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Sakaue S, Hirata J, Maeda Y, Kawakami E, Nii T, Kishikawa T, Ishigaki K, Terao C, Suzuki K, Akiyama M, Suita N, Masuda T, Ogawa K, Yamamoto K, Saeki Y, Matsushita M, Yoshimura M, Matsuoka H, Ikari K, Taniguchi A, Yamanaka H, Kawaji H, Lassmann T, Itoh M, Yoshitomi H, Ito H, Ohmura K, R Forrest AR, Hayashizaki Y, Carninci P, Kumanogoh A, Kamatani Y, de Hoon M, Yamamoto K, Okada Y. Integration of genetics and miRNA-target gene network identified disease biology implicated in tissue specificity. Nucleic Acids Res 2019; 46:11898-11909. [PMID: 30407537 PMCID: PMC6294505 DOI: 10.1093/nar/gky1066] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) modulate the post-transcriptional regulation of target genes and are related to biology of complex human traits, but genetic landscape of miRNAs remains largely unknown. Given the strikingly tissue-specific miRNA expression profiles, we here expand a previous method to quantitatively evaluate enrichment of genome-wide association study (GWAS) signals on miRNA-target gene networks (MIGWAS) to further estimate tissue-specific enrichment. Our approach integrates tissue-specific expression profiles of miRNAs (∼1800 miRNAs in 179 cells) with GWAS to test whether polygenic signals enrich in miRNA-target gene networks and whether they fall within specific tissues. We applied MIGWAS to 49 GWASs (nTotal = 3 520 246), and successfully identified biologically relevant tissues. Further, MIGWAS could point miRNAs as candidate biomarkers of the trait. As an illustrative example, we performed differentially expressed miRNA analysis between rheumatoid arthritis (RA) patients and healthy controls (n = 63). We identified novel biomarker miRNAs (e.g. hsa-miR-762) by integrating differentially expressed miRNAs with MIGWAS results for RA, as well as novel associated loci with significant genetic risk (rs56656810 at MIR762 at 16q11; n = 91 482, P = 3.6 × 10-8). Our result highlighted that miRNA-target gene network contributes to human disease genetics in a cell type-specific manner, which could yield an efficient screening of miRNAs as promising biomarkers.
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Affiliation(s)
- Saori Sakaue
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Allergy and Rheumatology, Graduate School of Medicine, the University of Tokyo, Tokyo 113-8655, Japan
| | - Jun Hirata
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Pharmaceutical Discovery Research Laboratories, TEIJIN PHARMA LIMITED, Hino 191-8512, Japan
| | - Yuichi Maeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo 100-0004, Japan
| | - Eiryo Kawakami
- Healthcare and Medical Data Driven AI based Predictive Reasoning Development Unit, Medical Sciences Innovation Hub Program (MIH), RIKEN, Yokohama 230-0045, Japan.,Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan.,Japan Agency for Medical Research and Development-Core Research for Evolutional Science and Technology, Tokyo 100-0004, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Otorhinolaryngology - Head and Neck Surgery, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Chikashi Terao
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Clinical Research Center, Shizuoka General Hospital, Shizuoka 420-0881, Japan.,The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.,Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Ken Suzuki
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka 812-8582, Japan
| | - Naomasa Suita
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Discovery Technology Research Laboratories, Tsukuba Research Institute, Ono Pharmaceutical Co., Ltd., Tsukuba 300-4247, Japan
| | - Tatsuo Masuda
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Obstetrics and Gynecology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kotaro Ogawa
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Neurology, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Department of Pediatrics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan
| | - Yukihiko Saeki
- Department of Clinical Research, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Masato Matsushita
- Department of Rheumatology and Allergology, Saiseikai Senri Hospital, Suita 565-0862, Japan.,Department of Rheumatology and Allergology, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, National Hospital Organization (NHO) Osaka Minami Medical Center, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Tokyo 162-0054, Japan
| | - Atsuo Taniguchi
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan
| | - Hisashi Yamanaka
- Institute of Rheumatology, Tokyo Women's Medical University, Tokyo 162-0054, Japan
| | - Hideya Kawaji
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan.,Preventive Medicine and Applied Genomics Unit, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Timo Lassmann
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Telethon Kids Institute, the University of Western Australia, Western Australia 6008, Australia
| | - Masayoshi Itoh
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Hiroyuki Yoshitomi
- Laboratory of Tissue Regeneration, Department of Regeneration Science and Engineering, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.,Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Hiromu Ito
- Department of Orthopaedic Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, the University of Western Australia, Western Australia 6009, Australia
| | - Yoshihide Hayashizaki
- RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program (PMI), Saitama 351-0198, Japan
