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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, Kouno 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 T, Abe M, Harada M, Taniai M, Zeniya M, Ohira H, Shimoda S, Komori A, Tanaka A, Ishigaki K, Nagasaki M, Tokunaga K, Nakamura M. A genome-wide association study identified PTPN2 as a population-specific susceptibility gene locus for primary biliary cholangitis. Hepatology 2024:01515467-990000000-00853. [PMID: 38652555 DOI: 10.1097/hep.0000000000000894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 02/22/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND AIMS Previous genome-wide association studies (GWAS) have indicated the involvement of shared (population-non-specific) and non-shared (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 RESULTS Protein tyrosine phosphatase non-receptor type 2 (PTPN2) was identified as a novel PBC susceptibility gene locus through a GWAS and subsequent genome-wide meta-analysis involving 2,181 cases and 2,699 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 (Tfh) and plasmacytoid dendritic cells (pDCs). Infiltration of PTPN2-positive T-cells and pDCs were 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 via an insufficient negative feedback loop caused by the PTPN2 risk allele of rs2292758 in IFN 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 Kouno
- 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
- 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 and Rheumatic Diseases, Fukushima Medical University of Medicine, 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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Shimada M, Omae Y, Kakita A, Gabdulkhaev R, Hitomi Y, Miyagawa T, Honda M, Fujimoto A, Tokunaga K. Identification of region-specific gene isoforms in the human brain using long-read transcriptome sequencing. Sci Adv 2024; 10:eadj5279. [PMID: 38266094 PMCID: PMC10807796 DOI: 10.1126/sciadv.adj5279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
In neurological and neuropsychiatric diseases, different brain regions are affected, and differences in gene expression patterns could potentially explain this mechanism. However, limited studies have precisely explored gene expression in different regions of the human brain. In this study, we performed long-read RNA sequencing on three different brain regions of the same individuals: the cerebellum, hypothalamus, and temporal cortex. Despite stringent filtering criteria excluding isoforms predicted to be artifacts, over half of the isoforms expressed in multiple samples across multiple regions were found to be unregistered in the GENCODE reference. We then especially focused on genes with different major isoforms in each brain region, even with similar overall expression levels, and identified that many of such genes including GAS7 might have distinct roles in dendritic spine and neuronal formation in each region. We also found that DNA methylation might, in part, drive different isoform expressions in different regions. These findings highlight the significance of analyzing isoforms expressed in disease-relevant sites.
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Affiliation(s)
- Mihoko Shimada
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Center for Clinical Sciences, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Yosuke Omae
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Ramil Gabdulkhaev
- Department of Pathology, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Taku Miyagawa
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Makoto Honda
- Sleep Disorders Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
- Japan Somnology Center and Seiwa Hospital, Institute of Neuropsychiatry, Tokyo, Japan
| | - Akihiro Fujimoto
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
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Hitomi Y, Ueno K, Aiba Y, Nishida N, Kawai Y, Kawashima M, Khor SS, Takada S, Iwabuchi C, Nagasaki M, Tokunaga K, Nakamura M. rs10924104 in the expression enhancer motif of CD58 confers susceptibility to human autoimmune diseases. Hum Genet 2024; 143:19-33. [PMID: 37994973 DOI: 10.1007/s00439-023-02617-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/28/2023] [Indexed: 11/24/2023]
Abstract
CD58 plays roles in cell adhesion and co-stimulation with antigen presentation from major histocompatibility complex class II on antigen-presenting cells to T-cell antigen receptors on naïve T cells. CD58 reportedly contributes to the development of various human autoimmune diseases. Recently, genome-wide association studies (GWASs) identified CD58 as a susceptibility locus for autoimmune diseases such as systemic lupus erythematosus (SLE), multiple sclerosis (MS), and primary biliary cholangitis (PBC). However, the primary functional variant and molecular mechanisms of susceptibility to autoimmune diseases in the CD58 locus were not clarified. Here, rs10924104, located in the ZNF35-binding motif within the gene expression regulatory motif, was identified as the primary functional variant for SLE, MS, and PBC among genetic variants showing stronger linkage disequilibrium (LD) with GWAS-lead variants in the CD58 locus. Expression-quantitative trait locus (e-QTL) data for each distinct blood cell type and in vitro functional analysis using the CRISPR/Cas9 system corroborated the functional role of rs10924104 in the upregulation of CD58 transcription by the disease-risk allele. Additionally, the strength of disease susceptibility observed in the CD58 locus could be accounted for by the strength of LD between rs10924104 and each GWAS-lead variant. In conclusion, the present study demonstrated for the first time the existence of a shared autoimmune disease-related primary functional variant (i.e., rs10924104) that regulates the expression of CD58. Clarifying the molecular mechanism of disease susceptibility derived from such a shared genetic background is important for understanding human autoimmune diseases and human immunology.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan.
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Nao Nishida
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Minae Kawashima
- Database Center for Life Science, Research Organization of Information and Systems, Kashiwa, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sanami Takada
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Chisato Iwabuchi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Japan
| | - Masao Nagasaki
- Division of Biomedical Information Analysis, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
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Koganebuchi K, Matsunami M, Imamura M, Kawai Y, Hitomi Y, Tokunaga K, Maeda S, Ishida H, Kimura R. Demographic history of Ryukyu islanders at the southern part of the Japanese Archipelago inferred from whole-genome resequencing data. J Hum Genet 2023; 68:759-767. [PMID: 37468573 PMCID: PMC10597838 DOI: 10.1038/s10038-023-01180-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 05/29/2023] [Accepted: 06/17/2023] [Indexed: 07/21/2023]
Abstract
The Ryukyu Islands are located in the southernmost part of the Japanese Archipelago and consist of several island groups. Each island group has its own history and culture, which differ from those of mainland Japan. People of the Ryukyu Islands are genetically subdivided; however, their detailed demographic history remains unclear. We report the results of a whole-genome sequencing analysis of a total of 50 Ryukyu islanders, focusing on genetic differentiation between Miyako and Okinawa islanders. We confirmed that Miyako and Okinawa islanders cluster differently in principal component analysis and ADMIXTURE analysis and that there is a population structure among Miyako islanders. The present study supports the hypothesis that population differentiation is primarily caused by genetic drift rather than by differences in the rate of migration from surrounding regions, such as the Japanese main islands or Taiwan. In addition, the genetic cline observed among Miyako and Okinawa islanders can be explained by recurrent migration beyond the bounds of these islands. Our analysis also suggested that the presence of multiple subpopulations during the Neolithic Ryukyu Jomon period is not crucial to explain the modern Ryukyu populations. However, the assumption of multiple subpopulations during the time of admixture with mainland Japanese is necessary to explain the modern Ryukyu populations. Our findings add insights that could help clarify the complex history of populations in the Ryukyu Islands.
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Affiliation(s)
- Kae Koganebuchi
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan.
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Masatoshi Matsunami
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
| | - Minako Imamura
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, 903-0215, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Yuki Hitomi
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, 142-8501, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Shiro Maeda
- Department of Advanced Genomic and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
- Division of Clinical Laboratory and Blood Transfusion, University of the Ryukyus Hospital, Nishihara, 903-0215, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan
- Mt. Olive Hospital, Naha, 903-0804, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, 903-0215, Japan.
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Khor SS, Ueno K, Nishida N, Kawashima M, Kawai Y, Aiba Y, Hitomi Y, Nagasaki M, Nakamura M, Tokunaga K. Novel HLA allele associations with susceptibility, staging, symptomatic state, autoimmune hepatitis and hepatocellular carcinoma events for primary biliary cholangitis in the Japanese population. Front Immunol 2023; 14:1151502. [PMID: 37325616 PMCID: PMC10264690 DOI: 10.3389/fimmu.2023.1151502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a rare autoimmune disease with a clear predisposition for human leukocyte antigen (HLA)-DR/DQ-associated loss of immune tolerance for the E2 component of the pyruvate dehydrogenase complex. Three-field-resolution HLA imputation of 1,670 Japanese PBC patients and 2,328 healthy controls was conducted using Japanese population-specific HLA reference panels. Eighteen previously reported Japanese PBC-associated HLA alleles were confirmed and extended to 3-field-resolution, including HLA-DRB1*08:03 to HLA-DRB1*08:03:02, HLA-DQB1*03:01 to HLA-DQB1*03:01:01, HLA-DQB1*04:01 to HLA-DQB1*04:01:01 and HLA-DQB1*06:04 to HLA-DQB1*06:04:01. In addition, additional significant novel HLA alleles were identified, including 3 novel susceptible HLA-DQA1 alleles: HLA-DQA1*03:03:01, HLA-DQA1*04:01:01, HLA-DQA1*01:04:01 and 1 novel protective HLA-DQA1 allele, HLA-DQA1*05:05:01. In addition, PBC patients carrying HLA-DRB1*15:01:01 and HLA-DQA1*03:03:01 would have a higher predisposition toward developing concomitant autoimmune hepatitis (AIH). Further, late-stage and symptomatic PBC shared the same susceptible HLA alleles of HLA-A*26:01:01, HLA-DRB1*09:01:02 and HLA-DQB1*03:03:02. Lastly, HLA-DPB1*05:01:01 was identified as a potential risk HLA allele for development of hepatocellular carcinoma (HCC) in PBC patients. In conclusion, we have extended the current knowledge of HLA allele associations to 3-field resolution and identified novel HLA allele associations with predisposition risk, staging, symptomatic state, and AIH and HCC events for Japanese PBC patients.
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Affiliation(s)
- Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
- The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Minae Kawashima
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems, Chiba, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
- Headquarters of Primary Biliary Cholangitis (PBC) Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. Corrigendum to: "An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs" [J Hepatol 75 (2021) 572-581]. J Hepatol 2023; 78:883. [PMID: 36639314 DOI: 10.1016/j.jhep.2022.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, USA
| | | | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, USA
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
| | | | | | | | | | | | | |
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7
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Nakamura T, Matsumoto M, Amano K, Enokido Y, Zolensky ME, Mikouchi T, Genda H, Tanaka S, Zolotov MY, Kurosawa K, Wakita S, Hyodo R, Nagano H, Nakashima D, Takahashi Y, Fujioka Y, Kikuiri M, Kagawa E, Matsuoka M, Brearley AJ, Tsuchiyama A, Uesugi M, Matsuno J, Kimura Y, Sato M, Milliken RE, Tatsumi E, Sugita S, Hiroi T, Kitazato K, Brownlee D, Joswiak DJ, Takahashi M, Ninomiya K, Takahashi T, Osawa T, Terada K, Brenker FE, Tkalcec BJ, Vincze L, Brunetto R, Aléon-Toppani A, Chan QHS, Roskosz M, Viennet JC, Beck P, Alp EE, Michikami T, Nagaashi Y, Tsuji T, Ino Y, Martinez J, Han J, Dolocan A, Bodnar RJ, Tanaka M, Yoshida H, Sugiyama K, King AJ, Fukushi K, Suga H, Yamashita S, Kawai T, Inoue K, Nakato A, Noguchi T, Vilas F, Hendrix AR, Jaramillo-Correa C, Domingue DL, Dominguez G, Gainsforth Z, Engrand C, Duprat J, Russell SS, Bonato E, Ma C, Kawamoto T, Wada T, Watanabe S, Endo R, Enju S, Riu L, Rubino S, Tack P, Takeshita S, Takeichi Y, Takeuchi A, Takigawa A, Takir D, Tanigaki T, Taniguchi A, Tsukamoto K, Yagi T, Yamada S, Yamamoto K, Yamashita Y, Yasutake M, Uesugi K, Umegaki I, Chiu I, Ishizaki T, Okumura S, Palomba E, Pilorget C, Potin SM, Alasli A, Anada S, Araki Y, Sakatani N, Schultz C, Sekizawa O, Sitzman SD, Sugiura K, Sun M, Dartois E, De Pauw E, Dionnet Z, Djouadi Z, Falkenberg G, Fujita R, Fukuma T, Gearba IR, Hagiya K, Hu MY, Kato T, Kawamura T, Kimura M, Kubo MK, Langenhorst F, Lantz C, Lavina B, Lindner M, Zhao J, Vekemans B, Baklouti D, Bazi B, Borondics F, Nagasawa S, Nishiyama G, Nitta K, Mathurin J, Matsumoto T, Mitsukawa I, Miura H, Miyake A, Miyake Y, Yurimoto H, Okazaki R, Yabuta H, Naraoka H, Sakamoto K, Tachibana S, Connolly HC, Lauretta DS, Yoshitake M, Yoshikawa M, Yoshikawa K, Yoshihara K, Yokota Y, Yogata K, Yano H, Yamamoto Y, Yamamoto D, Yamada M, Yamada T, Yada T, Wada K, Usui T, Tsukizaki R, Terui F, Takeuchi H, Takei Y, Iwamae A, Soejima H, Shirai K, Shimaki Y, Senshu H, Sawada H, Saiki T, Ozaki M, Ono G, Okada T, Ogawa N, Ogawa K, Noguchi R, Noda H, Nishimura M, Namiki N, Nakazawa S, Morota T, Miyazaki A, Miura A, Mimasu Y, Matsumoto K, Kumagai K, Kouyama T, Kikuchi S, Kawahara K, Kameda S, Iwata T, Ishihara Y, Ishiguro M, Ikeda H, Hosoda S, Honda R, Honda C, Hitomi Y, Hirata N, Hirata N, Hayashi T, Hayakawa M, Hatakeda K, Furuya S, Fukai R, Fujii A, Cho Y, Arakawa M, Abe M, Watanabe S, Tsuda Y. Formation and evolution of carbonaceous asteroid Ryugu: Direct evidence from returned samples. Science 2023; 379:eabn8671. [PMID: 36137011 DOI: 10.1126/science.abn8671] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Samples of the carbonaceous asteroid Ryugu were brought to Earth by the Hayabusa2 spacecraft. We analyzed 17 Ryugu samples measuring 1 to 8 millimeters. Carbon dioxide-bearing water inclusions are present within a pyrrhotite crystal, indicating that Ryugu's parent asteroid formed in the outer Solar System. The samples contain low abundances of materials that formed at high temperatures, such as chondrules and calcium- and aluminum-rich inclusions. The samples are rich in phyllosilicates and carbonates, which formed through aqueous alteration reactions at low temperature, high pH, and water/rock ratios of <1 (by mass). Less altered fragments contain olivine, pyroxene, amorphous silicates, calcite, and phosphide. Numerical simulations, based on the mineralogical and physical properties of the samples, indicate that Ryugu's parent body formed ~2 million years after the beginning of Solar System formation.
