title: Human primary biliary cirrhosis-susceptible allele of rs4979462 enhances TNFSF15 expression by binding NF-1.
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.
authors.affiliation: Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan, yhitomi-tky@umin.ac.jp.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Hitomi
authors.forename: Minae
authors.initials: M
authors.lastname: Kawashima
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Aiba
authors.forename: Nao
authors.initials: N
authors.lastname: Nishida
authors.forename: Mika
authors.initials: M
authors.lastname: Matsuhashi
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Okazaki
authors.forename: Minoru
authors.initials: M
authors.lastname: Nakamura
authors.forename: Katsushi
authors.initials: K
authors.lastname: Tokunaga
mesh_terms: D000483:Alleles; D016022:Case-Control Studies; D005260:Female; D005786:Gene Expression Regulation; D055106:Genome-Wide Association Study; D006801:Humans; D019169:Jurkat Cells; D008105:Liver Cirrhosis, Biliary / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D008297:Male; D025542:Neurofibromin 1 / Q000235:genetics / Q000378:metabolism; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D053380:Tumor Necrosis Factor Ligand Superfamily Member 15 / Q000235:genetics / Q000378:metabolism
chemical_list: D025542:Neurofibromin 1; C117026:TNFSF15 protein, human; D053380:Tumor Necrosis Factor Ligand Superfamily Member 15