XXX was significantly higher compared with in controls as well as the known birth rate of Klinefelter syndrome or 47,XXX. Conclusion Klinefelter syndrome (47,XXY) is associated with SSc and idiopathic inflammatory myopathies, similar to other autoimmune diseases with type 1 interferon pathogenesis, namely, systemic lupus erythematosus and Sjögren syndrome.
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Affiliation(s)
- R Hal Scofield
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Valerie M Lewis
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Joshua Cavitt
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Biji T Kurien
- Oklahoma Medical Research Foundation, College of Medicine, University of Oklahoma Health Sciences Center, and Oklahoma City US Department of Veterans Affairs Medical Center, Oklahoma City
| | - Shervin Assassi
- University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas, PTS, Granada, Spain
| | - Olga Gorlova
- Geisel School of Medicine, Dartmouth College and Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Peter Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Annette Lee
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Manhasset, New York, USA
| | - Lisa G Rider
- National Institute of Environmental Health Science, National Institutes of Health, Bethesda, Maryland, USA
| | - Terrance O'Hanlon
- National Institute of Environmental Health Science, National Institutes of Health, Bethesda, Maryland, USA
| | | | - James Lilleker
- School of Biological Sciences, The University of Manchester, Manchester, UK, and Salford Royal National Health Service Foundation Trust, Salford, UK
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- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuta Kochi
- Tokyo, Japan, and RIKEN Center for Integrative Medical Sciences, Tokyo Medical and Dental University, Yokohama, Japan
| | - Chikacshi Terao
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan, and Shizuoka General Hospital and School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Ann Igoe
- Oklahoma Medical Research Foundation, Oklahoma City
| | - Wendy Stevens
- St. Vincent's Hospital, Melbourne, Victoria, Australia
| | - Joanne Sahhar
- Monash Medical Centre, Melbourne, Victoria, Australia
| | - Janet Roddy
- Fiona Stanley Hospital, Murdoch, Western Australia, Australia
| | - Maureen Rischmueller
- The Queen Elizabeth Hospital and University of Adelaide, Woodville, South Australia, Australia
| | - Sue Lester
- The Queen Elizabeth Hospital and University of Adelaide, Woodville, South Australia, Australia
| | | | - Sixia Chen
- College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City
| | - Matthew A Brown
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Maureen D Mayes
- University of Texas Health Science Center at Houston McGovern Medical School, Houston, Texas, USA
| | | | - Frederick W Miller
- National Institute of Environmental Health Science, National Institutes of Health, Bethesda, Maryland, USA
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31
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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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32
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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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Bakutenko IY, Haurylchyk ID, Nikitchenko NV, Sechko E, Kozyro IA, Tchitchko AM, Batyan GM, Sukalo AV, Ryabokon NI. Neutrophil cytosolic factor 2 (NCF2) gene polymorphism is associated with juvenile-onset systemic lupus erythematosus, but probably not with other autoimmune rheumatic diseases in children. Mol Genet Genomic Med 2022; 10:e1859. [PMID: 34971477 PMCID: PMC8801135 DOI: 10.1002/mgg3.1859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 11/08/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Genetic variations of neutrophil cytosolic factor 2 (NCF2), a subunit of NADPH oxidase, are usually associated with chronic granulomatous disease, and their relationship with autoimmune disorders through the defective NADPH oxidase function during phagocytosis is suggested. Our study aimed to explore whether there is an association between the non-synonymous single nucleotide polymorphism in the NCF2 gene (rs17849502, NC_000001.11:g.183563445G>T) and the development of juvenile autoimmune rheumatic diseases. METHODS In order to test this hypothesis, we conducted a pilot case-control study. In total, 709 children and adolescents, all Belarusians, were involved in the study including patients with juvenile-onset systemic lupus erythematosus (JSLE), juvenile idiopathic arthritis (JIA), Kawasaki disease (KD), and subjects without autoimmune and inflammatory diseases as the clinical control, as well as health newborns as the population control. Real-time polymerase chain reaction was used for genotyping. RESULTS The minor T allele of NCF2 occurred most frequently in patients with JSLE (OR = 2.60, 95% CI = 1.18-5.73, p = 0.023 as compared to the clinical control). In groups with JIA and KD, its frequency did not differ from the control. The TT genotype was only observed in 5.7% of patients with JSLE (p = 0.007), but not in other groups. CONCLUSION Therefore, our study suggested that NCF2 rs17849502 polymorphism is a potential genetic risk factor for JSLE, while it is probably not for such autoimmune rheumatic diseases as JIA or KD.
