We explore the development mechanism of PBC by searching for susceptibility gene of exhaustive PBC over the whole genome.
原発性胆汁性胆管炎(PBC)は、肝臓内にある小さな胆管(胆汁排泄のための管)に炎症が起こり、胆管が破壊され胆汁が肝臓にうっ滞することによって起こる病気です。その発症には、自己の免疫システムが誤って自己の組織(胆管細胞)を攻撃してしまう「自己免疫」の関与が示唆されていますが、その発症や病態に関しては、多くが不明なままとなっています。
私たちは、長崎大学の中村稔教授、京都大学学際融合教育研究推進センターの長崎正朗特定教授、などとの共同研究により、ゲノムワイド関連解析(GWAS)という手法を用いて、全ゲノムに渡る網羅的なPBCの感受性遺伝子探索を実施しています。
7. PBCを対象としたHLA解析
全ゲノムに渡るおよそ60万ヶ所のマーカーSNPに対し、PBC患者1,274例・健常者1,091例を用いたGWASを実施した結果、HLA遺伝子群、TNFSF15、POU2AF1が疾患感受性との強い関連を示しました。(Nakamura M et al, Am J Hum Genet 2012)
サンプル数を拡大したGWAS (PBC患者1,406例・健常者7,541例)にて、合計8ヶ所の疾患感受性遺伝子を同定しました。(Kawashima M et al, Hum Mol Genet 2017)
さらに、新たに収集したサンプルを対象に実施したGWAS(PBC患者668例・健常者480例)と、これまでのGWASとのメタ・アナリシスにて、これまでにはアジア人で報告されていなかった新規疾患感受性遺伝子領域Chromosome 3q13.33を同定しました。(Hitomi Y, Ueno K, et al, Sci Rep 2019)
Hitomi Y, Ueno K, Aiba Y, Nishida N, Kawai Y, Kawashima M, Khor SS, Takada S, Iwabuchi C, Nagasaki M, Tokunaga K, and Nakamura M: rs10924104 in the expression enhancer motif of CD58 confers susceptibility to human autoimmune diseases. Hum. Genet. 2023 Nov. Online ahead of print. |
Khor SS, Ueno K, Nishida N, Kawashima M, Kawai Y, Aiba Y, Hitomi Y, Nagasaki M, Nakamura M, and 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. 14:1151502, 2023. |
Hitomi Y, Aiba Y, Ueno K, Nishida N, Kawai Y, Kawashima M, Tsuiji M, Iwabuchi C, Takada S, Miyake N, Nagasaki M, Tokunaga K, and Nakamura M: rs2013278 in the multiple immunological-trait susceptibility locus CD28 regulates the production of non-functional splicing isoforms. Hum. Genomics 16(1): 46, 2022. |
Hitomi Y, Aiba Y, Ueno K, Nishida N, Kawai Y, Kawashima M, Yasunami M, Gervais O, Ito M, Cordell HJ, Mells GF, Nagasaki M, Tokunaga K, Tsuiji M, and Nakamura M: rs9459874 and rs1012656 in CCR6/FGFR1OP confer susceptibility to primary biliary cholangitis. J. Autoimmun. 126: e102775, 2022. |
Gervais, Olivier, Kazuko Ueno, Yosuke Kawai, Yuki Hitomi, Yoshihiro Aiba, Mayumi Ueta, Minoru Nakamura, Katsushi Tokunaga, and Masao Nagasaki. Regional Heritability Mapping Identifies Several Novel Loci (STAT4, ULK4, and KCNH5) for Primary Biliary Cholangitis in the Japanese Population. European Journal of Human Genetics. 2021. |
Cordell, Heather J., James J. Fryett, Kazuko Ueno, Rebecca Darlay, Yoshihiro Aiba, Yuki Hitomi, Minae Kawashima, Nao Nishida, Seik-Soon Khor, Olivier Gervais, Yosuke Kawai, Masao Nagasaki, Katsushi Tokunaga, Ruqi Tang, Yongyong Shi, Zhiqiang Li, Brian D. Juran, Elizabeth J. Atkinson, Alessio Gerussi, Marco Carbone, Rosanna Asselta, Angela Cheung, Mariza de Andrade, Aris Baras, Julie Horowitz, Manuel A. R. Ferreira, Dylan Sun, David E. Jones, Steven Flack, Ann Spicer, Victoria L. Mulcahy, Jinyoung Byan, Younghun Han, Richard N. Sandford, Konstantinos N. Lazaridis, Christopher I. Amos, Gideon