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Affiliation(s)
- T Nakamura
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M Matsumoto
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - K Amano
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Y Enokido
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M E Zolensky
- NASA Johnson Space Center; Houston, TX 77058, USA
| | - T Mikouchi
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - H Genda
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - S Tanaka
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - M Y Zolotov
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA
| | - K Kurosawa
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - S Wakita
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - R Hyodo
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H Nagano
- Department of Mechanical Systems Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - D Nakashima
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Y Takahashi
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.,Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Y Fujioka
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M Kikuiri
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - E Kagawa
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M Matsuoka
- Laboratoire d'Etudes Spatiales et d'Instrumentation en Astrophysique (LESIA), Observatoire de Paris, Meudon 92195 France.,Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - A J Brearley
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131, USA
| | - A Tsuchiyama
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan.,Key Laboratory of Mineralogy and Metallogeny, Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou 510640, China.,Center for Excellence in Deep Earth Science, CAS, Guangzhou 510640, China
| | - M Uesugi
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - J Matsuno
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Y Kimura
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - M Sato
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - R E Milliken
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - E Tatsumi
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.,Instituto de Astrofísica de Canarias, University of La Laguna, Tenerife 38205, Spain
| | - S Sugita
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan.,Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Hiroi
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - K Kitazato
- Aizu Research Center for Space Informatics, The University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - D Brownlee
- Department of Astronomy, University of Washington, Seattle, WA 98195 USA
| | - D J Joswiak
- Department of Astronomy, University of Washington, Seattle, WA 98195 USA
| | - M Takahashi
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - K Ninomiya
- Institute for Radiation Sciences, Osaka University, Toyonaka 560-0043, Japan
| | - T Takahashi
- Kavli Institute for the Physics and Mathematics of the Universe, The University of Tokyo, Kashiwa 277-8583, Japan.,Department of Physics, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Osawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - K Terada
- Department of Earth and Space Science, Osaka University, Toyonaka 560-0043, Japan
| | - F E Brenker
- Institute of Geoscience, Goethe University, Frankfurt, 60438 Frankfurt am Main, Germany
| | - B J Tkalcec
- Institute of Geoscience, Goethe University, Frankfurt, 60438 Frankfurt am Main, Germany
| | - L Vincze
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - R Brunetto
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - A Aléon-Toppani
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - Q H S Chan
- Department of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
| | - M Roskosz
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Muséum National d'Histoire Naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, Paris, France
| | - J-C Viennet
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Muséum National d'Histoire Naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, Paris, France
| | - P Beck
- Institut de Planétologie et d'Astrophysique de Grenoble, CNRS, Université Grenoble Alpes, 38000 Grenoble, France
| | - E E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - T Michikami
- Faculty of Engineering, Kindai University, Higashi-Hiroshima 739-2116, Japan
| | - Y Nagaashi
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan.,Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - T Tsuji
- Department of Earth Resources Engineering, Kyushu University, Fukuoka 819-0395, Japan.,School of Engineering, The University of Tokyo, Tokyo 113-0033, Japan
| | - Y Ino
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Physics, Kwansei Gakuin University, Sanda 669-1330, Japan
| | - J Martinez
- NASA Johnson Space Center; Houston, TX 77058, USA
| | - J Han
- Department of Earth and Atmospheric Sciences, University of Houston, Houston, TX 77204, USA
| | - A Dolocan
- Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - R J Bodnar
- Department of Geoscience, Virginia Tech, Blacksburg, VA 24061, USA
| | - M Tanaka
- Materials Analysis Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
| | - H Yoshida
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K Sugiyama
- Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan
| | - A J King
- Department of Earth Science, Natural History Museum, London SW7 5BD, UK
| | - K Fukushi
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - H Suga
- Spectroscopy Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - S Yamashita
- Department of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - T Kawai
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K Inoue
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - A Nakato
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Noguchi
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan.,Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
| | - F Vilas
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - A R Hendrix
- Planetary Science Institute, Tucson, AZ 85719, USA
| | | | - D L Domingue
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - G Dominguez
- Department of Physics, California State University, San Marcos, CA 92096, USA
| | - Z Gainsforth
- Space Sciences Laboratory, University of California, Berkeley, CA 94720, USA
| | - C Engrand
- Laboratoire de Physique des 2 Infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - J Duprat
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Muséum National d'Histoire Naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, Paris, France
| | - S S Russell
- Department of Earth Science, Natural History Museum, London SW7 5BD, UK
| | - E Bonato
- Institute for Planetary Research, Deutsches Zentrum für Luftund Raumfahrt, Rutherfordstraße 2 12489 Berlin, Germany
| | - C Ma
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena CA 91125, USA
| | - T Kawamoto
- Department of Geosciences, Shizuoka University, Shizuoka 422-8529, Japan
| | - T Wada
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - S Watanabe
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Kavli Institute for the Physics and Mathematics of the Universe, The University of Tokyo, Kashiwa 277-8583, Japan
| | - R Endo
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - S Enju
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - L Riu
- European Space Astronomy Centre, 28692 Villanueva de la Cañada, Spain
| | - S Rubino
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - P Tack
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - S Takeshita
- High Energy Accelerator Research Organization, Tokai 319-1106, Japan
| | - Y Takeichi
- Department of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Tsukuba 305-0801, Japan.,Department of Applied Physics, Osaka University, Suita 565-0871, Japan
| | - A Takeuchi
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - A Takigawa
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - D Takir
- NASA Johnson Space Center; Houston, TX 77058, USA
| | | | - A Taniguchi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori 590-0494, Japan
| | - K Tsukamoto
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - T Yagi
- National Metrology Institute of Japan, AIST, Tsukuba 305-8565, Japan
| | - S Yamada
- Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - K Yamamoto
- Japan Fine Ceramics Center, Nagoya 456-8587, Japan
| | - Y Yamashita
- National Metrology Institute of Japan, AIST, Tsukuba 305-8565, Japan
| | - M Yasutake
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - K Uesugi
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - I Umegaki
- High Energy Accelerator Research Organization, Tokai 319-1106, Japan.,Toyota Central Research and Development Laboratories, Nagakute 480-1192, Japan
| | - I Chiu
- Institute for Radiation Sciences, Osaka University, Toyonaka 560-0043, Japan
| | - T Ishizaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S Okumura
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - E Palomba
- Istituto di Astrofisica e Planetologia Spaziali, Istituto Nazionale di Astrofisica, Rome 00133, Italy
| | - C Pilorget
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France.,Institut Universitaire de France, Paris, France
| | - S M Potin
- Laboratoire d'Etudes Spatiales et d'Instrumentation en Astrophysique (LESIA), Observatoire de Paris, Meudon 92195 France.,Faculty of Aerospace Engineering, Delft University of Technology, Delft, Netherlands
| | - A Alasli
- Department of Mechanical Systems Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - S Anada
- Japan Fine Ceramics Center, Nagoya 456-8587, Japan
| | - Y Araki
- Department of Physical Sciences, Ritsumeikan University, Shiga 525-0058, Japan
| | - N Sakatani
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - C Schultz
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - O Sekizawa
- Spectroscopy Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - S D Sitzman
- Physical Sciences Laboratory, The Aerospace Corporation, CA 90245, USA
| | - K Sugiura
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - M Sun
- Key Laboratory of Mineralogy and Metallogeny, Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou 510640, China.,Center for Excellence in Deep Earth Science, CAS, Guangzhou 510640, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - E Dartois
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - E De Pauw
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - Z Dionnet
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - Z Djouadi
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - G Falkenberg
- Deutsches Elektronen-Synchrotron Photon Science, 22603 Hamburg, Germany
| | - R Fujita
- Department of Mechanical Systems Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - T Fukuma
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - I R Gearba
- Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - K Hagiya
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - M Y Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - T Kato
- Japan Fine Ceramics Center, Nagoya 456-8587, Japan
| | - T Kawamura
- Institut de Physique du Globe de Paris, Université de Paris, Paris 75205, France
| | - M Kimura
- Department of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - M K Kubo
- Division of Natural Sciences, International Christian University, Mitaka 181-8585, Japan
| | - F Langenhorst
- Institute of Geosciences, Friedrich-Schiller-Universität Jena, 07745 Jena, Germany
| | - C Lantz
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - B Lavina
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - M Lindner
- Institute of Geoscience, Goethe University, Frankfurt, 60438 Frankfurt am Main, Germany
| | - J Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - B Vekemans
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - D Baklouti
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - B Bazi
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - F Borondics
- Optimized Light Source of Intermediate Energy to LURE (SOLEIL) L'Orme des Merisiers, Gif sur Yvette F-91192, France
| | - S Nagasawa
- Kavli Institute for the Physics and Mathematics of the Universe, The University of Tokyo, Kashiwa 277-8583, Japan.,Department of Physics, The University of Tokyo, Tokyo 113-0033, Japan
| | - G Nishiyama
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K Nitta
- Spectroscopy Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - J Mathurin
- Institut Chimie Physique, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - T Matsumoto
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - I Mitsukawa
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - H Miura
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - A Miyake
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Y Miyake
- High Energy Accelerator Research Organization, Tokai 319-1106, Japan
| | - H Yurimoto
- Department of Natural History Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - R Okazaki
- Department of Earth and Planetary Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - H Yabuta
- Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - H Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - K Sakamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S Tachibana
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - H C Connolly
- Department of Geology, Rowan University, Glassboro, NJ 08028, USA
| | - D S Lauretta
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA
| | - M Yoshitake
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Yoshikawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - K Yoshikawa
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - K Yoshihara
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Yokota
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Yogata
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H Yano
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - Y Yamamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - D Yamamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Yamada
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - T Yamada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Yada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Wada
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - T Usui
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - R Tsukizaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - F Terui
- Department of Mechanical Engineering, Kanagawa Institute of Technology, Atsugi 243-0292, Japan
| | - H Takeuchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - Y Takei
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - A Iwamae
- Marine Works Japan, Yokosuka 237-0063, Japan
| | - H Soejima
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - K Shirai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Shimaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H Senshu
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - H Sawada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Saiki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Ozaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - G Ono
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - T Okada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - N Ogawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Ogawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - R Noguchi
- Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - H Noda
- National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - M Nishimura
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - N Namiki
- Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan.,National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - S Nakazawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Morota
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - A Miyazaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - A Miura
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Mimasu
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Matsumoto
- Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan.,National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - K Kumagai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - T Kouyama
- Digital Architecture Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - S Kikuchi
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan.,National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - K Kawahara
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S Kameda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - T Iwata
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - Y Ishihara
- JAXA Space Exploration Center, JAXA, Sagamihara 252-5210, Japan
| | - M Ishiguro
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - H Ikeda
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - S Hosoda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - R Honda
- Department of Information Science, Kochi University, Kochi 780-8520, Japan.,Center for Data Science, Ehime University, Matsuyama 790-8577, Japan
| | - C Honda
- Aizu Research Center for Space Informatics, The University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - Y Hitomi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - N Hirata
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - N Hirata
- Aizu Research Center for Space Informatics, The University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - T Hayashi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Hayakawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Hatakeda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - S Furuya
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - R Fukai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - A Fujii
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Cho
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - M Arakawa
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - M Abe
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - S Watanabe
- Department of Earth and Environmental Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Y Tsuda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
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8
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Hitomi Y, Nakamura M. The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update. Genes (Basel) 2023; 14:405. [PMID: 36833332 PMCID: PMC9957238 DOI: 10.3390/genes14020405] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits the strongest involvement of genetic heritability in disease development. As at December 2022, genome-wide association studies (GWASs) and associated meta-analyses identified approximately 70 PBC susceptibility gene loci in various populations, including those of European and East Asian descent. However, the molecular mechanisms through which these susceptibility loci affect the pathogenesis of PBC are not fully understood. This study provides an overview of current data regarding the genetic factors of PBC as well as post-GWAS approaches to identifying primary functional variants and effector genes in disease-susceptibility loci. Possible mechanisms of these genetic factors in the development of PBC are also discussed, focusing on four major disease pathways identified by in silico gene set analyses, namely, (1) antigen presentation by human leukocyte antigens, (2) interleukin-12-related pathways, (3) cellular responses to tumor necrosis factor, and (4) B cell activation, maturation, and differentiation pathways.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, 2-1001-1 Kubara, Omura 856-8562, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
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9
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Ashouri S, Khor SS, Hitomi Y, Sawai H, Nishida N, Sugiyama M, Kawai Y, Posuwan N, Tangkijvanich P, Komolmit P, Tsuiji M, Shotelersuk V, Poovorawan Y, Mizokami M, Tokunaga K. Genome-Wide Association Study for Chronic Hepatitis B Infection in the Thai Population. Front Genet 2022; 13:887121. [PMID: 35769989 PMCID: PMC9234442 DOI: 10.3389/fgene.2022.887121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/16/2022] [Indexed: 11/19/2022] Open
Abstract
To identify novel host genetic variants that predispose to hepatitis B virus (HBV) persistence, we performed the first genome-wide association study in the Thai population involving 318 cases of chronic hepatitis B and 309 healthy controls after quality control measures. We detected the genome-wide significant association of the HLA class II region (HLA-DPA1/DPB1, rs7770370, p-value = 7.71 × 10−10, OR = 0.49) with HBV chronicity. Subsequent HLA allele imputation revealed HLA-DPA1*01:03 (Pc = 1.21 × 10−6, OR = 0.53), HLA-DPB1*02:01 (Pc = 2.17 × 10−3, OR = 0.50), and HLA-DQB1*06:09 (Pc = 2.17 × 10−2, OR = 0.07) as protective alleles, and HLA-DPA1*02:02 (Pc = 6.32 × 10−5, OR = 1.63), HLA-DPB1*05:01 (Pc = 1.13 × 10−4, OR = 1.72), HLA-DPB1*13:01 (Pc = 4.68 × 10−2, OR = 1.60), and HLA-DQB1*03:03 (Pc = 1.11 × 10−3, OR = 1.84) as risk alleles for HBV persistence. We also detected suggestive associations in the PLSCR1 (rs35766154), PDLIM5 (rs62321986), SGPL1 (rs144998273), and MGST1 (rs1828682) loci. Among single-nucleotide polymorphisms in the PLSCR1 locus, rs1061307 was identified as the primary functional variant by in silico/in vitro functional analysis. In addition to replicating the association of the HLA class II region, we detected novel candidate loci that provide new insights into the pathophysiology of chronic hepatitis B.
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Affiliation(s)
- Saeideh Ashouri
- Genome Medical Science Project, National Center for Global Health and Medicine, Toyama, Tokyo,Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- *Correspondence: Saeideh Ashouri, ; Katsushi Tokunaga,
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Toyama, Tokyo,Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Hitomi
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Toyama, Tokyo,Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nawarat Posuwan
- Chulabhorn International College of Medicine, Thammasat University, Rangsit Campus, Pathum Thani, Thailand
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Piyawat Komolmit
- Center of Excellence in Liver Diseases, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
- Liver Fibrosis and Cirrhosis Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Makoto Tsuiji
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Vorasuk Shotelersuk
- Department of Pediatrics, Center of Excellence for Medical Genomics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Masashi Mizokami
- Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Toyama, Tokyo,Japan
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- *Correspondence: Saeideh Ashouri, ; Katsushi Tokunaga,
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10
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MA, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byun J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. Corrigendum to 'An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs' [J Hepatol 2021;75(3):572-581]. J Hepatol 2022; 76:489. [PMID: 34895949 PMCID: PMC8935376 DOI: 10.1016/j.jhep.2021.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Heather J. Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J. Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan,Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan,Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China,Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D. Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J. Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy,Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E. Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L. Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N. Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M. Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy,European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A. Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada,Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - George F. Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom,Corresponding author. Address: Academic Department of Medical Genetics, University of Cambridge, Box 238, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, United Kingdom.