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Affiliation(s)
- Ivan Y. Bakutenko
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
| | - Irena D. Haurylchyk
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
| | - Natalia V. Nikitchenko
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
| | - Elena V. Sechko
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Inna A. Kozyro
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Alexei M. Tchitchko
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Galina M. Batyan
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Alexander V. Sukalo
- 1st Department of Childhood DiseasesBelarusian State Medical UniversityMinskBelarus
| | - Nadezhda I. Ryabokon
- Laboratory of Molecular Basis of Genome StabilityInstitute of Genetics and CytologyNational Academy of Sciences of BelarusMinskBelarus
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Dahlqvist J, Ekman D, Sennblad B, Kozyrev SV, Nordin J, Karlsson Å, Meadows JRS, Hellbacher E, Rantapää-Dahlqvist S, Berglin E, Stegmayr B, Baslund B, Palm Ø, Haukeland H, Gunnarsson I, Bruchfeld A, Segelmark M, Ohlsson S, Mohammad AJ, Svärd A, Pullerits R, Herlitz H, Söderbergh A, Rosengren Pielberg G, Hultin Rosenberg L, Bianchi M, Murén E, Omdal R, Jonsson R, Eloranta ML, Rönnblom L, Söderkvist P, Knight A, Eriksson P, Lindblad-Toh K. Identification and Functional Characterization of a Novel Susceptibility Locus for Small Vessel Vasculitis with MPO-ANCA. Rheumatology (Oxford) 2021; 61:3461-3470. [PMID: 34888651 PMCID: PMC9348767 DOI: 10.1093/rheumatology/keab912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 12/01/2021] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE To identify and characterize genetic loci associated with the risk of developing anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitides (AAV). METHODS Genetic association analyses were performed after Illumina sequencing of 1,853 genes and subsequent replication with genotyping of selected SNPs in a total cohort of 1110 Scandinavian cases with granulomatosis with polyangiitis (GPA) or microscopic polyangiitis (MPA) and 1589 controls. A novel AAV-associated SNP was analysed for allele-specific effects on gene expression using luciferase reporter assay. RESULTS Proteinase 3 ANCA positive (PR3-ANCA+) AAV was significantly associated with two independent loci in the HLA-DPB1/A1 region (rs1042335, p= 6.3 x 1 0 -61, Odds ratio (OR)= 0.10; rs9277341, p= 1.5 x 1 0 -44, OR = 0.22) and with rs28929474 in the SERPINA1 gene (p= 2.7 x 1 0 -10, OR = 2.9). Myeloperoxidase (MPO)-ANCA+ AAV was significantly associated with the HLA-DQB1/HLA-DQA2 locus (rs9274619, p= 5.4 x 1 0 -25, OR = 3.7) and with a rare variant in the BACH2 gene (rs78275221, p= 7.9 x 1 0 -7, OR = 3.0), the latter a novel susceptibility locus for MPO-ANCA+ GPA/MPA. The rs78275221-A risk allele reduced luciferase gene expression in endothelial cells, specifically, as compared with the non-risk allele. CONCLUSION We identified a novel susceptibility locus for MPO-ANCA+ AAV and propose that the associated variant is of mechanistic importance, exerting a regulatory function on gene expression in specific cell types.
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Affiliation(s)
- Johanna Dahlqvist
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
| | - Diana Ekman
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Sweden
| | - Bengt Sennblad
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sergey V Kozyrev
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jessika Nordin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Åsa Karlsson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jennifer R S Meadows
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Hellbacher
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | | | - Ewa Berglin
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Bernd Stegmayr
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Bo Baslund
- Copenhagen Lupus and Vasculitis Clinic, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Øyvind Palm
- Department of Rheumatology, Oslo University Hospital, Oslo, Norway
| | - Hilde Haukeland
- Department of Rheumatology, Martina Hansens Hospital, Oslo, Norway
| | - Iva Gunnarsson
- Department of Medicine, Division of Rheumatology, Karolinska Institutet, Stockholm, Sweden.,Unit of Rheumatology, Karolinska University Hospital, Stockholm, Sweden
| | - Annette Bruchfeld
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden.,Department of Renal Medicine, Karolinska University Hospital and CLINTEC Karolinska Institutet, Stockholm, Sweden
| | - Mårten Segelmark
- Department of Clinical Sciences, Division of Nephrology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Sophie Ohlsson
- Department of Clinical Sciences, Division of Nephrology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Aladdin J Mohammad
- Department of Clinical Sciences Lund, Section of Rheumatology, Skåne University Hospital, Lund University, Lund, Sweden.,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Anna Svärd
- Center for Clinical Research Dalarna, Uppsala University, Uppsala, Sweden
| | - Rille Pullerits
- Department of Rheumatology and Inflammation Research, Institution of Medicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Immunology and Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Hans Herlitz