M. Hirschfield, Michael F. Seldin, Pietro Invernizzi, Katherine A. Siminovitch, Xiong Ma, Minoru Nakamura, George F. Mells, Katherine A. Siminovitch, Gideon M. Hirschfield, Andrew Mason, Catherine Vincent, Gang Xie, Jinyi Zhang, Ruqi Tang, Xiong Ma, Zhiqiang Li, Yongyong Shi, Andrea Affronti, Piero L. Almasio, Domenico Alvaro, Pietro Andreone, Angelo Andriulli, Francesco Azzaroli, Pier Maria Battezzati, Antonio Benedetti, MariaConsiglia Bragazzi, Maurizia Brunetto, Savino Bruno, Vincenza Calvaruso, Vincenzo Cardinale, Giovanni Casella, Nora Cazzagon, Antonio Ciaccio, Barbara Coco, Agostino Colli, Guido Colloredo, Massimo Colombo, Silvia Colombo, Laura Cristoferi, Carmela Cursaro, Lory Saveria Croce, Andrea Crosignani, Daphne D’Amato, Francesca Donato, Gianfranco Elia, Stefano Fagiuoli, Carlo Ferrari, Annarosa Floreani, Andrea Galli, Edoardo Giannini, Ignazio Grattagliano, Pietro Lampertico, Ana Lleo, Federica Malinverno, Clara Mancuso, Fabio Marra, Marco Marzioni, Sara Massironi, Alberto Mattalia, Luca Miele, Chiara Milani, Lorenzo Morini, Filomena Morisco, Luigi Muratori, Paolo Muratori, Grazia A. Niro, Sarah O’Donnell, Antonio Picciotto, Piero Portincasa, Cristina Rigamonti, Vincenzo Ronca, Floriano Rosina, Giancarlo Spinzi, Mario Strazzabosco, Mirko Tarocchi, Claudio Tiribelli, Pierluigi Toniutto, Luca Valenti, Maria Vinci, Massimo Zuin, Hitomi Nakamura, Seigo Abiru, Shinya Nagaoka, Atsumasa Komori, Hiroshi Yatsuhashi, Hiromi Ishibashi, Masahiro Ito, Kiyoshi Migita, Hiromasa Ohira, Shinji Katsushima, Atsushi Naganuma, Kazuhiro Sugi, Tatsuji Komatsu, Tomohiko Mannami, Kouki Matsushita, Kaname Yoshizawa, Fujio Makita, Toshiki Nikami, Hideo Nishimura, Hiroshi Kouno, Hirotaka Kouno, Hajime Ota, Takuya Komura, Yoko Nakamura, Masaaki Shimada, Noboru Hirashima, Toshiki Komeda, Keisuke Ario, Makoto Nakamuta, Tsutomu Yamashita, Kiyoshi Furuta, Masahiro Kikuchi, Noriaki Naeshiro, Hironao Takahashi, Yutaka Mano, Seiji Tsunematsu, Iwao Yabuuchi, Yusuke Shimada, Kazuhiko Yamauchi, Rie Sugimoto, Hironori Sakai, Eiji Mita, Masaharu Koda, Satoru Tsuruta, Hiroshi Kamitsukasa, Takeaki Sato, Naohiko Masaki, Tatsuro Kobata, Nobuyoshi Fukushima, Yukio Ohara, Toyokichi Muro, Eiichi Takesaki, Hitoshi Takaki, Tetsuo Yamamoto, Michio Kato, Yuko Nagaoki, Shigeki Hayashi, Jinya Ishida, Yukio Watanabe, Masakazu Kobayashi, Michiaki Koga, Takeo Saoshiro, Michiyasu Yagura, Keisuke Hirata, Atsushu Tanaka, Hajime Takikawa, Mikio Zeniya, Masanori Abe, Morikazu Onji, Shuichi Kaneko, Masao Honda, Kuniaki Arai, Teruko Arinaga-Hino, Etsuko Hashimoto, Makiko Taniai, Takeji Umemura, Satoru Joshita, Kazuhiko Nakao, Tatsuki Ichikawa, Hidetaka Shibata, Satoshi Yamagiwa, Masataka Seike, Koichi Honda, Shotaro Sakisaka, Yasuaki Takeyama, Masaru Harada, Michio Senju, Osamu Yokosuka, Tatsuo Kanda, Yoshiyuki Ueno, Kentaro Kikuchi, Hirotoshi Ebinuma, Takashi Himoto, Michio Yasunami, Kazumoto Murata, Masashi Mizokami, Kazuhito Kawata, Shinji Shimoda, Yasuhiro Miyake, Akinobu Takaki, Kazuhide Yamamoto, Katsuji Hirano, Takafumi Ichida, Akio Ido, Hirohito Tsubouchi, Kazuaki Chayama, Kenichi Harada, Yasuni Nakanuma, Yoshihiko Maehara, Akinobu Taketomi, Ken Shirabe, Yuji Soejima, Akira Mori, Shintaro Yagi, Shinji Uemoto, H. 