| | - Canadian PBC ConsortiumSiminovitchKatherine A.252627HirschfieldGideon M.28MasonAndrew29VincentCatherine30XieGang31ZhangJinyi32Departments of Medicine, Immunology and Medical Sciences, University of Toronto, CanadaMount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute, CanadaToronto General Research Institute, Toronto, Ontario, CanadaToronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, CanadaDept of Medicine, University of Alberta, Edmonton, Alberta, CanadaUniversite de Montreal Hospital Centre, Saint-Luc Hospital, Montreal, Quebec, CanadaLunenfeld Tanenbaum Research Institute, Toronto, CanadaLunenfeld Tanenbaum Research Institute, Toronto, Canada
| | - Chinese PBC ConsortiumTangRuqi33MaXiong33LiZhiqiang3435ShiYongyong3435Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, ChinaBio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, ChinaAffiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, China
| | - Italian PBC Study GroupAffrontiAndrea36AlmasioPiero L.37AlvaroDomenico38AndreonePietro39AndriulliAngelo40AzzaroliFrancesco41BattezzatiPier Maria42BenedettiAntonio43BragazziMaria Consiglia44BrunettoMaurizia45BrunoSavino46CalvarusoVincenza47CardinaleVincenzo48CasellaGiovanni49CazzagonNora50CiaccioAntonio51CocoBarbara52ColliAgostino53ColloredoGuido54ColomboMassimo55ColomboSilvia56CristoferiLaura57CursaroCarmela58CrocèLory Saveria59CrosignaniAndrea60D’AmatoDaphne61DonatoFrancesca62EliaGianfranco63FabrisLuca64FagiuoliStefano65FerrariCarlo66FloreaniAnnarosa67GalliAndrea68GianniniEdoardo69GrattaglianoIgnazio70LamperticoPietro71LleoAna72MalinvernoFederica73MancusoClara74MarraFabio75MarzioniMarco76MassironiSara77MattaliaAlberto78MieleLuca79MilaniChiara80MoriniLorenzo81MoriscoFilomena82MuratoriLuigi83MuratoriPaolo84NiroGrazia A.85O’DonnellSarah86PicciottoAntonio87PortincasaPiero88RigamontiCristina89RoncaVincenzo90RosinaFloriano91SpinziGiancarlo92StrazzaboscoMario93TarocchiMirko94TiribelliClaudio95ToniuttoPierluigi96ValentiLuca97VinciMaria98ZuinMassimo99Azienda Ospedaliera Ospedali Riuniti Villa Sofia-Cervello, Palermo, ItalyGastroenterology & Hepatology Unit, Di.Bi.M.I.S., University of Palermo, Palermo, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, University Sapienza of Rome; Eleonora Lorillard Spencer-Cenci Foundation, Rome, ItalyDepartment of Medical and Surgical Sciences, Bologna University, Bologna, ItalyIRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, ItalyDepartment of Medical and Surgical Sciences (DIMEC) University of Bologna, Bologna, ItalySan Paolo Hospital Medical School, Università di Milano, Milan, ItalyUniversitàPolitecnica delle Marche, Ancona, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Polo Pontino, University Sapienza of Rome, Rome, ItalyAzienda Ospedaliera Universitaria Pisana, Pisa, ItalyDepartment of Internal Medicine, Ospedale Fatebene Fratelli e Oftalmico, Milan, ItalySezione di Gastroenterologia e Epatologia, Dipartimento Biomedico di Medicina Interna e Specialistica (Di.Bi.M.I.S.) University of Palermo, Palermo, ItalyDepartment of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Viale dell'Università37, 00185, Rome, ItalyMedical Department, Desio Hospital, Desio, ItalyDepartment of Surgery, Oncology and Gastroenterology, University of Padua, Padova, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyAzienda Ospedaliera Universitaria Pisana, Pisa, ItalyDepartment of Internal Medicine, AO Provincia di Lecco, Lecco, ItalyDepartment of Internal Medicine, San Pietro Hospital, Bergamo, Ponte San Pietro, ItalyHumanitas Clinical and Research Center, IRCCS, Rozzano, ItalyTreviglio Hospital, Treviglio, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyHepatology Unit, Department of Medical and Surgical Sciences, University Hospital of Bologna, ItalyUniversity of Trieste, & Fondazione Italiana Fegato (FIF) Trieste, ItalySan Paolo Hospital Medical School, Universitàdi Milano, Milan, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyFondazione IRCCS Ca’ Granda, Ospedale Maggiore Policlinico, Milan, ItalyAzienda Ospedaliero-Universitaria di Parma, Parma, ItalyUniversity of Padova, Padova, ItalyGastroenterologia Epatologia e Trapiantologia, Papa Giovanni XXIII Hospital, Bergamo, ItalyAzienda Ospedaliero-Universitaria di Parma, Parma, ItalyDepartment. of Surgical, Oncological and Gastroenterological Sciences, University of Padova, Padova, ItalyUniversity of Florence, Florence, ItalyGastroenterology Unit, Department Internal Medicine, Policlinico San Martino, University of Genoa, Genoa, ItalyItalian College of General Practicioners, ASL Bari, ItalyDivision of Gastroenterology and Hepatology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, ItalyDepartment of Biomedical Sciences, Humanitas University, Division of Internal Medicine and Hepatology, Department of Gastroenterology, Humanitas Clinical and Research Center IRCCS, Via A. Manzoni 56, 20089 Rozzano (MI), ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyUniversity of Florence, Florence, ItalyUniversità Politecnica delle Marche, Ancona, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalySanta Croce Carle Hospital, Cuneo, ItalyInternal Medicine, Gastroenterology and Liver Unit, A. Gemelli Polyclinic, Sacro Cuore Catholic University, 20123 Rome, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyMagenta Hospital, Magenta, ItalyUniversity of Naples, Federico II, Naples, ItalyDepartment of Clinical Medicine, University of Bologna, Bologna, ItalyDepartment of Clinical Medicine, University of Bologna, Bologna, ItalyIRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyUniversity of Genoa, Genoa, ItalyDepartment of Interdisciplinary Medicine, University Medical School, Bari, ItalyDepartment of Translational Medicine, Universitàdel Piemonte Orientale UPO, 28100 Novara, ItalyDivision of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, ItalyDivision of Gastroenterology & Hepatology, Center for Predictive Medicine, Gradenigo Hospital, Turin, ItalyAzienda Ospedaliera Valduce, Como, ItalyYale University, New Haven, Connecticut, USAUniversity of Florence, Florence, ItalyUniversity of Trieste, & Fondazione Italiana Fegato (FIF) Trieste, ItalyUniversity of Udine, Udine, ItalyInternal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Policlinico Milano, Department of Pathophysiology and Transplantation, Universitàdegli Studi di Milano, Milan, ItalyOspedale Niguarda, Milan, ItalySan Paolo Hospital Medical School, Università di Milano, Milan, Italy
| | - Japan-PBC-GWAS ConsortiumNakamuraHitomi100AbiruSeigo100NagaokaShinya100KomoriAtsumasa100YatsuhashiHiroshi100IshibashiHiromi100ItoMasahiro100MigitaKiyoshi101OhiraHiromasa101KatsushimaShinji102NaganumaAtsushi102SugiKazuhiro102KomatsuTatsuji102MannamiTomohiko102MatsushitaKouki102YoshizawaKaname102MakitaFujio102NikamiToshiki102NishimuraHideo102KounoHiroshi102KounoHirotaka102OtaHajime102KomuraTakuya102NakamuraYoko102ShimadaMasaaki102HirashimaNoboru102KomedaToshiki102ArioKeisuke102NakamutaMakoto102YamashitaTsutomu102FurutaKiyoshi102KikuchiMasahiro102NaeshiroNoriaki102TakahashiHironao102ManoYutaka102TsunematsuSeiji102YabuuchiIwao102ShimadaYusuke102YamauchiKazuhiko102SugimotoRie102SakaiHironori102MitaEiji102KodaMasaharu102TsurutaSatoru102KamitsukasaHiroshi102SatoTakeaki102MasakiNaohiko102KobataTatsuro102FukushimaNobuyoshi102OharaYukio102MuroToyokichi102TakesakiEiichi102TakakiHitoshi102YamamotoTetsuo102KatoMichio102NagaokiYuko102HayashiShigeki102IshidaJinya102WatanabeYukio102KobayashiMasakazu102KogaMichiaki102SaoshiroTakeo102YaguraMichiyasu102HirataKeisuke102TanakaAtsushu103TakikawaHajime103ZeniyaMikio104AbeMasanori105OnjiMorikazu105KanekoShuichi106HondaMasao106AraiKuniaki106Arinaga-HinoTeruko107HashimotoEtsuko108TaniaiMakiko108UmemuraTakeji109JoshitaSatoru109NakaoKazuhiko110IchikawaTatsuki110ShibataHidetaka110YamagiwaSatoshi111SeikeMasataka112HondaKoichi112SakisakaShotaro113TakeyamaYasuaki113HaradaMasaru114SenjuMichio114YokosukaOsamu115KandaTatsuo115UenoYoshiyuki116KikuchiKentaro117EbinumaHirotoshi118HimotoTakashi119YasunamiMichio120MurataKazumoto121MizokamiMasashi121KawataKazuhito122ShimodaShinji123MiyakeYasuhiro124TakakiAkinobu124YamamotoKazuhide124HiranoKatsuji125IchidaTakafumi125IdoAkio126TsubouchiHirohito126ChayamaKazuaki127HaradaKenichi128NakanumaYasuni128MaeharaYoshihiko129TaketomiAkinobu129ShirabeKen129SoejimaYuji129MoriAkira130YagiShintaro130UemotoShinji130HEgawa131TanakaTomohiro132YamashikiNoriyo132TamuraSumito133SugawaraYasuhiro133KokudoNorihiro133Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, JapanDepartment of Gastroenterology and Rheumatic Diseases, Fukushima Medical University of Medicine, Fukushima, JapanHeadquaters of PBC Research in the NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Nagasaki, JapanDepartment of Medicine, Teikyo University School of Medicine, Tokyo, JapanDepartment of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, JapanDepartment of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, JapanDepartment of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, JapanDivision of Gastroenterology, Department of Medicine, Kurume University School of Medicine, Kurume, JapanDepartment of Medicine and Gastroenterology, Tokyo Women’s Medical University, Tokyo, JapanDepartment of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, Matsumoto, JapanDepartment of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, JapanDivision of Gastroenterology and Hepatology,Niigata University Graduate School of Medical and Dental Sciences, Niigata, JapanFaculty of Medicine, Oita University, Oita, JapanDepartment of Gastroenterology and Medicine, Fukuoka University School of Medicine, Fukuoka, JapanThe Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, JapanDepartment of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, JapanDepartment of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, JapanDepartment of Internal Medicine, Teikyo University Mizonokuchi Hospital, Kawasaki, JapanDivision of Gastroenterology and Hepatology, Department of Internal Medicine, Keio Graduate School of Medicine, Tokyo, JapanDepartment of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, JapanDepartment of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasakin, JapanThe Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, JapanHepatology Division, Department of Internal Medicine II, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka JapanDepartment of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, JapanDepartment of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, JapanDepartment of Gastroenterology and Hepatology, Juntendo University Shizuoka Hospital, Shizuoka, JapanDepartment of Digestive and Lifestyle–Related Disease, Kagoshima University Graduate School of Medical and Dental Science, Kagoshima, JapanDepartment of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, JapanDepartment of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, JapanDepartment of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, JapanDivision of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, JapanDepartment of Surgery, Tokyo Women’s Medical University, Tokyo, JapanOrgan Transplantation Service, The University of Tokyo, Tokyo, JapanHepatobiliary and Pancreatic Surgery Division and Artificial Organ and Transplantation Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Japan
| | - US PBC ConsortiumJuranBrian D.134AtkinsonElizabeth J.135CheungAngela136de AndradeMariza137LazaridisKonstantinos N.138ChalasaniNaga139LuketicVel140OdinJoseph141ChopraKapil142BarasAris143HorowitzJulie143AbecasisGoncalo143CantorMichael143CoppolaGiovanni143EconomidesAris143LottaLuca A.143OvertonJohn D.143ReidJeffrey G.143ShuldinerAlan143BeechertChristina143ForsytheCaitlin143FullerErin D.143GuZhenhua143LattariMichael143LopezAlexander143OvertonJohn D.143SchleicherThomas D.143PadillaMaria Sotiropoulos143ToledoKarina143WidomLouis143WolfSarah E.143PradhanManasi143ManoochehriKia143UlloaRicardo H.143BaiXiaodong143BalasubramanianSuganthi143BarnardLeland143BlumenfeldAndrew143EomGisu143HabeggerLukas143HawesAlicia143KhalidShareef143ReidJeffrey G.143MaxwellEvan K.143SalernoWilliam143StaplesJeffrey C.143JonesMarcus B.143MitnaulLyndon J.143Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesDivision of Biomedical Statistics and Informatics Mayo Clinic, Rochester, Minnesota, United StatesDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesDivision of Biomedical Statistics and Informatics Mayo Clinic, Rochester, Minnesota, United StatesDivision of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United StatesIndiana University, Indiana, United StatesVirginia Commonwealth University, Virginia, United StatesIcahn School of Medicine, Mount Sinai, New York, United StatesUniversity of Pittsburgh, United StatesRegeneron, United States
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11
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Cordell HJ, Fryett JJ, Ueno K, Darlay R, Aiba Y, Hitomi Y, Kawashima M, Nishida N, Khor SS, Gervais O, Kawai Y, Nagasaki M, Tokunaga K, Tang R, Shi Y, Li Z, Juran BD, Atkinson EJ, Gerussi A, Carbone M, Asselta R, Cheung A, de Andrade M, Baras A, Horowitz J, Ferreira MAR, Sun D, Jones DE, Flack S, Spicer A, Mulcahy VL, Byan J, Han Y, Sandford RN, Lazaridis KN, Amos CI, Hirschfield GM, Seldin MF, Invernizzi P, Siminovitch KA, Ma X, Nakamura M, Mells GF. An international genome-wide meta-analysis of primary biliary cholangitis: Novel risk loci and candidate drugs. J Hepatol 2021; 75:572-581. [PMID: 34033851 PMCID: PMC8811537 DOI: 10.1016/j.jhep.2021.04.055] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 03/11/2021] [Accepted: 04/07/2021] [Indexed: 01/15/2023]
Abstract
BACKGROUNDS & AIMS Primary biliary cholangitis (PBC) is a chronic liver disease in which autoimmune destruction of the small intrahepatic bile ducts eventually leads to cirrhosis. Many patients have inadequate response to licensed medications, motivating the search for novel therapies. Previous genome-wide association studies (GWAS) and meta-analyses (GWMA) of PBC have identified numerous risk loci for this condition, providing insight into its aetiology. We undertook the largest GWMA of PBC to date, aiming to identify additional risk loci and prioritise candidate genes for in silico drug efficacy screening. METHODS We combined new and existing genotype data for 10,516 cases and 20,772 controls from 5 European and 2 East Asian cohorts. RESULTS We identified 56 genome-wide significant loci (20 novel) including 46 in European, 13 in Asian, and 41 in combined cohorts; and a 57th genome-wide significant locus (also novel) in conditional analysis of the European cohorts. Candidate genes at newly identified loci include FCRL3, INAVA, PRDM1, IRF7, CCR6, CD226, and IL12RB1, which each play key roles in immunity. Pathway analysis reiterated the likely importance of pattern recognition receptor and TNF signalling, JAK-STAT signalling, and differentiation of T helper (TH)1 and TH17 cells in the pathogenesis of this disease. Drug efficacy screening identified several medications predicted to be therapeutic in PBC, some of which are well-established in the treatment of other autoimmune disorders. CONCLUSIONS This study has identified additional risk loci for PBC, provided a hierarchy of agents that could be trialled in this condition, and emphasised the value of genetic and genomic approaches to drug discovery in complex disorders. LAY SUMMARY Primary biliary cholangitis (PBC) is a chronic liver disease that eventually leads to cirrhosis. In this study, we analysed genetic information from 10,516 people with PBC and 20,772 healthy individuals recruited in Canada, China, Italy, Japan, the UK, or the USA. We identified several genetic regions associated with PBC. Each of these regions contains several genes. For each region, we used diverse sources of evidence to help us choose the gene most likely to be involved in causing PBC. We used these 'candidate genes' to help us identify medications that are currently used for treatment of other conditions, which might also be useful for treatment of PBC.
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Affiliation(s)
- Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - James J Fryett
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Rebecca Darlay
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Brian D Juran
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Angela Cheung
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - Julie Horowitz
- Regeneron Genetics Center, Tarrytown, New York, United States
| | | | - Dylan Sun
- Regeneron Genetics Center, Tarrytown, New York, United States
| | - David E Jones
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Steven Flack
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ann Spicer
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Victoria L Mulcahy
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Jinyoung Byan
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Richard N Sandford
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, United States
| | - Gideon M Hirschfield
- Toronto Centre for Liver Disease, Division of Gastroenterology and Hepatology, University of Toronto, Toronto, Ontario, Canada
| | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Xiong Ma
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan; Department of Hepatology, Nagasaki Graduate School of Biomedical Sciences, Japan
| | - George F Mells
- Academic Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom.
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12
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Oku T, Kaneko Y, Ishii R, Hitomi Y, Tsuiji M, Toyoshima S, Tsuji T. Coronin-1 is phosphorylated at Thr-412 by protein kinase Cα in human phagocytic cells. Biochem Biophys Rep 2021; 27:101041. [PMID: 34189278 PMCID: PMC8220002 DOI: 10.1016/j.bbrep.2021.101041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/17/2021] [Accepted: 05/31/2021] [Indexed: 11/25/2022] Open
Abstract
Coronin-1, a hematopoietic cell-specific actin-binding protein, is thought to be involved in the phagocytic process through its interaction with actin filaments. The dissociation of coronin-1 from phagosomes after its transient accumulation on the phagosome surface is associated with lysosomal fusion. We previously reported that 1) coronin-1 is phosphorylated by protein kinase C (PKC), 2) coronin-1 has two phosphorylation sites, Ser-2 and Thr-412, and 3) Thr-412 of coronin-1 is phosphorylated during phagocytosis. In this study, we examined which PKC isoform is responsible for the phosphorylation of coronin-1 at Thr-412 by using isotype-specific PKC inhibitors and small interfering RNAs (siRNAs). Thr-412 phosphorylation of coronin-1 was suppressed by Gö6976, an inhibitor of PKCα and PKCβI. This phosphorylation was attenuated by siRNA for PKCα, but not by siRNA for PKCβ. Furthermore, Thr-412 of coronin-1 was phosphorylated by recombinant PKCα in vitro, but not by recombinant PKCβ. We next examined the effects of Gö6976 on the intracellular distribution of coronin-1 in HL60 cells during phagocytosis. The confocal fluorescence microscopic observation showed that coronin-1 was not dissociated from phagosomes in Gö6976-treated cells. These results indicate that phosphorylation of coronin-1 at Thr-412 by PKCα regulates intracellular distribution during phagocytosis. Phosphorylation of coronin-1 at Thr-412 is suppressed by PKCα/β inhibitor. PKCα not PKCβ phosphorylates coronin-1 at Thr-412 in vitro. Dissociation of coronin-1 from phagosome is regulated by PKCα. Phosphorylation of coronin-1 at Thr-412 may trigger phagosome maturation.
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Affiliation(s)
- Teruaki Oku
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
- Corresponding author.
| | - Yutaka Kaneko
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Rie Ishii
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Yuki Hitomi
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Makoto Tsuiji
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
| | - Satoshi Toyoshima
- Japan Pharmacists Education Center, 1-9-13 Akasaka, Minato-ku, Tokyo, 107-0052, Japan
| | - Tsutomu Tsuji
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
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Asselta R, Paraboschi EM, Gerussi A, Cordell HJ, Mells GF, Sandford RN, Jones DE, Nakamura M, Ueno K, Hitomi Y, Kawashima M, Nishida N, Tokunaga K, Nagasaki M, Tanaka A, Tang R, Li Z, Shi Y, Liu X, Xiong M, Hirschfield G, Siminovitch KA, Carbone M, Cardamone G, Duga S, Gershwin ME, Seldin MF, Invernizzi P. X Chromosome Contribution to the Genetic Architecture of Primary Biliary Cholangitis. Gastroenterology 2021; 160:2483-2495.e26. [PMID: 33675743 PMCID: PMC8169555 DOI: 10.1053/j.gastro.2021.02.061] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 02/15/2021] [Accepted: 02/25/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Genome-wide association studies in primary biliary cholangitis (PBC) have failed to find X chromosome (chrX) variants associated with the disease. Here, we specifically explore the chrX contribution to PBC, a sexually dimorphic complex autoimmune disease. METHODS We performed a chrX-wide association study, including genotype data from 5 genome-wide association studies (from Italy, United Kingdom, Canada, China, and Japan; 5244 case patients and 11,875 control individuals). RESULTS Single-marker association analyses found approximately 100 loci displaying P < 5 × 10-4, with the most significant being a signal within the OTUD5 gene (rs3027490; P = 4.80 × 10-6; odds ratio [OR], 1.39; 95% confidence interval [CI], 1.028-1.88; Japanese cohort). Although the transethnic meta-analysis evidenced only a suggestive signal (rs2239452, mapping within the PIM2 gene; OR, 1.17; 95% CI, 1.09-1.26; P = 9.93 × 10-8), the population-specific meta-analysis showed a genome-wide significant locus in East Asian individuals pointing to the same region (rs7059064, mapping within the GRIPAP1 gene; P = 6.2 × 10-9; OR, 1.33; 95% CI, 1.21-1.46). Indeed, rs7059064 tags a unique linkage disequilibrium block including 7 genes: TIMM17B, PQBP1, PIM2, SLC35A2, OTUD5, KCND1, and GRIPAP1, as well as a superenhancer (GH0XJ048933 within OTUD5) targeting all these genes. GH0XJ048933 is also predicted to target FOXP3, the main T-regulatory cell lineage specification factor. Consistently, OTUD5 and FOXP3 RNA levels were up-regulated in PBC case patients (1.75- and 1.64-fold, respectively). CONCLUSIONS This work represents the first comprehensive study, to our knowledge, of the chrX contribution to the genetics of an autoimmune liver disease and shows a novel PBC-related genome-wide significant locus.