- Department of Molecular and Clinical Medicine/Nephrology, Institute of Medicine, the Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Annika Söderbergh
- Department of Rheumatology, Örebro University Hospital, Örebro, Sweden
| | - Gerli Rosengren Pielberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Lina Hultin Rosenberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Matteo Bianchi
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Eva Murén
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Roald Omdal
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | | | - Lars Rönnblom
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Peter Söderkvist
- Department of Biomedical and Clinical Sciences, Division of Cell Biology, Linköping University, Linköping, Sweden
| | - Ann Knight
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Per Eriksson
- Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection, Linköping University, Linköping, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Broad Institute of MIT and Harvard University, Cambridge, MA, USA
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Wolter M, Grant ET, Boudaud M, Steimle A, Pereira GV, Martens EC, Desai MS. Leveraging diet to engineer the gut microbiome. Nat Rev Gastroenterol Hepatol 2021; 18:885-902. [PMID: 34580480 DOI: 10.1038/s41575-021-00512-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/06/2021] [Indexed: 12/12/2022]
Abstract
Autoimmune diseases, including inflammatory bowel disease, multiple sclerosis and rheumatoid arthritis, have distinct clinical presentations but share underlying patterns of gut microbiome perturbation and intestinal barrier dysfunction. Their potentially common microbial drivers advocate for treatment strategies aimed at restoring appropriate microbiome function, but individual variation in host factors makes a uniform approach unlikely. In this Perspective, we consolidate knowledge on diet-microbiome interactions in local inflammation, gut microbiota imbalance and host immune dysregulation. By understanding and incorporating the effects of individual dietary components on microbial metabolic output and host physiology, we examine the potential for diet-based therapies for autoimmune disease prevention and treatment. We also discuss tools targeting the gut microbiome, such as faecal microbiota transplantation, probiotics and orthogonal niche engineering, which could be optimized using custom dietary interventions. These approaches highlight paths towards leveraging diet for precise engineering of the gut microbiome at a time of increasing autoimmune disease.
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Affiliation(s)
- Mathis Wolter
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Erica T Grant
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg.,Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marie Boudaud
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | - Alex Steimle
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
| | | | - Eric C Martens
- University of Michigan Medical School, Ann Arbor, MI, USA
| | - Mahesh S Desai
- Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg. .,Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark.
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36
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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: 61] [Impact Index Per Article: 20.3] [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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Rahimizadeh P, Rezaieyazdi Z, Behzadi F, Hajizade A, Lim SI. Nanotechnology as a promising platform for rheumatoid arthritis management: Diagnosis, treatment, and treatment monitoring. Int J Pharm 2021; 609:121137. [PMID: 34592396 DOI: 10.1016/j.ijpharm.2021.121137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/16/2021] [Accepted: 09/23/2021] [Indexed: 12/18/2022]
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease that develops in about 5 per 1000 people. Over the past years, substantial progresses in knowledge of the disease's pathophysiology, effective diagnosis methods, early detection, and efficient treatment strategies have been made. Notably, nanotechnology has emerged as a game-changer in the efficacious management of many diseases, especially for RA. Joint replacement, photothermal therapy (PTT), photodynamic therapy (PDT), RA diagnosis, and treatment monitoring are nano-based avenues in RA management. Here, we present a brief overview of the pathogenesis of RA, risk factors, conventional diagnostic methods and treatment approaches, and then discuss the role of nanomedicine in RA diagnosis, treatment, and treatment monitoring with an emphasis on functional characteristics distinctive from other RA therapeutics.
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Affiliation(s)
- Parastou Rahimizadeh
- Department of Chemical Engineering, Pukyong National University, Busan 48513, South Korea
| | - Zahra Rezaieyazdi
- Rheumatic Disease Research Center, Mashhad University of Medical Science, Mashhad, Iran
| | - Faezeh Behzadi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Abbas Hajizade
- Biology Research Centre, Faculty of Basic Sciences, Imam Hossein University, Tehran, Iran.
| | - Sung In Lim
- Department of Chemical Engineering, Pukyong National University, Busan 48513, South Korea.