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Thomson, Andrew Bell, Voi Shim Wong, Richard Kia, Ian Gee, Richard Keld, Rupert Ransford, James Gotto, Charles Millson, Brian D. Juran, Elizabeth J. Atkinson, Angela Cheung, Mariza de Andrade, Konstantinos N. Lazaridis, Naga Chalasani, Vel Luketic, Joseph Odin, Kapil Chopra, Aris Baras, Julie Horowitz, Goncalo Abecasis, Michael Cantor, Giovanni Coppola, Aris Economides, Luca A. Lotta, John D. Overton, Jeffrey G. Reid, Alan Shuldiner, Christina Beechert, Caitlin Forsythe, Erin D. Fuller, Zhenhua Gu, Michael Lattari, Alexander Lopez, John D. Overton, Thomas D. Schleicher, Maria Sotiropoulos Padilla, Karina Toledo, Louis Widom, Sarah E. Wolf, Manasi Pradhan, Kia Manoochehri, Ricardo H. Ulloa, Xiaodong Bai, Suganthi Balasubramanian, Leland Barnard, Andrew Blumenfeld, Gisu Eom, Lukas Habegger, Alicia Hawes, Shareef Khalid, Jeffrey G. Reid, Evan K. Maxwell, William Salerno, Jeffrey C. Staples, Marcus B. Jones, and Lyndon J. Mitnaul. 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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; Canadian-US PBC Consortium; Italian PBC Genetics Study Group; UK-PBC Consortium; Japan PBC-GWAS Consortium, 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 Jun;160(7):2483-2495.e26. |
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 Feb 25;11(1):4557. |
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; PBC‐GWAS Consortium in Japan. Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis. Hepatol Commun. 2020 Mar 15;4(5):724-738. |
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 9: 102, 2019. |
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 7: 515-532, 2019. |
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 8: 11808, 2018. |
Nishida N, Aiba Y, Hitomi Y, Kawashima M, Kojima K, Kawai Y, Ueno K, Nakamura H, Yamashiki N, Tanaka T, Tamura S, Mori A, Yagi S, Soejima Y, Yoshizumi T, Takatsuki M, Tanaka A, Harada K, Shimoda S, Komori A, Eguchi S, Maehara Y, Uemoto S, Kokudo N, Nagasaki M, Tokunaga K, Nakamura M. NELFCD and CTSZ loci are associated with jaundice-stage progression in primary biliary cholangitis in the Japanese population. Sci Rep 8: 8071, 2018. |
Im C, Sapkota Y, Moon W, Kawashima M, Nakamura M, Tokunaga K, Yasui Y. Genome-wide haplotype association analysis of primary biliary cholangitis risk in Japanese. Sci Rep 8: 7806, 2018. |