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Affiliation(s)
- Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Elvezia M Paraboschi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Alessio Gerussi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, United Kingdom
| | - George F Mells
- Academic Department of Medical Genetics, Cambridge University, Cambridge, United Kingdom
| | - Richard N Sandford
- Academic Department of Medical Genetics, Cambridge University, Cambridge, United Kingdom
| | - David E Jones
- Faculty of Medical Sciences, Newcastle University, Newcastle, United Kingdom
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Nagasaki, Japan; Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan; Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan; Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Ruqi Tang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Zhiqiang Li
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yongyong Shi
- Affiliated Hospital of Qingdao University and Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, Institute of Life Sciences, Southeast University, Nanjing, Jiangsu, China
| | - Ma Xiong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Gideon Hirschfield
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada; Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Katherine A Siminovitch
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada; Mount Sinai Hospital, Lunenfeld Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada; Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Marco Carbone
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy
| | - Giulia Cardamone
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy; IRCCS Humanitas Research Hospital, Milan, Italy
| | | | | | - Pietro Invernizzi
- Division of Gastroenterology and Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; European Reference Network on Hepatological Diseases, San Gerardo Hospital, Monza, Italy.
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14
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Hitomi Y, Aiba Y, Kawai Y, Kojima K, Ueno K, Nishida N, Kawashima M, Gervais O, Khor SS, Nagasaki M, Tokunaga K, Nakamura M, Tsuiji M. rs1944919 on chromosome 11q23.1 and its effector genes COLCA1/COLCA2 confer susceptibility to primary biliary cholangitis. Sci Rep 2021; 11:4557. [PMID: 33633225 PMCID: PMC7907150 DOI: 10.1038/s41598-021-84042-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/11/2020] [Accepted: 02/11/2021] [Indexed: 01/12/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which intrahepatic bile ducts are destroyed by an autoimmune reaction. Our previous genome-wide association study (GWAS) identified chromosome 11q23.1 as a susceptibility gene locus for PBC in the Japanese population. Here, high-density association mapping based on single nucleotide polymorphism (SNP) imputation and in silico/in vitro functional analyses identified rs1944919 as the primary functional variant. Expression-quantitative trait loci analyses showed that the PBC susceptibility allele of rs1944919 was significantly associated with increased COLCA1/COLCA2 expression levels. Additionally, the effects of rs1944919 on COLCA1/COLCA2 expression levels were confirmed using genotype knock-in versions of cell lines constructed using the CRISPR/Cas9 system and differed between rs1944919-G/G clones and -T/T clones. To our knowledge, this is the first study to demonstrate the contribution of COLCA1/COLCA2 to PBC susceptibility.
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Affiliation(s)
- Yuki Hitomi
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan.,The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | | | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| | - Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- 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, National Center for Global Health and Medicine, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan.,Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Makoto Tsuiji
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan.
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15
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Alborzian Deh Sheikh A, Gomaa S, Li X, Routledge M, Saigoh K, Numoto N, Angata T, Hitomi Y, Takematsu H, Tsuiji M, Ito N, Kusunoki S, Tsubata T. A Guillain-Barré syndrome-associated SIGLEC10 rare variant impairs its recognition of gangliosides. J Autoimmun 2020; 116:102571. [PMID: 33223341 DOI: 10.1016/j.jaut.2020.102571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 01/05/2023]
Abstract
Guillain-Barré syndrome (GBS), including its variant Miller Fisher syndrome (MFS), is an acute peripheral neuropathy that involves autoimmune mechanisms leading to the production of autoantibodies to gangliosides; sialic acid-containing glycosphingolipids. Although association with various genetic polymorphisms in the major histocompatibility complex (MHC) is shown in other autoimmune diseases, GBS is an exception, showing no such link. No significant association was found by genome wide association studies, suggesting that GBS is not associated with common variants. To address the involvement of rare variants in GBS, we analyzed Siglec-10, a sialic acid-recognizing inhibitory receptor expressed on B cells. Here we demonstrate that two rare variants encoding R47Q and A108V substitutions in the ligand-binding domain are significantly accumulated in patients with GBS. Because of strong linkage disequilibrium, there was no patient carrying only one of them. Recombinant Siglec-10 protein containing R47Q but not A108V shows impaired binding to gangliosides. Homology modeling revealed that the R47Q substitution causes marked alteration in the ligand-binding site. Thus, GBS is associated with a rare variant of the SIGLEC10 gene that impairs ligand binding of Siglec-10. Because Siglec-10 regulates antibody production to sialylated antigens, our finding suggests that Siglec-10 regulates development of GBS by suppressing antibody production to gangliosides, with defects in its function predisposing to disease.
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Affiliation(s)
- Amin Alborzian Deh Sheikh
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Soha Gomaa
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan; Division of Immunology and Biotechnology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xuexin Li
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Matthew Routledge
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazumasa Saigoh
- Department of Neurology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Nobutaka Numoto
- Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takashi Angata
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yuki Hitomi
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Hiromu Takematsu
- Faculty of Medical Technology, Fujita Health University, Toyoake, Aichi, Japan
| | - Makoto Tsuiji
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Nobutoshi Ito
- Department of Structural Biology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Susumu Kusunoki
- Department of Neurology, Faculty of Medicine, Kindai University, Osaka, Japan
| | - Takeshi Tsubata
- Department of Immunology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
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16
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Jia X, Yamamura T, Gbadegesin R, McNulty MT, Song K, Nagano C, Hitomi Y, Lee D, Aiba Y, Khor SS, Ueno K, Kawai Y, Nagasaki M, Noiri E, Horinouchi T, Kaito H, Hamada R, Okamoto T, Kamei K, Kaku Y, Fujimaru R, Tanaka R, Shima Y, Baek J, Kang HG, Ha IS, Han KH, Yang EM, Abeyagunawardena A, Lane B, Chryst-Stangl M, Esezobor C, Solarin A, Dossier C, Deschênes G, Vivarelli M, Debiec H, Ishikura K, Matsuo M, Nozu K, Ronco P, Cheong HI, Sampson MG, Tokunaga K, Iijima K. Common risk variants in NPHS1 and TNFSF15 are associated with childhood steroid-sensitive nephrotic syndrome. Kidney Int 2020; 98:1308-1322. [PMID: 32554042 DOI: 10.1016/j.kint.2020.05.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 04/23/2020] [Accepted: 05/01/2020] [Indexed: 12/16/2022]
Abstract
To understand the genetics of steroid-sensitive nephrotic syndrome (SSNS), we conducted a genome-wide association study in 987 childhood SSNS patients and 3,206 healthy controls with Japanese ancestry. Beyond known associations in the HLA-DR/DQ region, common variants in NPHS1-KIRREL2 (rs56117924, P=4.94E-20, odds ratio (OR) =1.90) and TNFSF15 (rs6478109, P=2.54E-8, OR=0.72) regions achieved genome-wide significance and were replicated in Korean, South Asian and African populations. Trans-ethnic meta-analyses including Japanese, Korean, South Asian, African, European, Hispanic and Maghrebian populations confirmed the significant associations of variants in NPHS1-KIRREL2 (Pmeta=6.71E-28, OR=1.88) and TNFSF15 (Pmeta=5.40E-11, OR=1.33) loci. Analysis of the NPHS1 risk alleles with glomerular NPHS1 mRNA expression from the same person revealed allele specific expression with significantly lower expression of the transcript derived from the risk haplotype (Wilcox test p=9.3E-4). Because rare pathogenic variants in NPHS1 cause congenital nephrotic syndrome of the Finnish type (CNSF), the present study provides further evidence that variation along the allele frequency spectrum in the same gene can cause or contribute to both a rare monogenic disease (CNSF) and a more complex, polygenic disease (SSNS).
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Affiliation(s)
- Xiaoyuan Jia
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomohiko Yamamura
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Rasheed Gbadegesin
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Michelle T McNulty
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA
| | - Kyuyong Song
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - China Nagano
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Dongwon Lee
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA; Harvard Medical School, Boston, Massachussetts, USA
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuko Ueno
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eisei Noiri
- Department of Hemodialysis and Apheresis, The University of Tokyo Hospital, Tokyo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Hiroshi Kaito
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan; Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Riku Hamada
- Department of Nephrology, Tokyo Metropolitan Children's Medical Center, Tokyo, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Yoshitsugu Kaku
- Department of Nephrology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Rika Fujimaru
- Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | | | - Jiwon Baek
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Gyung Kang
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Il-Soo Ha
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Kyoung Hee Han
- Department of Pediatrics, Jeju National University School of Medicine, Jeju, Korea
| | - Eun Mi Yang
- Department of Pediatrics, Chonnam National University Children's Hospital, Gwangju, Korea
| | | | - Asiri Abeyagunawardena
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Brandon Lane
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Megan Chryst-Stangl
- Department of Pediatrics, Division of Nephrology, Duke University Medical Center, Durham, North Carolina, USA
| | - Christopher Esezobor
- Department of Paediatrics, College of Medicine, University of Lagos, Lagos, Nigeria
| | - Adaobi Solarin
- Department of Pediatrics, Lagos State University Teaching Hospital, Ikeja, Nigeria
| | | | - Claire Dossier
- Department of Paediatric Nephrology, Public Assistance Hospital of Paris, Robert-Debré Hospital, Paris, France
| | - Georges Deschênes
- Center of Research on Inflammation, Institut National de la Santé et de la Recherche Médicale UMR 1149, University Sorbonne-Paris, Paris, France
| | | | - Marina Vivarelli
- Division of Nephrology and Dialysis, Bambino Gesù Children's Hospital and Research Institute, Rome, Italy
| | - Hanna Debiec
- Sorbonne University, INSERM UMR_S1155, and Nephrology Day Hospital, Department of Nephrology, Hôpital Tenon, Paris France
| | - Kenji Ishikura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Masafumi Matsuo
- Research Center for Locomotion Biology, Kobe Gakuin University, Kobe, Japan; KNC Department of Nucleic Acid Drug Discovery, Faculty of Rehabilitation, Kobe Gakuin University, Kobe, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Pierre Ronco
- Sorbonne University, INSERM UMR_S1155, and Nephrology Day Hospital, Department of Nephrology, Hôpital Tenon, Paris France
| | - Hae Il Cheong
- Department of Pediatrics, Seoul National University Children's Hospital, Seoul, Korea
| | - Matthew G Sampson
- Department of Medicine-Nephrology, Boston Children's Hospital, Boston, Massachussetts, USA; Medical and Population Genetics, Broad Institute, Cambridge, Massachussetts, USA; Harvard Medical School, Boston, Massachussetts, USA
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan.
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17
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Ueno K, Aiba Y, Hitomi Y, Shimoda S, Nakamura H, Gervais O, Kawai Y, Kawashima M, Nishida N, Kohn SS, Kojima K, Katsushima S, Naganuma A, Sugi K, Komatsu T, Mannami T, Matsushita K, Yoshizawa K, Makita F, Nikami T, Nishimura H, Kouno H, Kouno H, Ohta H, Komura T, Tsuruta S, Yamauchi K, Kobata T, Kitasato A, Kuroki T, Abiru S, Nagaoka S, Komori A, Yatsuhashi H, Migita K, Ohira H, Tanaka A, Takikawa H, Nagasaki M, Tokunaga K, Nakamura M. Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis. Hepatol Commun 2020; 4:724-738. [PMID: 32363322 PMCID: PMC7193132 DOI: 10.1002/hep4.1497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/16/2019] [Accepted: 12/21/2019] [Indexed: 12/18/2022] Open
Abstract
Genome‐wide association studies (GWASs) in European and East Asian populations have identified more than 40 disease‐susceptibility genes in primary biliary cholangitis (PBC). The aim of this study is to computationally identify disease pathways, upstream regulators, and therapeutic targets in PBC through integrated GWAS and messenger RNA (mRNA) microarray analysis. Disease pathways and upstream regulators were analyzed with ingenuity pathway analysis in data set 1 for GWASs (1,920 patients with PBC and 1,770 controls), which included 261 annotated genes derived from 6,760 single‐nucleotide polymorphisms (P < 0.00001), and data set 2 for mRNA microarray analysis of liver biopsy specimens (36 patients with PBC and 5 normal controls), which included 1,574 genes with fold change >2 versus controls (P < 0.05). Hierarchical cluster analysis and categorization of cell type–specific genes were performed for data set 2. There were 27 genes, 10 pathways, and 149 upstream regulators that overlapped between data sets 1 and 2. All 10 pathways were immune‐related. The most significant common upstream regulators associated with PBC disease susceptibility identified were interferon‐gamma (IFNG) and CD40 ligand (CD40L). Hierarchical cluster analysis of data set 2 revealed two distinct groups of patients with PBC by disease activity. The most significant upstream regulators associated with disease activity were IFNG and CD40L. Several molecules expressed in B cells, T cells, Kupffer cells, and natural killer–like cells were identified as potential therapeutic targets in PBC with reference to a recently reported list of cell type–specific gene expression in the liver. Conclusion: Our integrated analysis using GWAS and mRNA microarray data sets predicted that IFNG and CD40L are the central upstream regulators in both disease susceptibility and activity of PBC and identified potential downstream therapeutic targets.
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Affiliation(s)
- Kazuko Ueno
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Yoshihiro Aiba
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan
| | - Yuki Hitomi
- Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan.,Department of Microbiology Hoshi University School of Pharmacy and Pharmaceutical Sciences Tokyo Japan
| | - Shinji Shimoda
- Department of Medicine and Biosystemic Science Kyushu University Graduate School of Medical Sciences Fukuoka Japan
| | - Hitomi Nakamura
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan
| | - Olivier Gervais
- Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto Japan
| | - Yosuke Kawai
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | | | - Nao Nishida
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Seik-Soon Kohn
- Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Kaname Kojima
- Tohoku Medical Megabank Organization Tohoku University Sendai Japan
| | - Shinji Katsushima
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Atsushi Naganuma
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Kazuhiro Sugi
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Tatsuji Komatsu
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Tomohiko Mannami
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Kouki Matsushita
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Kaname Yoshizawa
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Fujio Makita
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Toshiki Nikami
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Hideo Nishimura
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Hiroshi Kouno
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Hirotaka Kouno
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Hajime Ohta
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Takuya Komura
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Satoru Tsuruta
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Kazuhiko Yamauchi
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Tatsuro Kobata
- Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan
| | - Amane Kitasato
- Department of Surgery National Hospital Organization of Nagasaki Medical Center Omura Japan
| | - Tamotsu Kuroki
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan.,Department of Surgery National Hospital Organization of Nagasaki Medical Center Omura Japan.,Department of Hepatology Graduate School of Biomedical Sciences Nagasaki University Omura Japan
| | - Seigo Abiru
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan
| | - Shinya Nagaoka
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan
| | - Atsumasa Komori
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan.,Department of Hepatology Graduate School of Biomedical Sciences Nagasaki University Omura Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan.,Department of Hepatology Graduate School of Biomedical Sciences Nagasaki University Omura Japan
| | - Kiyoshi Migita
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan.,Department of Gastroenterology and Rheumatic Diseases Fukushima Medical University of Medicine Fukushima Japan
| | - Hiromasa Ohira
- Department of Gastroenterology and Rheumatic Diseases Fukushima Medical University of Medicine Fukushima Japan
| | - Atsushi Tanaka
- Department of Medicine Teikyo University School of Medicine Tokyo Japan
| | - Hajime Takikawa
- Department of Medicine Teikyo University School of Medicine Tokyo Japan
| | - Masao Nagasaki
- 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 National Center for Global Health and Medicine Tokyo Japan.,Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan
| | - Minoru Nakamura
- Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan.,Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan.,Department of Hepatology Graduate School of Biomedical Sciences Nagasaki University Omura Japan.,Headquarters of PBC-GWAS Consortium in Japan National Hospital Organization of Nagasaki Medical Center Graduate School of Biomedical Sciences Nagasaki University Omura Japan
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18
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Ohno O, Terasaki T, Sano T, Hitomi Y, Miyamoto J, Matsuno K. Inhibitory effects of biseokeaniamide A against lipopolysaccharide-induced signal transduction. Bioorg Med Chem Lett 2020; 30:127069. [PMID: 32173199 DOI: 10.1016/j.bmcl.2020.127069] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/22/2020] [Accepted: 02/27/2020] [Indexed: 12/16/2022]
Abstract
Lipopolysaccharides (LPS) are associated with various inflammatory diseases; therefore, the inhibition of LPS-induced nitric oxide (NO) production may have extensive therapeutic applications. We searched for inhibitors of NO production in the LPS-stimulated murine macrophage-like cell line RAW264.7 from MeOH extracts of marine organisms. The MeOH extract of the marine cyanobacterium Okeania sp., collected in Okinawa, Japan, showed inhibitory activity. Biseokeaniamide A was isolated from the MeOH extract by chromatographic separation. Biseokeaniamide A inhibited NO production without cytotoxicity. It reduced inducible nitric oxide synthase levels and suppressed the expression of IL-1β in LPS-stimulated RAW264.7 cells. Biseokeaniamide A did not inhibit IκBα degradation but inhibited IκBα expression. Thus, biseokeaniamide A, a naturally occurring lipopeptide, was identified as a selective inhibitor of LPS signal transduction.
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Affiliation(s)
- Osamu Ohno
- Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan.
| | - Takuro Terasaki
- Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Takuya Sano
- Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Yuki Hitomi
- Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Junichiro Miyamoto
- Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan
| | - Kenji Matsuno
- Department of Chemistry and Life Science, School of Advanced Engineering, Kogakuin University, 2665-1 Nakano, Hachioji, Tokyo 192-0015, Japan.