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Qi YY, Zhao XY, Liu XR, Wang YN, Zhai YL, Zhang XX, Wang XY, Zhang LJ, Zhao YF, Cui Y, Ning XH, Zhou XJ. Lupus susceptibility region containing CTLA4 rs17268364 functionally reduces CTLA4 expression by binding EWSR1 and correlates IFN-α signature. Arthritis Res Ther 2021; 23:279. [PMID: 34736521 PMCID: PMC8567630 DOI: 10.1186/s13075-021-02664-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/23/2021] [Indexed: 11/10/2022] Open
Abstract
Background Dysregulation of T cells mediated immune responses is a hallmark in the development of systemic lupus erythematosus (SLE). Recent genome wide association study (GWAS) revealed the genetic contribution of variants located in the cytotoxic T lymphocyte-associated protein-4 (CTLA4)-inducible T cell co-stimulator (ICOS) intergenic region to SLE susceptibility. Our aim is to find a functional variant in this region. Methods The genetic association results in the CTLA4-ICOS region from previous GWAS were adopted to select the potential variant which was further replicated in two independent cohorts (Henan cohort 2053 SLE patients and 1845 healthy controls, Beijing cohort 2303 SLE patients and 19,262 healthy). In order to explore the functional significance in SLE, bioinformatics with validation experiments (including electrophoretic mobility shift assay and luciferase reporter assay) and mRNA expression analysis were also performed. Results A variant located in the CTLA4-ICOS intergenic region, rs17268364, was associated with susceptibility to SLE patients in Chinese populations (risk allele, pmeta = 7.02×10−11, OR 1.19, 95%CI 1.13–1.26). The bioinformatics suggested that rs17268364 might affect the expression of CTLA4, not ICOS. The rs17268364 risk G allele containing sequence reduced the expression of the reporter gene by binding transcriptional repressor Ewing sarcoma breakpoint region 1 (EWSR1). Following genotype-mRNA expression, the analysis also showed the risk allele of rs17268364 was associated with low CTLA4 expression in lupus nephritis (LN) patients. Healthy individuals carrying rs17268364 risk G allele was significantly correlated with higher levels of IFN-α signature including increased lymphocyte antigen 6E (LY6E) (p=0.031), interferon-stimulated gene 15 (ISG15) (p=0.038), interferon regulatory factor 9 (IRF9) (p=0.028), and interferon regulatory factor 5 (IRF5) (p=0.040) mRNA expression. Conclusions The present study confirmed the functional role of rs17268364 in the CTLA4-ICOS intergenic region that increased SLE susceptibility in the Chinese population. Supplementary Information The online version contains supplementary material available at 10.1186/s13075-021-02664-y.
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Affiliation(s)
- Yuan-Yuan Qi
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China. .,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.
| | - Xin-Yu Zhao
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xin-Ran Liu
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Yan-Na Wang
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China
| | - Ya-Ling Zhai
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xiao-Xue Zhang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xiao-Yang Wang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Li-Jie Zhang
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Ya-Fei Zhao
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Yan Cui
- Nephrology Hospital, the First Affiliated Hospital of Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China.,Institute of Nephrology, Zhengzhou University, No.1, Jianshe Road, Erqi District, Zhengzhou, Henan, 4500052, People's Republic of China
| | - Xiang-Hui Ning
- Department of Urology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 4500052, Henan, China
| | - Xu-Jie Zhou
- Renal Division, Peking University First Hospital, Peking University Institute of Nephrology, Beijing, China. .,Key Laboratory of Renal Disease, Ministry of Health of China, No.8 Xi Shi Ku Street, Xi Cheng District, Beijing, 100034, China. .,Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, No.8 Xi Shi Ku Street, Xi Cheng District, Beijing, 100034, China.
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Understanding the genomic architecture of clinical mastitis in Bos indicus. 3 Biotech 2021; 11:466. [PMID: 34745817 DOI: 10.1007/s13205-021-03012-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/01/2021] [Indexed: 12/26/2022] Open
Abstract
This study elucidated potential genetic variants and QTLs associated with clinical mastitis incidence traits in Bos indicus breed, Sahiwal. Estimated breeding values for the traits (calculated using Bayesian inference) were used as pseudo-phenotypes for association with genome-wide SNPs and further QTL regions underlying the traits were identified. In all, 25 SNPs were found to be associated with the traits at the genome-wide suggestive threshold (p ≤ 5 × 10-4) and these SNPs were used to define QTL boundaries based on the linkage disequilibrium structure. A total of 16 QTLs were associated with the trait EBVs including seven each for clinical mastitis incidence (CMI) in first and second lactations and two for CMI in third lactation. Nine out of sixteen QTLs overlapped with the already reported QTLs for mastitis traits, whereas seven were adjudged as novel ones. Important candidates for clinical mastitis in the identified QTL regions included DNAJB9, ELMO1, ARHGAP26, NR3C1, CACNB2, RAB4A, GRB2, NUP85, SUMO2, RBPJ, and RAB33B genes. These findings shed light on the genetic architecture of the disease in Bos indicus, and present potential regions for fine mapping and downstream analysis in future.
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Márquez A, Martín J. Genetic overlap between type 1 diabetes and other autoimmune diseases. Semin Immunopathol 2021; 44:81-97. [PMID: 34595540 DOI: 10.1007/s00281-021-00885-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Type 1 diabetes (T1D) is a chronic disease caused by the destruction of pancreatic β cells, which is driven by autoreactive T lymphocytes. It has been described that a high proportion of T1D patients develop other autoimmune diseases (AIDs), such as autoimmune thyroid disease, celiac disease, or vitiligo, which suggests the existence of common etiological factors among these disorders. In this regard, genetic studies have identified a high number of loci consistently associated with T1D that also represent established genetic risk factors for other AIDs. In addition, studies focused on identifying the shared genetic component in autoimmunity have described several common susceptibility loci with a potential role in T1D. Elucidation of this genetic overlap has been useful in identifying key molecular pathways with a pathogenic role in multiple disorders. In this review, we summarize recent advances in understanding the shared genetic component between T1D and other AIDs and discuss how the identification of common pathogenic mechanisms can help in the development of new therapeutic approaches as well as in improving the use of existing drugs.