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045 Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, WPI Immunology Frontier Research Center, Osaka University, Suita 565-0871, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8507, Japan
| | - Michiel de Hoon
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan.,RIKEN Omics Science Center (OSC), Yokohama 230-0045, Japan.,Laboratory for Applied Computational Genomics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045 Japan
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita 565-0871, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita 565-0871, Japan
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Okada Y, Suzuki A, Ikari K, Terao C, Kochi Y, Ohmura K, Higasa K, Akiyama M, Ashikawa K, Kanai M, Hirata J, Suita N, Teo YY, Xu H, Bae SC, Takahashi A, Momozawa Y, Matsuda K, Momohara S, Taniguchi A, Yamada R, Mimori T, Kubo M, Brown M, Raychaudhuri S, Matsuda F, Yamanaka H, Kamatani Y, Yamamoto K. Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis. Am J Hum Genet 2016; 99:366-74. [PMID: 27486778 DOI: 10.1016/j.ajhg.2016.06.019] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 06/21/2016] [Indexed: 01/11/2023] Open
Abstract
Despite the progress in human leukocyte antigen (HLA) causal variant mapping, independent localization of major histocompatibility complex (MHC) risk from classical HLA genes is challenging. Here, we conducted a large-scale MHC fine-mapping analysis of rheumatoid arthritis (RA) in a Japanese population (6,244 RA cases and 23,731 controls) population by using HLA imputation, followed by a multi-ethnic validation study including east Asian and European populations (n = 7,097 and 23,149, respectively). Our study identified an independent risk of a synonymous mutation at HLA-DOA, a non-classical HLA gene, on anti-citrullinated protein autoantibody (ACPA)-positive RA risk (p = 1.4 × 10(-9)), which demonstrated a cis-expression quantitative trait loci (cis-eQTL) effect on HLA-DOA expression. Trans-ethnic comparison revealed different linkage disequilibrium (LD) patterns in HLA-DOA and HLA-DRB1, explaining the observed HLA-DOA variant risk heterogeneity among ethnicities, which was most evident in the Japanese population. Although previous HLA fine-mapping studies have identified amino acid polymorphisms of the classical HLA genes as driving genetic susceptibility to disease, our study additionally identifies the dosage contribution of a non-classical HLA gene to disease etiology. Our study contributes to the understanding of HLA immunology in human diseases and suggests the value of incorporating additional ancestry in MHC fine-mapping.
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Okada Y, Muramatsu T, Suita N, Kanai M, Kawakami E, Iotchkova V, Soranzo N, Inazawa J, Tanaka T. Significant impact of miRNA-target gene networks on genetics of human complex traits. Sci Rep 2016; 6:22223. [PMID: 26927695 PMCID: PMC4772006 DOI: 10.1038/srep22223] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
Abstract
The impact of microRNA (miRNA) on the genetics of human complex traits, especially in the context of miRNA-target gene networks, has not been fully assessed. Here, we developed a novel analytical method, MIGWAS, to comprehensively evaluate enrichment of genome-wide association study (GWAS) signals in miRNA–target gene networks. We applied the method to the GWAS results of the 18 human complex traits from >1.75 million subjects, and identified significant enrichment in rheumatoid arthritis (RA), kidney function, and adult height (P < 0.05/18 = 0.0028, most significant enrichment in RA with P = 1.7 × 10−4). Interestingly, these results were consistent with current literature-based knowledge of the traits on miRNA obtained through the NCBI PubMed database search (adjusted P = 0.024). Our method provided a list of miRNA and target gene pairs with excess genetic association signals, part of which included drug target genes. We identified a miRNA (miR-4728-5p) that downregulates PADI2, a novel RA risk gene considered as a promising therapeutic target (rs761426, adjusted P = 2.3 × 10−9). Our study indicated the significant impact of miRNA–target gene networks on the genetics of human complex traits, and provided resources which should contribute to drug discovery and nucleic acid medicine.
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Affiliation(s)
- Yukinori Okada
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.,Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Tomoki Muramatsu
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Naomasa Suita
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.,Advanced Medicinal Research Laboratories, Tsukuba Research Institute, Ono Pharmaceutical CO., LTD., Tsukuba 300-4247, Japan
| | - Masahiro Kanai
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Eiryo Kawakami
- Laboratory for Disease Systems Modeling, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Valentina Iotchkova
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Hills Rd, Cambridge CB2 0AH, UK
| | - Nicole Soranzo
- Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK.,Department of Haematology, University of Cambridge, Hills Rd, Cambridge CB2 0AH, UK
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute and Graduate School of Medical and Dental Science, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Toshihiro Tanaka
- Department of Human Genetics and Disease Diversity, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.,Laboratory for Cardiovascular Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
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