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19
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Nakatani K, Ueta M, Khor SS, Hitomi Y, Okudaira Y, Masuya A, Wada Y, Sotozono C, Kinoshita S, Inoko H, Tokunaga K. Identification of HLA-A*02:06:01 as the primary disease susceptibility HLA allele in cold medicine-related Stevens-Johnson syndrome with severe ocular complications by high-resolution NGS-based HLA typing. Sci Rep 2019; 9:16240. [PMID: 31700100 PMCID: PMC6838058 DOI: 10.1038/s41598-019-52619-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN) are life-threatening acute inflammatory vesiculobullous reactions of the skin and mucous membranes. These severe cutaneous drug reactions are known to be caused by inciting drugs and infectious agents. Previously, we have reported the association of HLA-A*02:06 and HLA-B*44:03 with cold medicine (CM)-related SJS/TEN with severe ocular complications (SOCs) in the Japanese population. However, the conventional HLA typing method (PCR-SSOP) sometimes has ambiguity in the final HLA allele determination. In this study, we performed HLA-disease association studies in CM-SJS/TEN with SOCs at 3- or 4-field level. 120 CM-SJS/TEN patients with SOCs and 817 Japanese healthy controls are HLA genotyped using the high-resolution next-generation sequencing (NGS)-based HLA typing of HLA class I genes, including HLA-A, HLA-B, and HLA-C. Among the alleles of HLA class I genes, HLA-A*02:06:01 was strongly associated with susceptibility to CM-SJS/TEN (p = 1.15 × 10−18, odds ratio = 5.46). Four other alleles (HLA-A*24:02:01, HLA-B*52:01:01, HLA-B*46:01:01, and HLA-C*12:02:02) also demonstrated significant associations. HLA haplotype analyses indicated that HLA-A*02:06:01 is primarily associated with susceptibility to CM-SJS/TEN with SOCs. Notably, there were no specific disease-causing rare variants among the high-risk HLA alleles. This study highlights the importance of higher resolution HLA typing in the study of disease susceptibility, which may help to elucidate the pathogenesis of CM-SJS/TEN with SOCs.
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Affiliation(s)
- Ken Nakatani
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mayumi Ueta
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | | | - Yuki Wada
- The Center of Medical Innovation and Translational Research, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shigeru Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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20
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Joo J, Omae Y, Hitomi Y, Park B, Shin HJ, Yoon KA, Sawai H, Tsuiji M, Hayashi T, Kong SY, Tokunaga K, Kim JY. The association of integration patterns of human papilloma virus and single nucleotide polymorphisms on immune- or DNA repair-related genes in cervical cancer patients. Sci Rep 2019; 9:13132. [PMID: 31511581 PMCID: PMC6739467 DOI: 10.1038/s41598-019-49523-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 08/24/2019] [Indexed: 11/24/2022] Open
Abstract
The present study investigated the association between single nucleotide polymorphisms (SNPs) in immune- or DNA repair-related genes and the integration pattern of human papillomavirus (HPV), a promising prognostic marker in cervical cancer. The HPV integration patterns of cervical cancer patients were determined by polymerase chain reaction and in situ hybridization, and categorized as episomal (group A), single-copy or multi-copy tandem repetition integrated (group B), and undetectable HPV types (group C). After sample and SNP quality control, 166,505 SNPs in 161 samples (38, 111, and 12 patients in groups A, B, and C, respectively) were examined. None of the SNPs reached genome-wide significance, and several candidate SNPs for future study were selected, including rs10999435 on chromosome 10q22, rs1322054 on chromosome 9q32-33, and rs10902171 on chromosome 11p15. Luciferase assay identified rs1322054 as the primary functional variant to regulate gene expression in immune cell. Further studies are needed to determine the genetic background of different integration patterns of HPV in cervical cancer patients.
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Affiliation(s)
- Jungnam Joo
- Biometrics Research Branch, National Cancer Center, Goyang, Korea
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Boram Park
- Biometrics Research Branch, National Cancer Center, Goyang, Korea
| | - Hye-Jin Shin
- Particle Therapy Research Branch, National Cancer Center, Goyang, Korea
| | - Kyong-Ah Yoon
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
- Center for Breast Cancer, National Cancer Center, Goyang, Korea
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Makoto Tsuiji
- Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Tomonori Hayashi
- Department of Radiobiology and Molecular Epidemiology, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Sun-Young Kong
- Translational Research Branch, National Cancer Center, Goyang, Korea
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Genome Medical Science Project (Toyama), National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Joo-Young Kim
- Particle Therapy Research Branch, National Cancer Center, Goyang, Korea.
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21
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Hitomi Y, Kawai Y, Ueta M, Khor SS, Nakatani K, Sotozono C, Kinoshita S, Nagasaki M, Tokunaga K. P066 Identification of susceptibility gene loci for cold medicine-related stevens-johnson syndrome with severe ocular complications by whole-genome resequencing. Hum Immunol 2019. [DOI: 10.1016/j.humimm.2019.07.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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Khor SS, Hitomi Y, Omae Y, Ogawa A, Tokunaga K. Discovery of the novel HLA-B allele, HLA-B*51:01:01:36 in a Japanese individual. HLA 2019; 94:445-447. [PMID: 31389158 DOI: 10.1111/tan.13658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 12/01/2022]
Abstract
HLA-B*51:01:01:36 differs from HLA-B*51:01:01:01 by one nucleotide difference at position -230(G>T) with no amino acid change.
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Affiliation(s)
- Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Ayumi Ogawa
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
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23
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Khor SS, Hitomi Y, Omae Y, Ishibashi Y, Tokunaga K. Detection of the novel HLA-A allele, HLA-A*02:01:01:58, in a Japanese individual. HLA 2019; 94:435-436. [PMID: 31389186 DOI: 10.1111/tan.13657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/04/2019] [Accepted: 08/05/2019] [Indexed: 11/30/2022]
Abstract
HLA-A*02:01:01:58 differs from HLA-A*02:01:01:01 by one nucleotide difference at position 2126(G>T) with no amino acid change.
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Affiliation(s)
- Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshimi Ishibashi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
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24
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Khor SS, Hitomi Y, Omae Y, Ishibashi Y, Tokunaga K. Identification of the novel HLA-DQB1 allele, HLA-DQB1*05:03:01:04, in a Japanese individual. HLA 2019; 94:466-468. [PMID: 31381265 DOI: 10.1111/tan.13654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 08/01/2019] [Accepted: 08/02/2019] [Indexed: 11/29/2022]
Abstract
HLA-DQB1*05:03:01:04 differs from HLA-DQB1*05:03:01:01 by one nucleotide difference at position 5075(A > G) with no amino acid change.
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Affiliation(s)
- Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Microbiology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, Tokyo, Japan
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshimi Ishibashi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
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25
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Watanabe Y, Naka I, Khor SS, Sawai H, Hitomi Y, Tokunaga K, Ohashi J. Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period. Sci Rep 2019; 9:8556. [PMID: 31209235 PMCID: PMC6572846 DOI: 10.1038/s41598-019-44473-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/17/2019] [Indexed: 01/06/2023] Open
Abstract
The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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26
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Hitomi Y, Ueno K, Kawai Y, Nishida N, Kojima K, Kawashima M, Aiba Y, Nakamura H, Kouno H, Kouno H, Ohta H, Sugi K, Nikami T, Yamashita T, Katsushima S, Komeda T, Ario K, Naganuma A, Shimada M, Hirashima N, Yoshizawa K, Makita F, Furuta K, Kikuchi M, Naeshiro N, Takahashi H, Mano Y, Yamashita H, Matsushita K, Tsunematsu S, Yabuuchi I, Nishimura H, Shimada Y, Yamauchi K, Komatsu T, Sugimoto R, Sakai H, Mita E, Koda M, Nakamura Y, Kamitsukasa H, Sato T, Nakamuta M, Masaki N, Takikawa H, Tanaka A, Ohira H, Zeniya M, Abe M, Kaneko S, Honda M, Arai K, Arinaga-Hino T, Hashimoto E, Taniai M, Umemura T, Joshita S, Nakao K, Ichikawa T, Shibata H, Takaki A, Yamagiwa S, Seike M, Sakisaka S, Takeyama Y, Harada M, Senju M, Yokosuka O, Kanda T, Ueno Y, Ebinuma H, Himoto T, Murata K, Shimoda S, Nagaoka S, Abiru S, Komori A, Migita K, Ito M, Yatsuhashi H, Maehara Y, Uemoto S, Kokudo N, Nagasaki M, Tokunaga K, Nakamura M. POGLUT1, the putative effector gene driven by rs2293370 in primary biliary cholangitis susceptibility locus chromosome 3q13.33. Sci Rep 2019; 9:102. [PMID: 30643196 PMCID: PMC6331557 DOI: 10.1038/s41598-018-36490-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 06/06/2018] [Accepted: 11/13/2018] [Indexed: 12/28/2022] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic and cholestatic autoimmune liver disease caused by the destruction of intrahepatic small bile ducts. Our previous genome-wide association study (GWAS) identified six susceptibility loci for PBC. Here, in order to further elucidate the genetic architecture of PBC, a GWAS was performed on an additional independent sample set, then a genome-wide meta-analysis with our previous GWAS was performed based on a whole-genome single nucleotide polymorphism (SNP) imputation analysis of a total of 4,045 Japanese individuals (2,060 cases and 1,985 healthy controls). A susceptibility locus on chromosome 3q13.33 (including ARHGAP31, TMEM39A, POGLUT1, TIMMDC1, and CD80) was previously identified both in the European and Chinese populations and was replicated in the Japanese population (OR = 0.7241, P = 3.5 × 10-9). Subsequent in silico and in vitro functional analyses identified rs2293370, previously reported as the top-hit SNP in this locus in the European population, as the primary functional SNP. Moreover, e-QTL analysis indicated that the effector gene of rs2293370 was Protein O-Glucosyltransferase 1 (POGLUT1) (P = 3.4 × 10-8). This is the first study to demonstrate that POGLUT1 and not CD80 is the effector gene regulated by the primary functional SNP rs2293370, and that increased expression of POGLUT1 might be involved in the pathogenesis of PBC.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Kazuko Ueno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | | | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Hitomi Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Kouno
- 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
| | - Hajime Ohta
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - 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
| | - 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
| | - 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
| | - 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
| | - Toshiki Komeda
- 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - 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
| | - Masahiro Kikuchi
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Noriaki Naeshiro
- 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
| | - 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
| | - Haruhiro Yamashita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kouki Matsushita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Seiji Tsunematsu
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Iwao Yabuuchi
- 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
| | - Yusuke Shimada
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazuhiko Yamauchi
- 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
| | - 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
| | - Hironori Sakai
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Eiji Mita
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Masaharu Koda
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yoko Nakamura
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Kamitsukasa
- 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
| | - 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
| | - Naohiko Masaki
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hajime Takikawa
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Hiromasa Ohira
- Department of Gastroenterology and Rheumatic Diseases, Fukushima Medical University of Medicine, Fukushima, Japan
| | - Mikio Zeniya
- Department of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, Japan
| | - Masanori Abe
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Masao Honda
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, 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
| | - Etsuko Hashimoto
- Department of Medicine and Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Makiko Taniai
- Department of Medicine and Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Takeji Umemura
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Satoru Joshita
- Department of Medicine, Division of Gastroenterology and Hepatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Kazuhiko Nakao
- Department of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tatsuki Ichikawa
- Department of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hidetaka Shibata
- Department of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akinobu Takaki
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Satoshi Yamagiwa
- Division of Gastroenterology and Hepatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Shotaro Sakisaka
- Department of Gastroenterology and Medicine, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Yasuaki Takeyama
- Department of Gastroenterology and Medicine, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Masaru Harada
- The Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Michio Senju
- The Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Osamu Yokosuka
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tatsuo Kanda
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiyuki Ueno
- Department of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Hirotoshi Ebinuma
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio Graduate School of Medicine, Tokyo, Japan
| | - Takashi Himoto
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, Japan
| | - Kazumoto Murata
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Shinji Shimoda
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinya Nagaoka
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Seigo Abiru
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Atsumasa Komori
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Kiyoshi Migita
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Masahiro Ito
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinji Uemoto
- Division of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norihiro Kokudo
- National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.,Graduate School of Medicine, Tohoku University, Sendai, Japan.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, 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. .,Headquaters of PBC-GWAS study group in Japan, Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan.
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Hitomi Y, Nakatani K, Kojima K, Nishida N, Kawai Y, Kawashima M, Aiba Y, Nagasaki M, Nakamura M, Tokunaga K. NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants. Cell Mol Gastroenterol Hepatol 2018; 7:515-532. [PMID: 30528300 PMCID: PMC6396435 DOI: 10.1016/j.jcmgh.2018.11.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 01/03/2023]
Abstract
BACKGROUND & AIMS Primary biliary cholangitis (PBC) is a chronic and cholestatic liver disease that eventually leads to cirrhosis and hepatic failure. We recently identified several susceptibility genes included NFKB1 and MANBA for PBC in the Japanese population by genome-wide association study. However, the primary functional variants in the NFKB1/MANBA region and the molecular mechanism for conferring disease susceptibility to PBC have not yet been clarified. METHODS We performed high-density association mapping based on a single-nucleotide polymorphism (SNP) imputation analysis, using data from a whole-genome sequence reference panel of 1070 Japanese individuals and the previous genome-wide association study (1389 PBC patients, 1508 healthy controls). Among SNPs (P < 5.0 × 10-7) in the NFKB1/MANBA region, putative primary functional variants and the molecular mechanism for conferring disease susceptibility to PBC were identified by in silico/in vitro functional analysis. RESULTS Among the SNPs in the NFKB1/MANBA region, rs17032850 and rs227361, which changed the binding of transcription factors lymphoid enhancer-binding factor 1 (LEF-1) and retinoid X receptor α (RXRα), respectively, were identified as putative primary functional variants that regulate gene expression. In addition, expression-quantitative trait locus data and gene editing using a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system supported the potential role of rs17032850 and rs227361 in regulating NFKB1 and MANBA expression, respectively. CONCLUSIONS We identified independent putative primary functional variants in NFKB1/MANBA and showed the distinct molecular mechanism by which each putative primary functional variant conferred susceptibility to PBC. Our approach was useful to dissect the pathogenesis not only of PBC, but also other digestive diseases in which NFKB1/MANBA has been reported as a susceptibility locus.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Correspondence Address correspondence to: Yuki Hitomi, PhD, Department of Human Genetics, Graduate School of Medicine, University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan. fax: (81) 3-5802-8619.
| | - Ken Nakatani
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan,Japan Science and Technology Agency, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan,Graduate School of Medicine, Tohoku University, Sendai, Japan,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Minoru Nakamura
- Headquarters of Primary Biliary Cholangitis (PBC) Research in National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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28
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Latt KZ, Honda K, Thiri M, Hitomi Y, Omae Y, Sawai H, Kawai Y, Teraguchi S, Ueno K, Nagasaki M, Mabuchi A, Kaga H, Komatsuda A, Tokunaga K, Noiri E. Identification of a two-SNP PLA2R1 Haplotype and HLA-DRB1 Alleles as Primary Risk Associations in Idiopathic Membranous Nephropathy. Sci Rep 2018; 8:15576. [PMID: 30349113 PMCID: PMC6197221 DOI: 10.1038/s41598-018-33612-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 05/31/2018] [Accepted: 10/03/2018] [Indexed: 01/12/2023] Open
Abstract
The associations of single nucleotide polymorphisms (SNPs) in PLA2R1 and HLA-DQA1, as well as HLA-DRB1*15:01-DQB1*06:02 haplotype with idiopathic membranous nephropathy (IMN) is well known. However, the primary associations of these loci still need to be determined. We used Japanese-specific SNP genotyping array and imputation using 2,048 sequenced Japanese samples to fine-map PLA2R1 region in 98 patients and 413 controls. The most significant SNPs were replicated in a separate sample set of 130 patients and 288 controls. A two-SNP haplotype of intronic and missense SNPs showed the strongest association. The intronic SNP is strongly associated with PLA2R1 expression in the Genotype-Tissue Expression (GTEx) database, and the missense SNP is predicted to alter peptide binding with HLA-DRB1*15:01 by the Immune Epitope Database (IEDB). In HLA region, we performed relative predispositional effect (RPE) tests and identified additional risk alleles in both HLA-DRB1 and HLA-DQB1. We collapsed the risk alleles in each of HLA-DRB1 and HLA-DQB1 into single risk alleles. Reciprocal conditioning of these collapsed risk alleles showed more residual significance for HLA-DRB1 collapsed risk than HLA-DQB1 collapsed risk. These results indicate that changes in the expression levels of structurally different PLA2R protein confer risk for IMN in the presence of risk HLA-DRB1 alleles.
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Affiliation(s)
- Khun Zaw Latt
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenjiro Honda
- Department of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan
| | - Myo Thiri
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shunsuke Teraguchi
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuko Ueno
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Akihiko Mabuchi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hajime Kaga
- Department of Hematology, Nephrology, and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Atsushi Komatsuda
- Department of Hematology, Nephrology, and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Eisei Noiri
- Department of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan. .,Department of Hemodialysis and Apheresis, The University of Tokyo Hospital, Tokyo, Japan.