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Affiliation(s)
- Ana Márquez
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.,Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria Ibs. GRANADA, Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra. Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain.
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41
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Borcherding DC, He K, Amin NV, Hirbe AC. TYK2 in Cancer Metastases: Genomic and Proteomic Discovery. Cancers (Basel) 2021; 13:4171. [PMID: 34439323 PMCID: PMC8393599 DOI: 10.3390/cancers13164171] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Advances in genomic analysis and proteomic tools have rapidly expanded identification of biomarkers and molecular targets important to cancer development and metastasis. On an individual basis, personalized medicine approaches allow better characterization of tumors and patient prognosis, leading to more targeted treatments by detection of specific gene mutations, overexpression, or activity. Genomic and proteomic screens by our lab and others have revealed tyrosine kinase 2 (TYK2) as an oncogene promoting progression and metastases of many types of carcinomas, sarcomas, and hematologic cancers. TYK2 is a Janus kinase (JAK) that acts as an intermediary between cytokine receptors and STAT transcription factors. TYK2 signals to stimulate proliferation and metastasis while inhibiting apoptosis of cancer cells. This review focuses on the growing evidence from genomic and proteomic screens, as well as molecular studies that link TYK2 to cancer prevalence, prognosis, and metastasis. In addition, pharmacological inhibition of TYK2 is currently used clinically for autoimmune diseases, and now provides promising treatment modalities as effective therapeutic agents against multiple types of cancer.
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Affiliation(s)
- Dana C. Borcherding
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (D.C.B.); (K.H.); (N.V.A.)
| | - Kevin He
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (D.C.B.); (K.H.); (N.V.A.)
| | - Neha V. Amin
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (D.C.B.); (K.H.); (N.V.A.)
| | - Angela C. Hirbe
- Division of Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; (D.C.B.); (K.H.); (N.V.A.)
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
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The genetic architecture of primary biliary cholangitis. Eur J Med Genet 2021; 64:104292. [PMID: 34303876 DOI: 10.1016/j.ejmg.2021.104292] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/03/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022]
Abstract
Primary biliary cholangitis (PBC) is a rare autoimmune disease of the liver affecting the small bile ducts. From a genetic point of view, PBC is a complex trait and several genetic and environmental factors have been called in action to explain its etiopathogenesis. Similarly to other complex traits, PBC has benefited from the introduction of genome-wide association studies (GWAS), which identified many variants predisposing or protecting toward the development of the disease. While a progressive endeavour toward the characterization of candidate loci and downstream pathways is currently ongoing, there is still a relatively large portion of heritability of PBC to be revealed. In addition, genetic variation behind progression of the disease and therapeutic response are mostly to be investigated yet. This review outlines the state-of-the-art regarding the genetic architecture of PBC and provides some hints for future investigations, focusing on the study of gene-gene interactions, the application of whole-genome sequencing techniques, and the investigation of X chromosome that can be helpful to cover the missing heritability gap in PBC.
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Dato S, Crocco P, Rambaldi Migliore N, Lescai F. Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging. Front Genet 2021; 12:689824. [PMID: 34178042 PMCID: PMC8225294 DOI: 10.3389/fgene.2021.689824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Aging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration. Recent Advances In this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today. Critical Issues Although the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types. Future Directions We critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.
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Affiliation(s)
- Serena Dato
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Paolina Crocco
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | | | - Francesco Lescai
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy
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Peripheral Blood from Rheumatoid Arthritis Patients Shows Decreased T reg CD25 Expression and Reduced Frequency of Effector T reg Subpopulation. Cells 2021; 10:cells10040801. [PMID: 33916798 PMCID: PMC8067140 DOI: 10.3390/cells10040801] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/26/2021] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disease characterized by immune cell infiltration of the synovium, leading to the loss of cartilage, bone, and joint function. Although regulatory T (Treg) cells are thought to modulate the initiation and progression of RA, a consensus has yet to be reached regarding the function and composition of Treg cells in RA patients. To address these discrepancies, we analyzed not only the total Treg frequency but also that of Treg subpopulations in the peripheral blood of RA patients and healthy controls by flow cytometry. We found that the total Treg population was not significantly different between RA and control subjects. However, the effector Treg cell subgroup, defined as CD45RA−CD25hi, showed markedly decreased frequency in RA patients. In addition, the total Treg population from RA patients showed a significant decline in the expression of CD25. Both the naïve and effector Treg subgroups also showed marked reduction of CD25 expression in RA patients compared to controls. These data suggest that the decreased frequency of effector Treg cells and overall reduction of CD25 expression in Treg cells in the peripheral blood may be evidence of altered Treg homeostasis associated with RA pathogenesis.