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 7:11093, 2017. |
Hitomi Y (#), Kojima K (#), Kawashima M, Kawai Y, Nishida N, Aiba Y, Yasunami M, Nagasaki M, Nakamura M, Tokunaga K. Identification of the functional variant driving ORMDL3 and GSDMB expression in human chromosome 17q12-21 in primary biliary cholangitis. (#Equally contributed) Sci Rep 7: 2904, 2017. |
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, Nakamura M, Kohjima M, Komatsu T, Komeda T, Ohara Y, Muro T, Yamashita T, Yoshizawa K, Kamitsukasa Y, 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, 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, Kokubo N, Takikawa H, Ishibashi H, Chayama K, Mizokami M, Nagasaki M, Tokunaga K, Nakamura M. Genome-wide association studies identify PRKCB as a genetic susceptibility locus for primary biliary cirrhosis in the Japanese population. (#Equally contributed) Hum Mol Genet 26(3):650-659, 2017 |
Sun YH, Irwanto A, Toyo-oka L, Hong MH, Liu H, Andiappan AK, Choi HC, Hitomi Y, Yu GQ, Yu YX, Bao FF, Wang C, Fu X, Yue ZH, Wang HL, Zhang HM, Kawashima M, Kojima K, Nagasaki M, Nakamura M, Yang SK, Ye BD, Denise Y, Rotzschke O, Song KY, Tokunaga K, Zhang FR, Liu JJ. Fine-mapping analysis revealed complex pleiotropic effect and tissue-specific regulatory mechanism of TNFSF15 in primary biliary cholangitis, Crohn's disease and leprosy. Sci Rep 6: 31429, 2016. |
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 60(9):525-31, 2015. |
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 134(7):737-47, 2015. |
Aiba Y, Harada K, Komori A, Ito M, Shimoda S, Nakamura H, Nagaoka S, Abiru S, Migita K, Ishibashi H, Nakanuma Y, Nishida N, Kawashima M, Tokunaga K, Yatsuhashi H, Nakamura M.Systemic and local expression levels of TNF-like ligand 1A and its decoy receptor 3 are increased in primary biliary cirrhosis. Liver Int. 34(5):679-88, 2014. |
Nakamura M, Nishida N, Kawashima M, Aiba Y, Tanaka A, Yasunami M, Nakamura H, Komori A, Nakamuta M, Zeniya M, Hashimoto E, Ohira H, Yamamoto K, Onji M, Kaneko S, Honda M, Yamagiwa S, Nakao K, Ichida T, Takikawa H, Seike M, Umemura T, Ueno Y, Sakisaka S, Kikuchi K, Ebinuma H, Yamashiki N, Tamura S, Sugawara Y, Mori A, Yagi S, Shirabe K, Taketomi A, Arai K, Monoe K, Ichikawa T, Taniai M, Miyake Y, Kumagi T, Abe M, Yoshizawa K, Joshita S, Shimoda S, Honda K, Takahashi H, Hirano K, Takeyama Y, Harada K, Migita K, Ito M, Yatsuhashi H, Fukushima N, Ota H, Komatsu T, Saoshiro T, Ishida J, Kouno H, Kouno H, Yagura M, Kobayashi M, Muro T, Masaki N, Hirata K, Watanabe Y, Nakamura Y, Shimada M, Hirashima N, Komeda T, Sugi K, Koga M, Ario K, Takesaki E, Maehara Y, Uemoto S, Kokudo N, Tsubouchi H, Mizokami M, Nakanuma Y, Tokunaga K, Ishibashi H: Genome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population.Am J Hum Genet, 91(4):721-8, 2012. |