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Human primary biliary cirrhosis-susceptible allele of rs4979462 enhances TNFSF15 expression by binding NF-1

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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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Acknowledgments

We would like to thank all the patients and volunteers who enrolled in the study. We also thank Ms. Megumi Sageshima, Ms. Yuko Hirano, Ms. Natsumi Baba, Ms. Rieko Shirahashi, Ms. Ayumi Nakayama (The University of Tokyo), and Ms. Hitomi Nakamura (National Hospital Organization Nagasaki Medical Center) for technical and administrative assistance. This work was supported by Grant-in-Aid for Scientific Research from the Japan Society for the Promotion of Science (#23591006, #2629318) to M.N., Grant-in-Aid for Clinical Research from the NHO to M.N., Grant from the Research Program of Intractable Disease provided by the Ministry of Health, Labor, and Welfare of Japan to M.N., Grant from Core-to-Core program (Asia-Africa Science Platforms) from the Japan Society for the Promotion of Science to K.T., Uehara Memorial Foundation to Y.H., and Takeda Foundation to Y.H.

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Authors and Affiliations

  1. Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Yuki Hitomi, Minae Kawashima, Nao Nishida & Katsushi Tokunaga

  2. Japan Science and Technology Agency (JST), Tokyo, Japan

    Minae Kawashima

  3. Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Ōmura, Nagasaki, Japan

    Yoshihiro Aiba & Minoru Nakamura

  4. The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Chiba, Japan

    Nao Nishida

  5. Department of Transfusion Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan

    Mika Matsuhashi & Hitoshi Okazaki

  6. Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Ōmura, Nagasaki, Japan

    Minoru Nakamura

  7. Headquarters of PBC Research in NHOSLJ, Clinical Research Center, National Hospital Organization Nagasaki Medical Center, Ōmura, Nagasaki, Japan

    Minoru Nakamura

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  1. Yuki Hitomi
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  2. Minae Kawashima
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  3. Yoshihiro Aiba
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  8. Katsushi Tokunaga
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Correspondence to Yuki Hitomi.

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Hitomi, Y., Kawashima, M., Aiba, Y. et al. Human primary biliary cirrhosis-susceptible allele of rs4979462 enhances TNFSF15 expression by binding NF-1. Hum Genet 134, 737–747 (2015). https://doi.org/10.1007/s00439-015-1556-3

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