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Varadé J, Magadán S, González-Fernández Á. Human immunology and immunotherapy: main achievements and challenges. Cell Mol Immunol 2021; 18:805-828. [PMID: 32879472 PMCID: PMC7463107 DOI: 10.1038/s41423-020-00530-6] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/27/2020] [Accepted: 07/31/2020] [Indexed: 02/07/2023] Open
Abstract
The immune system is a fascinating world of cells, soluble factors, interacting cells, and tissues, all of which are interconnected. The highly complex nature of the immune system makes it difficult to view it as a whole, but researchers are now trying to put all the pieces of the puzzle together to obtain a more complete picture. The development of new specialized equipment and immunological techniques, genetic approaches, animal models, and a long list of monoclonal antibodies, among many other factors, are improving our knowledge of this sophisticated system. The different types of cell subsets, soluble factors, membrane molecules, and cell functionalities are some aspects that we are starting to understand, together with their roles in health, aging, and illness. This knowledge is filling many of the gaps, and in some cases, it has led to changes in our previous assumptions; e.g., adaptive immune cells were previously thought to be unique memory cells until trained innate immunity was observed, and several innate immune cells with features similar to those of cytokine-secreting T cells have been discovered. Moreover, we have improved our knowledge not only regarding immune-mediated illnesses and how the immune system works and interacts with other systems and components (such as the microbiome) but also in terms of ways to manipulate this system through immunotherapy. The development of different types of immunotherapies, including vaccines (prophylactic and therapeutic), and the use of pathogens, monoclonal antibodies, recombinant proteins, cytokines, and cellular immunotherapies, are changing the way in which we approach many diseases, especially cancer.
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Affiliation(s)
- Jezabel Varadé
- CINBIO, Centro de Investigaciones Biomédicas, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas, Marcosende, 36310, Vigo, Spain
- Instituto de Investigación Sanitaria Galicia Sur (IIS-Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Susana Magadán
- CINBIO, Centro de Investigaciones Biomédicas, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas, Marcosende, 36310, Vigo, Spain
- Instituto de Investigación Sanitaria Galicia Sur (IIS-Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - África González-Fernández
- CINBIO, Centro de Investigaciones Biomédicas, Universidade de Vigo, Immunology Group, Campus Universitario Lagoas, Marcosende, 36310, Vigo, Spain.
- Instituto de Investigación Sanitaria Galicia Sur (IIS-Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
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Caliskan M, Brown CD, Maranville JC. A catalog of GWAS fine-mapping efforts in autoimmune disease. Am J Hum Genet 2021; 108:549-563. [PMID: 33798443 PMCID: PMC8059376 DOI: 10.1016/j.ajhg.2021.03.009] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 03/05/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies (GWASs) have enabled unbiased identification of genetic loci contributing to common complex diseases. Because GWAS loci often harbor many variants and genes, it remains a major challenge to move from GWASs’ statistical associations to the identification of causal variants and genes that underlie these association signals. Researchers have applied many statistical and functional fine-mapping strategies to prioritize genetic variants and genes as potential candidates. There is no gold standard in fine-mapping approaches, but consistent results across different approaches can improve confidence in the fine-mapping findings. Here, we combined text mining with a systematic review and formed a catalog of 85 studies with evidence of fine mapping for at least one autoimmune GWAS locus. Across all fine-mapping studies, we compiled 230 GWAS loci with allelic heterogeneity estimates and predictions of causal variants and trait-relevant genes. These 230 loci included 455 combinations of locus-by-disease association signals with 15 autoimmune diseases. Using these estimates, we assessed the probability of mediating disease risk associations across genes in GWAS loci and identified robust signals of causal disease biology. We predict that this comprehensive catalog of GWAS fine-mapping efforts in autoimmune disease will greatly help distill the plethora of information in the field and inform therapeutic strategies.
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Affiliation(s)
- Minal Caliskan
- Department of Informatics and Predictive Sciences, Bristol Myers Squibb, Princeton, NJ 08540, USA.