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29
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Iwasaki K, Iwasaki A, Sumimoto S, Sano T, Hitomi Y, Ohno O, Suenaga K. Croissamide, a proline-rich cyclic peptide with an N-prenylated tryptophan from a marine cyanobacterium Symploca sp. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.09.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Aiba Y, Harada K, Ito M, Suematsu T, Aishima S, Hitomi Y, Nishida N, Kawashima M, Takatsuki M, Eguchi S, Shimoda S, Nakamura H, Komori A, Abiru S, Nagaoka S, Migita K, Yatsuhashi H, Tokunaga K, Nakamura M. Increased expression and altered localization of cathepsin Z are associated with progression to jaundice stage in primary biliary cholangitis. Sci Rep 2018; 8:11808. [PMID: 30087368 PMCID: PMC6081405 DOI: 10.1038/s41598-018-30146-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 03/07/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
Our recent genome-wide association study found that the NELFCD/CTSZ locus was significantly associated with progression of primary biliary cholangitis (PBC) to jaundice stage in the Japanese population. In this study, we investigated the role of cathepsin Z in the etiology and pathology of PBC. Serum cathepsin Z levels were measured using enzyme-linked immunosorbent assay. The expression and localization of cathepsin Z in liver specimens were analyzed by western blotting and immunohistochemistry. In PBC patients, serum cathepsin Z levels were significantly increased with disease progression. In addition, its levels were positively correlated with alanine transaminase, aspartate transaminase and total bilirubin, and were negatively correlated with platelet count and albumin. Cathepsin Z expression was markedly increased in hepatocytes at later stages of PBC, and its localization was altered from the peri-bile canaliculus to the cytoplasm, where a fraction was no longer colocalized with endosomal/lysosomal vesicles. Similar altered expression of cathepsin Z was observed in end-stage of other cholestatic liver diseases including sepsis, obstructive jaundice, and Alagille syndrome. Our results indicate that altered expression and localization of cathepsin Z in hepatocytes are characteristic features of PBC and other cholestatic liver diseases, and are implicated in the progression of PBC.
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Affiliation(s)
- Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Kenichi Harada
- Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Masahiro Ito
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Takashi Suematsu
- Central Electron Microscope Laboratory, Nagasaki University School of Medicine, Nagasaki, Nagasaki, Japan
| | - Shinichi Aishima
- Departments of Pathology & Microbiology, Faculty of Medicine, Saga University, Saga, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Nao Nishida
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan
| | | | - Mitsuhisa Takatsuki
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Susumu Eguchi
- Department of Surgery, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Shimoda
- Department of Medicine and Biosystemic Science Graduate School of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Hitomi Nakamura
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Atsumasa Komori
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Seigo Abiru
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Shinya Nagaoka
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan
| | - Kiyoshi Migita
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Omura, Japan. .,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Nagasaki, Japan. .,Headquarters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Omura, Japan.
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31
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Jia X, Horinouchi T, Hitomi Y, Shono A, Khor SS, Omae Y, Kojima K, Kawai Y, Nagasaki M, Kaku Y, Okamoto T, Ohwada Y, Ohta K, Okuda Y, Fujimaru R, Hatae K, Kumagai N, Sawanobori E, Nakazato H, Ohtsuka Y, Nakanishi K, Shima Y, Tanaka R, Ashida A, Kamei K, Ishikura K, Nozu K, Tokunaga K, Iijima K. Strong Association of the HLA-DR/DQ Locus with Childhood Steroid-Sensitive Nephrotic Syndrome in the Japanese Population. J Am Soc Nephrol 2018; 29:2189-2199. [PMID: 30012571 DOI: 10.1681/asn.2017080859] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 05/11/2018] [Indexed: 12/26/2022] Open
Abstract
Background Nephrotic syndrome is the most common cause of chronic glomerular disease in children. Most of these patients develop steroid-sensitive nephrotic syndrome (SSNS), but the loci conferring susceptibility to childhood SSNS are mainly unknown.Methods We conducted a genome-wide association study (GWAS) in the Japanese population; 224 patients with childhood SSNS and 419 adult healthy controls were genotyped using the Affymetrix Japonica Array in the discovery stage. Imputation for six HLA genes (HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1) was conducted on the basis of Japanese-specific references. We performed genotyping for HLA-DRB1/-DQB1 using a sequence-specific oligonucleotide-probing method on a Luminex platform. Whole-genome imputation was conducted using a phased reference panel of 2049 healthy Japanese individuals. Replication was performed in an independent Japanese sample set including 216 patients and 719 healthy controls. We genotyped candidate single-nucleotide polymorphisms using the DigiTag2 assay.Results The most significant association was detected in the HLA-DR/DQ region and replicated (rs4642516 [minor allele G], combined Pallelic=7.84×10-23; odds ratio [OR], 0.33; 95% confidence interval [95% CI], 0.26 to 0.41; rs3134996 [minor allele A], combined Pallelic=1.72×10-25; OR, 0.29; 95% CI, 0.23 to 0.37). HLA-DRB1*08:02 (Pc=1.82×10-9; OR, 2.62; 95% CI, 1.94 to 3.54) and HLA-DQB1*06:04 (Pc=2.09×10-12; OR, 0.10; 95% CI, 0.05 to 0.21) were considered primary HLA alleles associated with childhood SSNS. HLA-DRB1*08:02-DQB1*03:02 (Pc=7.01×10-11; OR, 3.60; 95% CI, 2.46 to 5.29) was identified as the most significant genetic susceptibility factor.Conclusions The most significant association with childhood SSNS was detected in the HLA-DR/DQ region. Further HLA allele/haplotype analyses should enhance our understanding of molecular mechanisms underlying SSNS.
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Affiliation(s)
- Xiaoyuan Jia
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoko Horinouchi
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akemi Shono
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yosuke Omae
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization.,Graduate School of Medicine, and.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization
| | - Masao Nagasaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization.,Graduate School of Medicine, and.,Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Yoshitsugu Kaku
- Department of Nephrology, Fukuoka Children's Hospital, Fukuoka, Japan
| | - Takayuki Okamoto
- Department of Pediatrics, Hokkaido University Hospital, Sapporo, Japan
| | - Yoko Ohwada
- Department of Pediatrics, Dokkyo Medical University School of Medicine, Tochigi, Japan
| | - Kazuhide Ohta
- Department of Pediatrics, Kanazawa Medical Center, Kanazawa, Japan
| | - Yusuke Okuda
- Department of Pediatrics, Shiga University of Medical Science, Shiga, Japan
| | - Rika Fujimaru
- Department of Pediatrics, Osaka City General Hospital, Osaka, Japan
| | - Ken Hatae
- Department of Pediatrics, Japanese Red Cross Fukuoka Hospital, Fukuoka, Japan
| | - Naonori Kumagai
- Department of Pediatrics, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Emi Sawanobori
- Department of Pediatrics, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Hitoshi Nakazato
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yasufumi Ohtsuka
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, Japan
| | - Koichi Nakanishi
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Yuko Shima
- Department of Pediatrics, Wakayama Medical University, Wakayama, Japan
| | - Ryojiro Tanaka
- Department of Nephrology, Hyogo Prefectural Kobe Children's Hospital, Kobe, Japan
| | - Akira Ashida
- Department of Pediatrics, Osaka Medical College, Osaka, Japan; and
| | - Koichi Kamei
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Kenji Ishikura
- Division of Nephrology and Rheumatology, National Center for Child Health and Development, Tokyo, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan;
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Kobe, Japan;
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32
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Ueta M, Hamuro J, Nishigaki H, Nakamura N, Shinomiya K, Mizushima K, Hitomi Y, Tamagawa-Mineoka R, Yokoi N, Naito Y, Tokunaga K, Katoh N, Sotozono C, Kinoshita S. Mucocutaneous inflammation in the Ikaros Family Zinc Finger 1-keratin 5-specific transgenic mice. Allergy 2018; 73:395-404. [PMID: 28914974 DOI: 10.1111/all.13308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Our genomewide association study documented an association between cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis (CM-SJS/TEN) and Ikaros Family Zinc Finger 1 (IKZF1). Few studies examined biological and pathological functions of IKZF1 in mucosal immunity. We hypothesized that IKZF1 contributes to the mucocutaneous inflammation. METHODS Human skin and conjunctival tissues were obtained for immunohistological studies. Primary human conjunctival epithelial cells (PHCjECs) and adult human epidermal keratinocytes (HEKa) also used for gene expression analysis. We also generated K5-Ikzf1-EGFP transgenic mice (Ikzf1 Tg) by introducing the Ik1 isoform into cells expressing keratin 5, which is expressed in epithelial tissues such as the epidermis and conjunctiva, and then examined them histologically and investigated gene expression of the epidermis. Moreover, Ikzf1 Tg were induced allergic contact dermatitis. RESULTS We found that human epidermis and conjunctival epithelium expressed IKZF1, and in PHCjECs and HEKa, the expression of IKZF1 mRNA was upregulated by stimulation with polyI:C, a TLR3 ligand. In Ikzf1 Tg, we observed dermatitis and mucosal inflammation including the ocular surface. In contact dermatitis model, inflammatory infiltrates in the skin of Ikzf1 Tg were significantly increased compared with wild type. Microarray analysis showed that Lcn2, Adh7, Epgn, Ifi202b, Cdo1, Gpr37, Duoxa1, Tnfrsf4, and Enpp5 genes were significantly upregulated in the epidermis of Ikzf1 Tg compared with wild type. CONCLUSION Our findings support the hypothesis that Ikaros might participate in mucocutaneous inflammation.
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Affiliation(s)
- M. Ueta
- Department of Frontier Medical Science and Technology for Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - J. Hamuro
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - H. Nishigaki
- Department of Frontier Medical Science and Technology for Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - N. Nakamura
- Department of Dermatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - K. Shinomiya
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - K. Mizushima
- Department of Molecular Gastroenterology and Hepatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - Y. Hitomi
- Department of Human Genetics; Graduate School of Medicine; University of Tokyo; Tokyo Japan
| | - R. Tamagawa-Mineoka
- Department of Dermatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - N. Yokoi
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - Y. Naito
- Department of Molecular Gastroenterology and Hepatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - K. Tokunaga
- Department of Human Genetics; Graduate School of Medicine; University of Tokyo; Tokyo Japan
| | - N. Katoh
- Department of Dermatology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - C. Sotozono
- Department of Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
| | - S. Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology; Kyoto Prefectural University of Medicine; Kyoto Japan
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33
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Kawashima M, Hitomi Y, Aiba Y, Nishida N, Kojima K, Kawai Y, Nakamura H, Tanaka A, Zeniya M, Hashimoto E, Ohira H, Yamamoto K, Abe M, Nakao K, Yamagiwa S, Kaneko S, Honda M, Umemura T, Ichida T, Seike M, Sakisaka S, Harada M, Yokosuka O, Ueno Y, Senju M, Kanda T, Shibata H, Himoto T, Murata K, Miyake Y, Ebinuma H, Taniai M, Joshita S, Nikami T, Ota H, Kouno H, Kouno H, Nakamuta M, Fukushima N, Kohjima M, Komatsu T, Komeda T, Ohara Y, Muro T, Yamashita T, Yoshizawa K, Nakamura Y, Shimada M, Hirashima N, Sugi K, Ario K, Takesaki E, Naganuma A, Mano H, Yamashita H, Matsushita K, Yamauchi K, Makita F, Nishimura H, Furuta K, Takahashi N, Kikuchi M, Masaki N, Tanaka T, Tamura S, Mori A, Yagi S, Shirabe K, Komori A, Migita K, Ito M, Nagaoka S, Abiru S, Yatsuhashi H, Yasunami M, Shimoda S, Harada K, Egawa H, Maehara Y, Uemoto S, Kokudo N, Takikawa H, Ishibashi H, Chayama K, Mizokami M, Nagasaki M, Tokunaga K, Nakamura M. Genome-wide association studies identify PRKCB as a novel genetic susceptibility locus for primary biliary cholangitis in the Japanese population. Hum Mol Genet 2017; 26:650-659. [PMID: 28062665 DOI: 10.1093/hmg/ddw406] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 11/23/2016] [Indexed: 12/13/2022] Open
Abstract
A previous genome-wide association study (GWAS) performed in 963 Japanese individuals (487 primary biliary cholangitis [PBC] cases and 476 healthy controls) identified TNFSF15 (rs4979462) and POU2AF1 (rs4938534) as strong susceptibility loci for PBC. In this study, we performed GWAS in additional 1,923 Japanese individuals (894 PBC cases and 1,029 healthy controls), and combined the results with the previous data. This GWAS, together with a subsequent replication study in an independent set of 7,024 Japanese individuals (512 PBC cases and 6,512 healthy controls), identified PRKCB (rs7404928) as a novel susceptibility locus for PBC (odds ratio [OR] = 1.26, P = 4.13 × 10-9). Furthermore, a primary functional variant of PRKCB (rs35015313) was identified by genotype imputation using a phased panel of 1,070 Japanese individuals from a prospective, general population cohort study and subsequent in vitro functional analyses. These results may lead to improved understanding of the disease pathways involved in PBC, forming a basis for prevention of PBC and development of novel therapeutics.
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Affiliation(s)
- Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Kaname Kojima
- Division of Biomedical Information Analysis, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yosuke Kawai
- Division of Biomedical Information Analysis, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hitomi Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Atsushi Tanaka
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Mikio Zeniya
- Department of Gastroenterology and Hepatology, Tokyo Jikei University School of Medicine, Tokyo, Japan
| | - Etsuko Hashimoto
- Department of Medicine and Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Hiromasa Ohira
- Department of Gastroenterology and Rheumatic Diseases, Fukushima Medical University of Medicine, Fukushima, Japan
| | - Kazuhide Yamamoto
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Masanori Abe
- Department of Gastroenterology and Metabology, Ehime University Graduate School of Medicine, Matsuyama, Japan
| | - Kazuhiko Nakao
- Department of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagaski, Japan
| | - Satoshi Yamagiwa
- Division of Gastroenterology and Hepatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Shuichi Kaneko
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Masao Honda
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Takeji Umemura
- Division of Gastroenterology and Hepatology, Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Takafumi Ichida
- Department of Gastroenterology and Hepatology, Juntendo University Shizuoka Hospital, Shizuoka, Japan
| | - Masataka Seike
- First Department of Internal Medicine, Faculty of Medicine, Oita University, Oita, Japan
| | - Shotaro Sakisaka
- Department of Gastroenterology and Medicine, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Masaru Harada
- The Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Osamu Yokosuka
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiyuki Ueno
- Department of Gastroenterology, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Michio Senju
- The Third Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Tatsuo Kanda
- Department of Medicine and Clinical Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidetaka Shibata
- Department of Gastroenterology and Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagaski, Japan
| | - Takashi Himoto
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, Kagawa, Japan
| | - Kazumoto Murata
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Yasuhiro Miyake
- Department of Gastroenterology and Hepatology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hirotoshi Ebinuma
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Keio Graduate School of Medicine, Tokyo, Japan
| | - Makiko Taniai
- Department of Medicine and Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Satoru Joshita
- Division of Gastroenterology and Hepatology, Department of Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Toshiki Nikami
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hajime Ota
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Kouno
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hirotaka Kouno
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Makoto Nakamuta
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Nobuyoshi Fukushima
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Motoyuki Kohjima
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tatsuji Komatsu
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Toshiki Komeda
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yukio Ohara
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Toyokichi Muro
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tsutomu Yamashita
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kaname Yoshizawa
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Yoko Nakamura
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Masaaki Shimada
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Noboru Hirashima
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazuhiro Sugi
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Keisuke Ario
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Eiichi Takesaki
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Atsushi Naganuma
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Mano
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Haruhiro Yamashita
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kouki Matsushita
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kazuhiko Yamauchi
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Fujio Makita
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Hideo Nishimura
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Kiyoshi Furuta
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Naohiro Takahashi
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Masahiro Kikuchi
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Naohiko Masaki
- Headquaters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Tomohiro Tanaka
- Organ Transplantation Service, The University of Tokyo, Tokyo, Japan
| | - Sumito Tamura
- Hepatobiliarypancreatic Surgery Division, Artificial Organ and Transplantation Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akira Mori
- Division of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shintaro Yagi
- Division of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ken Shirabe
- Department of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Atsumasa Komori
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Kiyoshi Migita
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Masahiro Ito
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Shinya Nagaoka
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Seigo Abiru
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Hiroshi Yatsuhashi
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Michio Yasunami
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Shinji Shimoda
- Department of Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Kenichi Harada
- Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
| | - Hiroto Egawa
- Department of Surgery, Institute of Gastroenterology, Tokyo Women's Medical University, Tokyo, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shinji Uemoto
- Division of Hepato-Biliary-Pancreatic and Transplant Surgery, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norihiro Kokudo
- Hepatobiliarypancreatic Surgery Division, Artificial Organ and Transplantation Division, Department of Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hajime Takikawa
- Department of Medicine, Teikyo University School of Medicine, Tokyo, Japan
| | - Hiromi Ishibashi
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
| | - Kazuaki Chayama
- Department of Gastroenterology and Metabolism, Applied Life Sciences, Institute of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masashi Mizokami
- The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Masao Nagasaki
- Division of Biomedical Information Analysis, Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan.,Headquaters of PBC Research in the National Hospital Organization 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.,Headquaters of gp210 Working Group in Intractable Liver Disease Research Project Team of the Ministry of Health and Welfare in Japan, Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
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Yasunami M, Nakamura H, Tokunaga K, Kawashima M, Nishida N, Hitomi Y, Nakamura M. Principal contribution of HLA-DQ alleles, DQB1*06:04 and DQB1*03:01, to disease resistance against primary biliary cholangitis in a Japanese population. Sci Rep 2017; 7:11093. [PMID: 28894202 PMCID: PMC5593890 DOI: 10.1038/s41598-017-11148-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 05/31/2017] [Accepted: 08/21/2017] [Indexed: 01/07/2023] Open
Abstract
Identification of the primary allele(s) in HLA class II associated diseases remains challenging because of a tight linkage between alleles of HLA-DR and -DQ loci. In the present study, we determined the genotypes of seven HLA loci (HLA-A, -B, -DRB1, -DQA1, -DQB1, -DPA1 and -DPB1) for 1200 Japanese patients with primary biliary cholangitis and 1196 controls. Observation of recombination derivatives facilitated an evaluation of the effects of individual HLA alleles consisting of disease-prone/disease-resistant HLA haplotypes. Consequently, a primary contribution of DQB1*06:04 (odds ratio: 0.19, p = 1.91 × 10−22), DQB1*03:01 (odds ratio: 0.50, p = 6.76 × 10−10), DRB1*08:03 (odds ratio: 1.75, p = 1.01 × 10−7) and DQB1*04:01 (odds ratio: 1.50, p = 9.20 × 10−6) was suggested. Epistasis of the protective DQB1*06:04 to risk conferred by DRB1*08:03 was demonstrated by subpopulation analysis, implicating the presence of an active immunological mechanism that alleviates pathogenic autoimmune reactions. Further, the contribution of the aforementioned HLA alleles as well as an HLA-DP allele, DPB1*02:01 to the association signals of 304 loci among 4103 SNPs in the HLA region at the genome-wide level of significance (p values less than 5 × 10−8) was demonstrated by the stepwise exclusion of the individuals possessing these HLA alleles from the comparison.
