Integrated GWAS and mRNA Microarray Analysis Identified IFNG and CD40L as the Central Upstream Regulators in Primary Biliary Cholangitis

Kazuko Ueno; Yoshihiro Aiba; Yuki Hitomi; Shinji Shimoda; Hitomi Nakamura; Olivier Gervais; Yosuke Kawai; Minae Kawashima; Nao Nishida; Seik-Soon Kohn; Kaname Kojima; 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 Ohta; Takuya Komura; Satoru Tsuruta; Kazuhiko Yamauchi; Tatsuro Kobata; Amane Kitasato; Tamotsu Kuroki; Seigo Abiru; Shinya Nagaoka; Atsumasa Komori; Hiroshi Yatsuhashi; Kiyoshi Migita; Hiromasa Ohira; Atsushi Tanaka; Hajime Takikawa; Masao Nagasaki; Katsushi Tokunaga; Minoru Nakamura; PBC‐GWAS Consortium in Japan

doi:10.1002/hep4.1497

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. doi: 10.1002/hep4.1497. eCollection 2020 May.

Authors

Kazuko Ueno^{1

2}, Yoshihiro Aiba³, Yuki Hitomi^{2

4}, Shinji Shimoda⁵, Hitomi Nakamura³, Olivier Gervais⁶, Yosuke Kawai^{1

2}, Minae Kawashima⁷, Nao Nishida^{1

2}, Seik-Soon Kohn^{1

2}, Kaname Kojima⁸, Shinji Katsushima⁹, Atsushi Naganuma⁹, Kazuhiro Sugi⁹, Tatsuji Komatsu⁹, Tomohiko Mannami⁹, Kouki Matsushita⁹, Kaname Yoshizawa⁹, Fujio Makita⁹, Toshiki Nikami⁹, Hideo Nishimura⁹, Hiroshi Kouno⁹, Hirotaka Kouno⁹, Hajime Ohta⁹, Takuya Komura⁹, Satoru Tsuruta⁹, Kazuhiko Yamauchi⁹, Tatsuro Kobata⁹, Amane Kitasato¹⁰, Tamotsu Kuroki^{3

10

11}, Seigo Abiru³, Shinya Nagaoka³, Atsumasa Komori^{3

11}, Hiroshi Yatsuhashi^{3

11}, Kiyoshi Migita^{3

12}, Hiromasa Ohira¹², Atsushi Tanaka¹³, Hajime Takikawa¹³, Masao Nagasaki⁶, Katsushi Tokunaga^{1

2}, Minoru Nakamura^{3

9

11

14}; PBC‐GWAS Consortium in Japan

Affiliations

¹ Genome Medical Science Project National Center for Global Health and Medicine Tokyo Japan.
² Department of Human Genetics Graduate School of Medicine University of Tokyo Tokyo Japan.
³ Clinical Research Center National Hospital Organization of Nagasaki Medical Center Omura Japan.
⁴ Department of Microbiology Hoshi University School of Pharmacy and Pharmaceutical Sciences Tokyo Japan.
⁵ Department of Medicine and Biosystemic Science Kyushu University Graduate School of Medical Sciences Fukuoka Japan.
⁶ Human Biosciences Unit for the Top Global Course Center for the Promotion of Interdisciplinary Education and Research Kyoto University Kyoto Japan.
⁷ Japan Science and Technology Agency Tokyo Japan.
⁸ Tohoku Medical Megabank Organization Tohoku University Sendai Japan.
⁹ Headquarters of PBC Research National Hospital Organization Study Group for Liver Disease in Japan Omura Japan.
¹⁰ Department of Surgery National Hospital Organization of Nagasaki Medical Center Omura Japan.
¹¹ Department of Hepatology Graduate School of Biomedical Sciences Nagasaki University Omura Japan.
¹² Department of Gastroenterology and Rheumatic Diseases Fukushima Medical University of Medicine Fukushima Japan.
¹³ Department of Medicine Teikyo University School of Medicine Tokyo Japan.
¹⁴ Headquarters of PBC-GWAS Consortium in Japan National Hospital Organization of Nagasaki Medical Center Graduate School of Biomedical Sciences Nagasaki University Omura Japan.

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.