| | - Christopher D Brown
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joseph C Maranville
- Department of Informatics and Predictive Sciences, Bristol Myers Squibb, Princeton, NJ 08540, USA
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Kitanaga Y, Imamura E, Nakahara Y, Fukahori H, Fujii Y, Kubo S, Nakayamada S, Tanaka Y. In vitro pharmacological effects of peficitinib on lymphocyte activation: a potential treatment for systemic sclerosis with JAK inhibitors. Rheumatology (Oxford) 2021; 59:1957-1968. [PMID: 31764973 PMCID: PMC7382595 DOI: 10.1093/rheumatology/kez526] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/06/2019] [Indexed: 12/13/2022] Open
Abstract
Objectives Peficitinib, a novel Janus kinase (JAK) inhibitor, demonstrated promising results in treating RA in phase 3 clinical trials. This in vitro study was undertaken to characterize the pharmacological properties of peficitinib and investigate the involvement of JAK and signal transducer and activator of transcription (STAT) pathways in the pathological processes of SSc, which is also an autoimmune disease. Methods Phosphorylation levels of STAT molecules were assessed in peripheral blood mononuclear cells collected from patients with RA or SSc and healthy subjects, and in skin specimens obtained from 19 patients with SSc. In vitro inhibition of STAT phosphorylation and cytokine/chemokine production by peficitinib, tofacitinib and baricitinib were also characterized. Results Higher spontaneous STAT1 or STAT3 phosphorylation was observed in peripheral T-cells and monocytes from patients with RA and SSc compared with healthy subjects. In skin sections from patients with SSc, phosphorylated STAT3–positive cells were found in almost all cases, irrespective of disease subtype or patient characteristics. Conversely, phosphorylated STAT1-positive cells were observed only in samples from untreated patients with diffuse disease of short duration. Peficitinib inhibited STAT phosphorylation induced by various cytokines, with comparable efficacy to tofacitinib and baricitinib. Peficitinib also suppressed cytokine and chemokine production by peripheral blood mononuclear cells and skin fibroblasts. Conclusion Our results suggest that JAK/STAT pathways are constitutively activated in SSc and RA, and that the JAK inhibitor may represent a novel therapeutic option for SSc.
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Affiliation(s)
- Yukihiro Kitanaga
- Drug Discovery Research, Astellas Pharma, Inc., Tsukuba, Ibaraki.,First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Emiko Imamura
- Drug Discovery Research, Astellas Pharma, Inc., Tsukuba, Ibaraki
| | - Yutaka Nakahara
- Drug Discovery Research, Astellas Pharma, Inc., Tsukuba, Ibaraki
| | | | - Yasutomo Fujii
- Drug Discovery Research, Astellas Pharma, Inc., Tsukuba, Ibaraki
| | - Satoshi Kubo
- First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Shingo Nakayamada
- First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Yoshiya Tanaka
- First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
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Genetic factors underlying the bidirectional relationship between autoimmune and mental disorders - Findings from a Danish population-based study. Brain Behav Immun 2021; 91:10-23. [PMID: 32534018 DOI: 10.1016/j.bbi.2020.06.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Previous studies have indicated the bidirectionality between autoimmune and mental disorders. However, genetic studies underpinning the co-occurrence of the two disorders have been lacking. In this study, we examined the potential genetic contribution to the association between autoimmune and mental disorders and investigated the genetic basis of overall autoimmune disease. METHODS We used diagnostic information from patients with seven autoimmune diseases and six mental disorders from the Danish population-based case-cohort sample (iPSYCH2012). We explored the epidemiological association using survival analysis and modelled the effect of polygenic risk scores (PRSs) on autoimmune and mental diseases. Genetic factors were investigated using GWAS and imputed HLA alleles in the iPSYCH cohort. RESULTS Of 64,039 individuals, a total of 43,902 (68.6%) were diagnosed with mental disorders and 1383 (2.2%) with autoimmune diseases. There was a significant comorbidity between the two disease classes (P = 2.67 × 10-7, OR = 1.38, 95%CI = 1.22-1.56), with an overall bidirectional association, wherein individuals with autoimmune diseases had an increased risk of subsequent mental disorders (HR = 1.13, 95%CI: 1.07-1.21, P = 7.95 × 10-5) and vice versa (HR = 1.27, 95%CI = 1.16-1.39, P = 8.77 × 10-15). Adding PRSs to these adjustment models did not have an impact on the associations. PRSs for autoimmune diseases were only slightly associated with increased risk of mental disorders (HR = 1.01, 95%CI: 1.00-1.02, p = 0.038), whereas PRSs for mental disorders were not associated with autoimmune diseases overall. Our GWAS highlighted 12 loci on chromosome 6 (minimum P = 2.74 × 10-36, OR = 1.80, 95% CI: 1.64-1.96), which were implicated in gene regulation through bioinformatic functional analyses, thereby identifying new candidate genes for overall autoimmune disease. Moreover, we observed 20 human leukocyte antigen (HLA) alleles strongly associated, either positively or negatively, with overall autoimmune disease, but we did not find significant evidence of their associations with overall mental disorders. A GWAS of a comorbid diagnosis of an autoimmune disease and a mental disorder identified a genome-wide significant locus on chromosome 7 as well (P = 1.43 × 10-8, OR = 10.65, 95%CI = 3.21-35.36). CONCLUSIONS Our findings confirm the overall comorbidity and bidirectionality between autoimmune diseases and mental disorders and identify HLA genes which are significantly associated with overall autoimmune disease. Additionally, we identified several new candidate genes for overall autoimmune disease and ranked them based on their association with the investigated diseases.