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Affiliation(s)
- Michio Yasunami
- Department of Medical Genomics, Life Science Institute, Saga-Ken Medical Centre Koseikan, Saga, 840-8571, Japan. .,Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan.
| | - Hitomi Nakamura
- Department of Clinical Medicine, Institute of Tropical Medicine, Nagasaki University, Nagasaki, 852-8523, Japan.,Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center and Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, 856-8562, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-0033, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-0033, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-0033, Japan.,The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, 272-8516, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, 113-0033, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center and Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, 856-8562, Japan. .,Headquarters of PBC Research in the NHO Study Group for Liver Disease in Japan (NHOSLJ), Omura, 856-8562, Japan. .,Headquarters of gp210 Working Group in Intractable Hepatobiliary Disease Study Group supported by the Ministry of Health, Labour and Welfare of Japan (gp210WG), Omura, 856-8562, Japan.
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Khor SS, Hitomi Y, Okudaira Y, Masuya A, Ozaki Y, Ueta M, Nakatani K, Nagato M, Ogawa T, Sotozono C, Kinoshita S, Inoko H, Tokunaga K. P258 Evaluation of high-resolution HLA typing of Japanese samples using NXType™ NGS HLA typing kit. Hum Immunol 2017. [DOI: 10.1016/j.humimm.2017.06.318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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36
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Aiba Y, Yamazaki K, Nishida N, Kawashima M, Hitomi Y, Nakamura H, Komori A, Fuyuno Y, Takahashi A, Kawaguchi T, Takazoe M, Suzuki Y, Motoya S, Matsui T, Esaki M, Matsumoto T, Kubo M, Tokunaga K, Nakamura M. Disease susceptibility genes shared by primary biliary cirrhosis and Crohn's disease in the Japanese population. J Hum Genet 2015; 60:525-31. [PMID: 26084578 DOI: 10.1038/jhg.2015.59] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/01/2015] [Accepted: 05/01/2015] [Indexed: 01/08/2023]
Abstract
We previously identified TNFSF15 as the most significant susceptibility gene at non-HLA loci for both primary biliary cirrhosis (PBC) and Crohn's diseases (CD) in the Japanese population. The aim of this study is to identify further disease susceptibility genes shared by PBC and CD. We selected 15 and 33 genetic variants that were significantly associated with PBC and CD, respectively, based on previously reported genome-wide association studies of the Japanese population. Next, an association study was independently performed for these genetic variants in CD (1312 CD patients and 3331 healthy controls) and PBC (1279 PBC patients and 1015 healthy controls) cohorts. Two CD susceptibility genes, ICOSLG rs2838519 and IL12B rs6556412, were also nominally associated with susceptibility to PBC (P=3.85 × 10(-2) and P=8.40 × 10(-3), respectively). Three PBC susceptibility genes, CXCR5 rs6421571, STAT4 rs7574865 and NFKB1 rs230534, were nominally associated with susceptibility to CD (P=2.82 × 10(-2), P=3.88 × 10(-2) and P=2.04 × 10(-2), respectively). The effect of ICOSLG and CXCR5 variants were concordant but the effect of STAT4, NFKB1 and IL12B variants were discordant for PBC and CD. TNFSF15 and ICOSLG-CXCR5 might constitute a shared pathogenic pathway in the development of PBC and CD in the Japanese population, whereas IL12B-STAT4-NFKB1 might constitute an opposite pathogenic pathway, reflecting the different balance between Th1 and Th17 in the two diseases.
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Affiliation(s)
- Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Keiko Yamazaki
- Laboratory for Genotyping Development, Center for Integrative Medical Science, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Minae Kawashima
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency (JST), Tokyo, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hitomi Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan
| | - Atsumasa Komori
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuta Fuyuno
- Laboratory for Genotyping Development, Center for Integrative Medical Science, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan.,Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Takahashi
- Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Tokyo, Japan
| | - Takaaki Kawaguchi
- Department of Medicine, Division of Gastroenterology, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Masakazu Takazoe
- Department of Medicine, Division of Gastroenterology, Tokyo Yamate Medical Center, Tokyo, Japan
| | - Yasuo Suzuki
- Department of Internal Medicine, Faculty of Medicine, Toho University, Chiba, Japan
| | - Satoshi Motoya
- Department of Gastroenterology, Sapporo Kosei Hospital, Sapporo, Japan
| | - Toshiyuki Matsui
- Laboratory for Genotyping Development, Center for Integrative Medical Science, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan.,Department of Gastroenterology, Fukuoka University Chikushi Hospital, Fukuoka, Japan
| | - Motohiro Esaki
- Department of Medicine and Clinical Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takayuki Matsumoto
- Division of Gastroenterology, Department of Internal Medicine, Iwate Medical University, Iwate, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, Center for Integrative Medical Science, Institute of Physical and Chemical Research (RIKEN), Yokohama, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan.,Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Headquarters of PBC Research in the National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ) and gp210 working in Research Program of Intractable Hepatoboliary Disease Study Group supported by the Ministry of Health, Labour, and Welfare of Japan, Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Nagasaki, Japan
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Hitomi Y, Kawashima M, Aiba Y, Nishida N, Matsuhashi M, Okazaki H, Nakamura M, Tokunaga K. Human primary biliary cirrhosis-susceptible allele of rs4979462 enhances TNFSF15 expression by binding NF-1. Hum Genet 2015; 134:737-47. [PMID: 25899471 DOI: 10.1007/s00439-015-1556-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 04/12/2015] [Indexed: 01/12/2023]
Abstract
A genome-wide association study (GWAS) identified tumor necrosis factor superfamily member 15 (TNFSF15) as the strongest associated gene with susceptibility to primary biliary cirrhosis (PBC) outside the HLA loci in the Japanese population. However, causal functional variants of the TNFSF15 locus and the molecular mechanism underlying disease susceptibility have not been clarified. Here, to identify the functional causal variants of the TNFSF15 locus, integrated analysis comprising in silico analysis, a case-control association study and in vitro functional analysis was performed. Initially, 32 functional candidate single-nucleotide polymorphisms (SNPs) in the expression regulatory motifs, the coding region, or the untranslated regions (UTRs) of the TNFSF15 locus were selected by in silico analysis. By the case-control association studies using PBC patients (n = 1279) and healthy controls (n = 1091) in the Japanese population, rs4979462 [P = 1.85 × 10(-14) (our previous study)], rs56211063 (P = 2.21 × 10(-14)), and rs55768522 (r(2) = 1 with rs4979462) were likely candidates for causal variants. Among these SNPs, rs4979462 was identified as the causal variant by in vitro functional analysis using luciferase assay and electrophoretic mobility shift assay (EMSA). Super-shift assay clarified that PBC-susceptible allele of rs4979462 generated a novel NF-1 binding site. Moreover, higher endogenous TNFSF15 protein and mRNA expression levels were observed in individuals with the PBC-susceptible allele of rs4979462. This study identified the causal variant for PBC susceptibility in the TNFSF15 locus and clarified its underlying molecular mechanism. TNFSF15 and NF-1 are considered to be potential targets for the treatment of PBC.
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Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan,
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Ueta M, Sawai H, Sotozono C, Hitomi Y, Kaniwa N, Kim MK, Seo KY, Yoon KC, Joo CK, Kannabiran C, Wakamatsu TH, Sangwan V, Rathi V, Basu S, Ozeki T, Mushiroda T, Sugiyama E, Maekawa K, Nakamura R, Aihara M, Matsunaga K, Sekine A, Gomes JÁP, Hamuro J, Saito Y, Kubo M, Kinoshita S, Tokunaga K. IKZF1, a new susceptibility gene for cold medicine-related Stevens-Johnson syndrome/toxic epidermal necrolysis with severe mucosal involvement. J Allergy Clin Immunol 2015; 135:1538-45.e17. [PMID: 25672763 DOI: 10.1016/j.jaci.2014.12.1916] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 11/27/2014] [Accepted: 12/15/2014] [Indexed: 12/28/2022]
Abstract
BACKGROUND Stevens-Johnson syndrome (SJS) and its severe form, toxic epidermal necrolysis (TEN), are acute inflammatory vesiculobullous reactions of the skin and mucous membranes, including the ocular surface, oral cavity, and genitals. These reactions are very rare but are often associated with inciting drugs, infectious agents, or both. OBJECTIVE We sought to identify susceptibility loci for cold medicine-related SJS/TEN (CM-SJS/TEN) with severe mucosal involvement (SMI). METHODS A genome-wide association study was performed in 808 Japanese subjects (117 patients with CM-SJS/TEN with SMI and 691 healthy control subjects), and subsequent replication studies were performed in 204 other Japanese subjects (16 cases and 188 control subjects), 117 Korean subjects (27 cases and 90 control subjects), 76 Indian subjects (20 cases and 56 control subjects), and 174 Brazilian subjects (39 cases and 135 control subjects). RESULTS In addition to the most significant susceptibility region, HLA-A, we identified IKZF1, which encodes Ikaros, as a novel susceptibility gene (meta-analysis, rs4917014 [G vs. T]; odds ratio, 0.5; P = 8.5 × 10(-11)). Furthermore, quantitative ratios of the IKZF1 alternative splicing isoforms Ik1 and Ik2 were significantly associated with rs4917014 genotypes. CONCLUSION We identified IKZF1 as a susceptibility gene for CM-SJS/TEN with SMI not only in Japanese subjects but also in Korean and Indian subjects and showed that the Ik2/Ik1 ratio might be influenced by IKZF1 single nucleotide polymorphisms, which were significantly associated with susceptibility to CM-SJS/TEN with SMI.
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Affiliation(s)
- Mayumi Ueta
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan; Research Center for Inflammation and Regenerative Medicine, Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan; Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Chie Sotozono
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Nahoko Kaniwa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Mee Kum Kim
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Korea
| | - Kyoung Yul Seo
- Department of Ophthalmology, Severance Hospital, Institute of Vision Research, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-Chul Yoon
- Department of Ophthalmology, Chonnam National University, Gwangju, Korea
| | - Choun-Ki Joo
- Department of Ophthalmology & Visual Science, Seoul St Mary's Hospital, College of Medicine, Catholic University of Korea, Seoul, Korea
| | - Chitra Kannabiran
- Prof Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | | | - Virender Sangwan
- Cornea and Anterior Segment Services, L V Prasad Eye Institute, Hyderabad, India
| | - Varsha Rathi
- Cornea and Anterior Segment Services, L V Prasad Eye Institute, Hyderabad, India
| | - Sayan Basu
- Cornea and Anterior Segment Services, L V Prasad Eye Institute, Hyderabad, India
| | - Takeshi Ozeki
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Taisei Mushiroda
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Emiko Sugiyama
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Keiko Maekawa
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Ryosuke Nakamura
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Michiko Aihara
- Department of Environmental Immuno-Dermatology, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kayoko Matsunaga
- Department of Dermatology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Akihiro Sekine
- EBM Research Center, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Junji Hamuro
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshiro Saito
- Division of Medicinal Safety Science, National Institute of Health Sciences, Tokyo, Japan
| | - Michiaki Kubo
- Research Group for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shigeru Kinoshita
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
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Ruzzo EK, Capo-Chichi JM, Ben-Zeev B, Chitayat D, Mao H, Pappas AL, Hitomi Y, Lu YF, Yao X, Hamdan FF, Pelak K, Reznik-Wolf H, Bar-Joseph I, Oz-Levi D, Lev D, Lerman-Sagie T, Leshinsky-Silver E, Anikster Y, Ben-Asher E, Olender T, Colleaux L, Décarie JC, Blaser S, Banwell B, Joshi RB, He XP, Patry L, Silver RJ, Dobrzeniecka S, Islam MS, Hasnat A, Samuels ME, Aryal DK, Rodriguiz RM, Jiang YH, Wetsel WC, McNamara JO, Rouleau GA, Silver DL, Lancet D, Pras E, Mitchell GA, Michaud JL, Goldstein DB. Deficiency of asparagine synthetase causes congenital microcephaly and a progressive form of encephalopathy. Neuron 2014; 80:429-41. [PMID: 24139043 DOI: 10.1016/j.neuron.2013.08.013] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2013] [Indexed: 12/30/2022]
Abstract
We analyzed four families that presented with a similar condition characterized by congenital microcephaly, intellectual disability, progressive cerebral atrophy, and intractable seizures. We show that recessive mutations in the ASNS gene are responsible for this syndrome. Two of the identified missense mutations dramatically reduce ASNS protein abundance, suggesting that the mutations cause loss of function. Hypomorphic Asns mutant mice have structural brain abnormalities, including enlarged ventricles and reduced cortical thickness, and show deficits in learning and memory mimicking aspects of the patient phenotype. ASNS encodes asparagine synthetase, which catalyzes the synthesis of asparagine from glutamine and aspartate. The neurological impairment resulting from ASNS deficiency may be explained by asparagine depletion in the brain or by accumulation of aspartate/glutamate leading to enhanced excitability and neuronal damage. Our study thus indicates that asparagine synthesis is essential for the development and function of the brain but not for that of other organs.
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Affiliation(s)
- Elizabeth K Ruzzo
- Center for Human Genome Variation, Duke University School of Medicine, Durham, NC 27708, USA
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Hitomi Y, Heinzen EL, Donatello S, Dahl HH, Damiano JA, McMahon JM, Berkovic SF, Scheffer IE, Legros B, Rai M, Weckhuysen S, Suls A, De Jonghe P, Pandolfo M, Goldstein DB, Van Bogaert P, Depondt C. Mutations in TNK2 in severe autosomal recessive infantile onset epilepsy. Ann Neurol 2013; 74:496-501. [PMID: 23686771 DOI: 10.1002/ana.23934] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 04/30/2013] [Accepted: 05/01/2013] [Indexed: 01/27/2023]
Abstract
We identified a small family with autosomal recessive, infantile onset epilepsy and intellectual disability. Exome sequencing identified a homozygous missense variant in the gene TNK2, encoding a brain-expressed tyrosine kinase. Sequencing of the coding region of TNK2 in 110 patients with a similar phenotype failed to detect further homozygote or compound heterozygote mutations. Pathogenicity of the variant is supported by the results of our functional studies, which demonstrated that the variant abolishes NEDD4 binding to TNK2, preventing its degradation after epidermal growth factor stimulation. Definitive proof of pathogenicity will require confirmation in unrelated patients.
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Affiliation(s)
- Yuki Hitomi
- Duke Center for Human Genome Variation, Duke University School of Medicine, Durham, NC
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Allen AS, Berkovic SF, Cossette P, Delanty N, Dlugos D, Eichler EE, Epstein MP, Glauser T, Goldstein DB, Han Y, Heinzen EL, Hitomi Y, Howell KB, Johnson MR, Kuzniecky R, Lowenstein DH, Lu YF, Madou MRZ, Marson AG, Mefford HC, Esmaeeli Nieh S, O'Brien TJ, Ottman R, Petrovski S, Poduri A, Ruzzo EK, Scheffer IE, Sherr EH, Yuskaitis CJ, Abou-Khalil B, Alldredge BK, Bautista JF, Berkovic SF, Boro A, Cascino GD, Consalvo D, Crumrine P, Devinsky O, Dlugos D, Epstein MP, Fiol M, Fountain NB, French J, Friedman D, Geller EB, Glauser T, Glynn S, Haut SR, Hayward J, Helmers SL, Joshi S, Kanner A, Kirsch HE, Knowlton RC, Kossoff EH, Kuperman R, Kuzniecky R, Lowenstein DH, McGuire SM, Motika PV, Novotny EJ, Ottman R, Paolicchi JM, Parent JM, Park K, Poduri A, Scheffer IE, Shellhaas RA, Sherr EH, Shih JJ, Singh R, Sirven J, Smith MC, Sullivan J, Lin Thio L, Venkat A, Vining EPG, Von Allmen GK, Weisenberg JL, Widdess-Walsh P, Winawer MR. De novo mutations in epileptic encephalopathies. Nature 2013; 501:217-21. [PMID: 23934111 PMCID: PMC3773011 DOI: 10.1038/nature12439] [Citation(s) in RCA: 1093] [Impact Index Per Article: 99.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022]
Abstract
Epileptic encephalopathies are a devastating group of severe childhood epilepsy disorders for which the cause is often unknown. Here we report a screen for de novo mutations in patients with two classical epileptic encephalopathies: infantile spasms (n = 149) and Lennox-Gastaut syndrome (n = 115). We sequenced the exomes of 264 probands, and their parents, and confirmed 329 de novo mutations. A likelihood analysis showed a significant excess of de novo mutations in the ∼4,000 genes that are the most intolerant to functional genetic variation in the human population (P = 2.9 × 10(-3)). Among these are GABRB3, with de novo mutations in four patients, and ALG13, with the same de novo mutation in two patients; both genes show clear statistical evidence of association with epileptic encephalopathy. Given the relevant site-specific mutation rates, the probabilities of these outcomes occurring by chance are P = 4.1 × 10(-10) and P = 7.8 × 10(-12), respectively. Other genes with de novo mutations in this cohort include CACNA1A, CHD2, FLNA, GABRA1, GRIN1, GRIN2B, HNRNPU, IQSEC2, MTOR and NEDD4L. Finally, we show that the de novo mutations observed are enriched in specific gene sets including genes regulated by the fragile X protein (P < 10(-8)), as has been reported previously for autism spectrum disorders.
