GWAS for systemic sclerosis identifies six novel susceptibility loci including one in the Fcγ receptor region

• Published in: Nature communications Vol. 15; no. 1; pp. 319 - 16
• Main Authors: Ishikawa, Yuki, Tanaka, Nao, Asano, Yoshihide, Kodera, Masanari, Shirai, Yuichiro, Akahoshi, Mitsuteru, Hasegawa, Minoru, Matsushita, Takashi, Saito, Kazuyoshi, Motegi, Sei-ichiro, Yoshifuji, Hajime, Yoshizaki, Ayumi, Kohmoto, Tomohiro, Takagi, Kae, Oka, Akira, Kanda, Miho, Tanaka, Yoshihito, Ito, Yumi, Nakano, Kazuhisa, Kasamatsu, Hiroshi, Utsunomiya, Akira, Sekiguchi, Akiko, Niiro, Hiroaki, Jinnin, Masatoshi, Makino, Katsunari, Makino, Takamitsu, Ihn, Hironobu, Yamamoto, Motohisa, Suzuki, Chisako, Takahashi, Hiroki, Nishida, Emi, Morita, Akimichi, Yamamoto, Toshiyuki, Fujimoto, Manabu, Kondo, Yuya, Goto, Daisuke, Sumida, Takayuki, Ayuzawa, Naho, Yanagida, Hidetoshi, Horita, Tetsuya, Atsumi, Tatsuya, Endo, Hirahito, Shima, Yoshihito, Kumanogoh, Atsushi, Hirata, Jun, Otomo, Nao, Suetsugu, Hiroyuki, Koike, Yoshinao, Tomizuka, Kohei, Yoshino, Soichiro, Liu, Xiaoxi, Ito, Shuji, Hikino, Keiko, Suzuki, Akari, Momozawa, Yukihide, Ikegawa, Shiro, Tanaka, Yoshiya, Ishikawa, Osamu, Takehara, Kazuhiko, Torii, Takeshi, Sato, Shinichi, Okada, Yukinori, Mimori, Tsuneyo, Matsuda, Fumihiko, Matsuda, Koichi, Amariuta, Tiffany, Imoto, Issei, Matsuo, Keitaro, Kuwana, Masataka, Kawaguchi, Yasushi, Ohmura, Koichiro, Terao, Chikashi
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 31-01-2024; Nature Publishing Group; Nature Portfolio
• Subjects: 45/23; 45/43; 45/61; 631/208/199; 631/208/200; 631/208/205/2138; 631/250/248; 692/4023/1670/122/1801; Binding sites; Fc receptors; Genetic Loci; Genetic Predisposition to Disease - genetics; Genetic Risk Score; Genome-wide association studies; Genome-Wide Association Study; Genomes; Humanities and Social Sciences; Humans; Interferon Regulatory Factors - genetics; Linkage disequilibrium; Lymphocytes B; Meta-analysis; multidisciplinary; Pathogenesis; Polymorphism, Single Nucleotide; Population genetics; Populations; Receptors, IgG - genetics; Risk; Science; Science (multidisciplinary); Scleroderma; Scleroderma, Systemic - genetics; Single-nucleotide polymorphism; Systemic sclerosis
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-44541-z

Here we report the largest Asian genome-wide association study (GWAS) for systemic sclerosis performed to date, based on data from Japanese subjects and comprising of 1428 cases and 112,599 controls. The lead SNP is in the FCGR/FCRL region, which shows a penetrating association in the Asian population, while a complete linkage disequilibrium SNP, rs10917688, is found in a cis-regulatory element for IRF8. IRF8 is also a significant locus in European GWAS for systemic sclerosis, but rs10917688 only shows an association in the presence of the risk allele of IRF8 in the Japanese population. Further analysis shows that rs10917688 is marked with H3K4me1 in primary B cells. A meta-analysis with a European GWAS detects 30 additional significant loci. Polygenic risk scores constructed with the effect sizes of the meta-analysis suggest the potential portability of genetic associations beyond populations. Prioritizing the top 5% of SNPs of IRF8 binding sites in B cells improves the fitting of the polygenic risk scores, underscoring the roles of B cells and IRF8 in the development of systemic sclerosis. The results also suggest that systemic sclerosis shares a common genetic architecture across populations.
Here, the authors identify six risk SNPs for systemic sclerosis by performing GWAS on Japanese patients and meta-analyzing Japanese and European GWAS datasets. Downstream analyses indicate that B cells contribute to pathogenesis.