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Baghfalaki T, Sugier PE, Truong T, Pettitt AN, Mengersen K, Liquet B. Bayesian meta-analysis models for cross cancer genomic investigation of pleiotropic effects using group structure. Stat Med 2020; 40:1498-1518. [PMID: 33368447 DOI: 10.1002/sim.8855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 10/23/2020] [Accepted: 11/26/2020] [Indexed: 12/11/2022]
Abstract
An increasing number of genome-wide association studies (GWAS) summary statistics is made available to the scientific community. Exploiting these results from multiple phenotypes would permit identification of novel pleiotropic associations. In addition, incorporating prior biological information in GWAS such as group structure information (gene or pathway) has shown some success in classical GWAS approaches. However, this has not been widely explored in the context of pleiotropy. We propose a Bayesian meta-analysis approach (termed GCPBayes) that uses summary-level GWAS data across multiple phenotypes to detect pleiotropy at both group-level (gene or pathway) and within group (eg, at the SNP level). We consider both continuous and Dirac spike and slab priors for group selection. We also use a Bayesian sparse group selection approach with hierarchical spike and slab priors that enables us to select important variables both at the group level and within group. GCPBayes uses a Bayesian statistical framework based on Markov chain Monte Carlo (MCMC) Gibbs sampling. It can be applied to multiple types of phenotypes for studies with overlapping or nonoverlapping subjects, and takes into account heterogeneity in the effect size and allows for the opposite direction of the genetic effects across traits. Simulations show that the proposed methods outperform benchmark approaches such as ASSET and CPBayes in the ability to retrieve pleiotropic associations at both SNP and gene-levels. To illustrate the GCPBayes method, we investigate the shared genetic effects between thyroid cancer and breast cancer in candidate pathways.
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Affiliation(s)
- Taban Baghfalaki
- Department of Statistics, Faculty of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Pierre-Emmanuel Sugier
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Queensland, Australia.,Laboratoire de Mathématiques et de leurs Applications de Pau, Université de Pau et des Pays de l'Adour, Pau, France.,CESP (Center for Research in Epidemiology and Population Health), INSERM, Paris-Saclay University, Paris-Sud University, Villejuif, France
| | - Therese Truong
- CESP (Center for Research in Epidemiology and Population Health), INSERM, Paris-Saclay University, Paris-Sud University, Villejuif, France.,Gustave Roussy, Villejuif, France
| | - Anthony N Pettitt
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kerrie Mengersen
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Benoit Liquet
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, Queensland University of Technology, Brisbane, Queensland, Australia.,Laboratoire de Mathématiques et de leurs Applications de Pau, Université de Pau et des Pays de l'Adour, Pau, France.,Department of Mathematics and Statistics, Macquarie University, Sydney, New South Wales, Australia
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González-Serna D, Villanueva-Martin G, Acosta-Herrera M, Márquez A, Martín J. Approaching Shared Pathophysiology in Immune-Mediated Diseases through Functional Genomics. Genes (Basel) 2020; 11:E1482. [PMID: 33317201 PMCID: PMC7762979 DOI: 10.3390/genes11121482] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/01/2020] [Accepted: 12/04/2020] [Indexed: 12/14/2022] Open
Abstract
Immune-mediated diseases (IMDs) are complex pathologies that are strongly influenced by environmental and genetic factors. Associations between genetic loci and susceptibility to these diseases have been widely studied, and hundreds of risk variants have emerged during the last two decades, with researchers observing a shared genetic pattern among them. Nevertheless, the pathological mechanism behind these associations remains a challenge that has just started to be understood thanks to functional genomic approaches. Transcriptomics, regulatory elements, chromatin interactome, as well as the experimental characterization of genomic findings, constitute key elements in the emerging understandings of how genetics affects the etiopathogenesis of IMDs. In this review, we will focus on the latest advances in the field of functional genomics, centering our attention on systemic rheumatic IMDs.
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Affiliation(s)
- David González-Serna
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (D.G.-S.); (G.V.-M.); (M.A.-H.); (A.M.)
| | - Gonzalo Villanueva-Martin
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (D.G.-S.); (G.V.-M.); (M.A.-H.); (A.M.)
| | - Marialbert Acosta-Herrera
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (D.G.-S.); (G.V.-M.); (M.A.-H.); (A.M.)
| | - Ana Márquez
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (D.G.-S.); (G.V.-M.); (M.A.-H.); (A.M.)
- Systemic Autoimmune Disease Unit, Hospital Clínico San Cecilio, Instituto de Investigación Biosanitaria ibs.GRANADA, 18016 Granada, Spain
| | - Javier Martín
- Institute of Parasitology and Biomedicine López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), 18016 Granada, Spain; (D.G.-S.); (G.V.-M.); (M.A.-H.); (A.M.)
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