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Honma T, Hatta K, Hitomi Y, Kambayashi Y, Hibino Y, Konoshita T, Nakamura H. Increased systemic inflammatory interleukin-1ß and interleukin-6 during agitation as predictors of Alzheimer's disease. Int J Geriatr Psychiatry 2013; 28:233-41. [PMID: 22535710 DOI: 10.1002/gps.3816] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 03/19/2012] [Indexed: 11/07/2022]
Abstract
OBJECTS Identification of biomarkers for Alzheimer's disease (AD) is important for its early diagnosis and prevention and a key in advancing our understanding of its pathophysiology. The aim of this study was to determine whether systemic inflammatory interleukin-1ß (IL-1ß) and interleukin-6 (IL-6) as well as hypertension (HT), diabetes mellitus (DM), and body mass index (BMI) are predictors of AD. METHODS We performed a 10-year follow-up study on 133 elderly who were institutionalized in a nursing home. The associations of IL-1ß and IL-6 at both rest and agitation, as well as HT, DM, and BMI at baseline, were analyzed with the incidences of vascular dementia (VD) and AD during a 10-year follow-up period. RESULTS The Kaplan-Meier method with log-rank test and Cox regression analyses for the total of 133 subjects showed significantly higher incidences of both VD and AD in subjects with DM or HT at baseline. Resting IL-1ß or IL-6 value, or agitation score, was not significantly associated with the subsequent development of VD or AD. The analyses of 40 subjects who had shown agitation at least once in the previous 3 months demonstrated that IL-1ß and IL-6 values at the agitation stage were significantly associated with AD, but not with VD. CONCLUSION Our results indicate that systemic inflammatory IL-1ß and IL-6 at the agitation stage are risk factors for the development of AD, but not VD. Inflammatory mechanisms for AD seem to be causal and specific to the development of AD.
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Affiliation(s)
- T Honma
- Department of Environmental and Preventive Medicine, Graduate School of Medical Science, Kanazawa University, Kanazawa, Japan
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Oz-Levi D, Ben-Zeev B, Ruzzo EK, Hitomi Y, Gelman A, Pelak K, Anikster Y, Reznik-Wolf H, Bar-Joseph I, Olender T, Alkelai A, Weiss M, Ben-Asher E, Ge D, Shianna KV, Elazar Z, Goldstein DB, Pras E, Lancet D. Mutation in TECPR2 reveals a role for autophagy in hereditary spastic paraparesis. Am J Hum Genet 2012. [PMID: 23176824 DOI: 10.1016/j.ajhg.2012.09.015] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We studied five individuals from three Jewish Bukharian families affected by an apparently autosomal-recessive form of hereditary spastic paraparesis accompanied by severe intellectual disability, fluctuating central hypoventilation, gastresophageal reflux disease, wake apnea, areflexia, and unique dysmorphic features. Exome sequencing identified one homozygous variant shared among all affected individuals and absent in controls: a 1 bp frameshift TECPR2 deletion leading to a premature stop codon and predicting significant degradation of the protein. TECPR2 has been reported as a positive regulator of autophagy. We thus examined the autophagy-related fate of two key autophagic proteins, SQSTM1 (p62) and MAP1LC3B (LC3), in skin fibroblasts of an affected individual, as compared to a healthy control, and found that both protein levels were decreased and that there was a more pronounced decrease in the lipidated form of LC3 (LC3II). siRNA knockdown of TECPR2 showed similar changes, consistent with aberrant autophagy. Our results are strengthened by the fact that autophagy dysfunction has been implicated in a number of other neurodegenerative diseases. The discovered TECPR2 mutation implicates autophagy, a central intracellular mechanism, in spastic paraparesis.
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Affiliation(s)
- Danit Oz-Levi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Need AC, Shashi V, Hitomi Y, Schoch K, Shianna KV, McDonald MT, Meisler MH, Goldstein DB. Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet 2012; 49:353-61. [PMID: 22581936 PMCID: PMC3375064 DOI: 10.1136/jmedgenet-2012-100819] [Citation(s) in RCA: 335] [Impact Index Per Article: 27.9] [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] [Indexed: 01/06/2023]
Abstract
Background There is considerable interest in the use of next-generation sequencing to help diagnose unidentified genetic conditions, but it is difficult to predict the success rate in a clinical setting that includes patients with a broad range of phenotypic presentations. Methods The authors present a pilot programme of whole-exome sequencing on 12 patients with unexplained and apparent genetic conditions, along with their unaffected parents. Unlike many previous studies, the authors did not seek patients with similar phenotypes, but rather enrolled any undiagnosed proband with an apparent genetic condition when predetermined criteria were met. Results This undertaking resulted in a likely genetic diagnosis in 6 of the 12 probands, including the identification of apparently causal mutations in four genes known to cause Mendelian disease (TCF4, EFTUD2, SCN2A and SMAD4) and one gene related to known Mendelian disease genes (NGLY1). Of particular interest is that at the time of this study, EFTUD2 was not yet known as a Mendelian disease gene but was nominated as a likely cause based on the observation of de novo mutations in two unrelated probands. In a seventh case with multiple disparate clinical features, the authors were able to identify homozygous mutations in EFEMP1 as a likely cause for macular degeneration (though likely not for other features). Conclusions This study provides evidence that next-generation sequencing can have high success rates in a clinical setting, but also highlights key challenges. It further suggests that the presentation of known Mendelian conditions may be considerably broader than currently recognised.
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Affiliation(s)
- Anna C Need
- Center for Human Genome Variation, Duke University School of Medicine, Box 91009, Durham, NC 27708, USA.
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Hitomi Y, Cirulli ET, Fellay J, McHutchison JG, Thompson AJ, Gumbs CE, Shianna KV, Urban TJ, Goldstein DB. Inosine triphosphate protects against ribavirin-induced adenosine triphosphate loss by adenylosuccinate synthase function. Gastroenterology 2011; 140:1314-21. [PMID: 21199653 DOI: 10.1053/j.gastro.2010.12.038] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/09/2010] [Accepted: 12/14/2010] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Genetic variation of inosine triphosphatase (ITPA) causing an accumulation of inosine triphosphate (ITP) has been shown to protect patients against ribavirin (RBV)-induced anemia during treatment for chronic hepatitis C infection by genome-wide association study (GWAS). However, the biologic mechanism by which this occurs is unknown. METHODS We examined whether ITP can be used by adenosine triphosphatase (ATPase) in human erythrocytes or recombinant human adenylosuccinate synthase (ADSS). RBV-induced adenosine triphosphate (ATP) reduction in erythrocytes was compared with the genetically determined low or normal activity of ITPA, leading respectively to high or normal ITP levels. RESULTS Although ITP is not used directly by human erythrocyte ATPase, it can be used for ATP biosynthesis via ADSS in place of guanosine triphosphate (GTP). With RBV challenge, erythrocyte ATP reduction was more severe in the wild-type ITPA genotype than in the hemolysis protective ITPA genotype. This difference also remains after inhibiting adenosine uptake using nitrobenzylmercaptopurine riboside (NBMPR). Interestingly, the alleviation of ATP reduction by the hemolysis protective ITPA genotype was canceled by the ADSS inhibitor 6-mercaptoethanol (6-MP). CONCLUSIONS ITP confers protection against RBV-induced ATP reduction by substituting for erythrocyte GTP, which is depleted by RBV, in the biosynthesis of ATP. Because patients with excess ITP appear largely protected against anemia, these results confirm that RBV-induced anemia is due primarily to the effect of the drug on GTP and consequently ATP levels in erythrocytes.
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Affiliation(s)
- Yuki Hitomi
- Center for Human Genome Variation, School of Medicine, Duke University, Durham, North Carolina, USA
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Harada M, Hirota T, Jodo AI, Hitomi Y, Sakashita M, Tsunoda T, Miyagawa T, Doi S, Kameda M, Fujita K, Miyatake A, Enomoto T, Noguchi E, Masuko H, Sakamoto T, Hizawa N, Suzuki Y, Yoshihara S, Adachi M, Ebisawa M, Saito H, Matsumoto K, Nakajima T, Mathias RA, Rafaels N, Barnes KC, Himes BE, Duan QL, Tantisira KG, Weiss ST, Nakamura Y, Ziegler SF, Tamari M. Thymic stromal lymphopoietin gene promoter polymorphisms are associated with susceptibility to bronchial asthma. Am J Respir Cell Mol Biol 2010; 44:787-93. [PMID: 20656951 DOI: 10.1165/rcmb.2009-0418oc] [Citation(s) in RCA: 162] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Thymic stromal lymphopoietin (TSLP) triggers dendritic cell--mediated T helper (Th) 2 inflammatory responses. A single-nucleotide polymorphism (SNP), rs3806933, in the promoter region of the TSLP gene creates a binding site for the transcription factor activating protein (AP)-1. The variant enhances AP-1 binding to the regulatory element, and increases the promoter--reporter activity of TSLP in response to polyinosinic-polycytidylic acid (poly[I:C]) stimulation in normal human bronchial epithelium (NHBE). We investigated whether polymorphisms including the SNP rs3806933 could affect the susceptibility to and clinical phenotypes of bronchial asthma. We selected three representative (i.e., Tag) SNPs and conducted association studies of the TSLP gene, using two independent populations (639 patients with childhood atopic asthma and 838 control subjects, and 641 patients with adult asthma and 376 control subjects, respectively). We further examined the effects of corticosteroids and a long-acting β(2)-agonist (salmeterol) on the expression levels of the TSLP gene in response to poly(I:C) in NHBE. We found that the promoter polymorphisms rs3806933 and rs2289276 were significantly associated with disease susceptibility in both childhood atopic and adult asthma. The functional SNP rs3806933 was associated with asthma (meta-analysis, P = 0.000056; odds ratio, 1.29; 95% confidence interval, 1.14-1.47). A genotype of rs2289278 was correlated with pulmonary function. Moreover, the induction of TSLP mRNA and protein expression induced by poly(I:C) in NHBE was synergistically impaired by a corticosteroid and salmeterol. TSLP variants are significantly associated with bronchial asthma and pulmonary function. Thus, TSLP may serve as a therapeutic target molecule for combination therapy.
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Affiliation(s)
- Michishige Harada
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research, Kanagawa, Japan
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Hitomi Y, Ebisawa M, Tomikawa M, Imai T, Komata T, Hirota T, Harada M, Sakashita M, Suzuki Y, Shimojo N, Kohno Y, Fujita K, Miyatake A, Doi S, Enomoto T, Taniguchi M, Higashi N, Nakamura Y, Tamari M. Associations of functional NLRP3 polymorphisms with susceptibility to food-induced anaphylaxis and aspirin-induced asthma. J Allergy Clin Immunol 2009; 124:779-85.e6. [PMID: 19767079 DOI: 10.1016/j.jaci.2009.07.044] [Citation(s) in RCA: 140] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 07/06/2009] [Accepted: 07/21/2009] [Indexed: 01/01/2023]
Abstract
BACKGROUND NLR family, pyrin domain containing 3 (NLRP3), controls the activity of inflammatory caspase-1 by forming inflammasomes, which leads to cleavage of the procytokines IL-1beta and IL-18. Recent studies have shown associations of human NLRP3 polymorphisms with susceptibility to various inflammatory diseases; however, the association with allergic diseases remains unclear. OBJECTIVE We sought to examine whether NLRP3 polymorphisms are associated with susceptibility to food allergy, food-induced anaphylaxis, and aspirin-induced asthma (AIA). METHODS We selected 15 tag single nucleotide polymorphisms (SNPs) of NLRP3 and conducted association analyses of NLRP3 using 574 and 1279 samples for food allergy and AIA, respectively. We further performed functional analyses of the susceptible SNPs. RESULTS Two NLRP3 SNPs (rs4612666 and rs10754558) were significantly associated with susceptibility to food-induced anaphylaxis (P = .00086 and P = .00068, respectively). The NLRP3 haplotype of the 2 SNPs also showed a significant association (P = .000098). We could confirm the association with susceptibility to another hypersensitivity phenotype, AIA (rs4612666, P = .0096). Functional analysis revealed that the risk alleles of rs4612666 and rs10754558 increased the enhancer activity of NLRP3 expression and NLRP3 mRNA stability, respectively. CONCLUSION Our results indicate that the NLRP3 SNPs might play an important role in the development of food-induced anaphylaxis and AIA in a gain-of-function manner. Further research on the NLRP3 inflammasome will contribute to the development of novel diagnostic and therapeutic methods for food-induced anaphylaxis and AIA.
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Affiliation(s)
- Yuki Hitomi
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, RIKEN, Kanagawa, Japan
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Harada M, Obara K, Hirota T, Yoshimoto T, Hitomi Y, Sakashita M, Doi S, Miyatake A, Fujita K, Enomoto T, Taniguchi M, Higashi N, Fukutomi Y, Nakanishi K, Nakamura Y, Tamari M. A functional polymorphism in IL-18 is associated with severity of bronchial asthma. Am J Respir Crit Care Med 2009; 180:1048-55. [PMID: 19745201 DOI: 10.1164/rccm.200905-0652oc] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
RATIONALE IL-18 is a unique cytokine that enhances innate immunity and both Th1- and Th2-driven immune responses. Recent murine and human genetic studies have shown its role in the pathogenesis of asthma. OBJECTIVES We conducted an association study in a Japanese population to discover variants of IL-18 that might have an effect on asthma susceptibility and/or progression and conducted functional analyses of the related variants. METHODS The IL-18 gene locus was resequenced in 48 human chromosomes. Asthma severity was determined according to the 2002 Global Initiative for Asthma Guidelines. Association and haplotype analyses were performed using 1,172 subjects. MEASUREMENTS AND MAIN RESULTS Although no polymorphisms differed significantly in frequency between the control and adult asthma groups, rs5744247 C>G was significantly associated with the severity of adult asthma (steps 1, 2 vs. steps 3, 4; P = 0.0034). We also found a positive association with a haplotype (P = 0.0026). By in vitro functional analyses, the rs5744247 variant was found to increase enhancer-reporter activity of the IL-18 gene in bronchial epithelial cells. Expression levels of IL-18 in response to LPS stimulation in monocytes were significantly greater in subjects homozygous for the susceptibility G allele at rs5744247 C>G. Furthermore, we found a significant correlation between the serum IL-18 level and the genotype of rs5744247 (P = 0.031). CONCLUSIONS Although the association results need to be replicated by other studies, IL-18 variants are significantly associated with asthma severity, and the rs5744247 variant reflects higher transcriptional activity and higher expression of IL-18 in LPS-stimulated monocytes and a higher serum IL-18 level.
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Affiliation(s)
- Michishige Harada
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research (RIKEN, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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Tamari M, Harada M, Hirota T, Hitomi Y. [Bronchial asthma and genes of the innate immunity]. Arerugi 2009; 58:766-771. [PMID: 19675409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Mayumi Tamari
- Laboratory for Respiratory Diseases, Center for Genomic Medicine (CGM), RIKEN.
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Hitomi Y, Tsuchiya N, Hasegawa M, Fujimoto M, Takehara K, Tokunaga K, Sato S. Association of CD22 gene polymorphism with susceptibility to limited cutaneous systemic sclerosis. ACTA ACUST UNITED AC 2007; 69:242-9. [PMID: 17493148 DOI: 10.1111/j.1399-0039.2007.00801.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Activating and inhibitory signal transducers, CD19 and CD22, have been substantially implicated both in human systemic sclerosis (SSc) and tight-skin mouse, a model for SSc. We previously showed that a single nucleotide polymorphism (SNP) in CD19 promoter region was significantly associated with increased CD19 expression level and with susceptibility to SSc. In the present study, we examined whether CD22 polymorphisms were associated with susceptibility to SSc. CD22 variations were genotyped in 126 Japanese patients with SSc [47 diffuse cutaneous SSc and 79 limited cutaneous SSc (lcSSc)] and 93 unrelated healthy controls. At the c.2304C > A SNP coding for a synonymous substitution in exon 13, A/A genotype was observed in six patients with SSc (4.8 %) but none in the controls (P=0.040). All six patients with A/A genotype belonged to the lcSSc subgroup (7.6%, P=0.008 vs controls). Surface expression level of CD22 tended to be lower in B cells from the patients with A/A genotype (n=5) as compared with C/A (n=7) or C/C (n=14) genotype (17% decrease, P=0.0032). Taken together with our previous observation on CD19 polymorphism, intrinsic difference in the expression level of CD19 and CD22 was suggested to play a causative role in a proportion of patients with lcSSc.
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Affiliation(s)
- Y Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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