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

• Published in: Human genetics 2015-07, Vol.134 (7), p.737-747
• Main Authors: Hitomi, Yuki, Kawashima, Minae, Aiba, Yoshihiro, Nishida, Nao, Matsuhashi, Mika, Okazaki, Hitoshi, Nakamura, Minoru, Tokunaga, Katsushi
• Format: Article
• Language: English
• Subjects: Alleles; Analysis; Biliary cirrhosis; Biomedical and Life Sciences; Biomedicine; Case-Control Studies; Disease; Female; Gene Expression Regulation; Gene Function; Genetic research; Genome-Wide Association Study; Genomes; Genomics; Human Genetics; Humans; Jurkat Cells; Liver cirrhosis; Liver Cirrhosis, Biliary - genetics; Liver Cirrhosis, Biliary - metabolism; Liver Cirrhosis, Biliary - pathology; Male; Medicine; Metabolic Diseases; Molecular Medicine; Neurofibromin 1 - genetics; Neurofibromin 1 - metabolism; Original Investigation; Polymorphism, Single Nucleotide; Protein Binding; Research centers; RNA; Single nucleotide polymorphisms; Tumor necrosis factor; Tumor Necrosis Factor Ligand Superfamily Member 15 - genetics; Tumor Necrosis Factor Ligand Superfamily Member 15 - metabolism; Tumor necrosis factor-TNF
• ISSN: 0340-6717; 1432-1203
• DOI: 10.1007/s00439-015-1556-3

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.