NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants

Yuki Hitomi; Ken Nakatani; Kaname Kojima; Nao Nishida; Yosuke Kawai; Minae Kawashima; Yoshihiro Aiba; Masao Nagasaki; Minoru Nakamura; Katsushi Tokunaga

doi:10.1016/j.jcmgh.2018.11.006

NFKB1 and MANBA Confer Disease Susceptibility to Primary Biliary Cholangitis via Independent Putative Primary Functional Variants

Cell Mol Gastroenterol Hepatol. 2019;7(3):515-532. doi: 10.1016/j.jcmgh.2018.11.006. Epub 2018 Dec 4.

Authors

Affiliations

¹ Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan. Electronic address: yhitomi-tky@umin.ac.jp.
² Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan.
³ Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Graduate School of Medicine, Tohoku University, Sendai, Japan.
⁴ Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan; The Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Ichikawa, Japan.
⁵ Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan; Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Graduate School of Medicine, Tohoku University, Sendai, Japan.
⁶ Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan; Japan Science and Technology Agency, Tokyo, Japan.
⁷ Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan.
⁸ Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan; Graduate School of Medicine, Tohoku University, Sendai, Japan; Graduate School of Information Sciences, Tohoku University, Sendai, Japan.
⁹ Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan; Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Headquarters of Primary Biliary Cholangitis (PBC) Research in National Hospital Organization Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization, Nagasaki Medical Center, Omura, Japan.

Abstract

Background & aims: Primary biliary cholangitis (PBC) is a chronic and cholestatic liver disease that eventually leads to cirrhosis and hepatic failure. We recently identified several susceptibility genes included NFKB1 and MANBA for PBC in the Japanese population by genome-wide association study. However, the primary functional variants in the NFKB1/MANBA region and the molecular mechanism for conferring disease susceptibility to PBC have not yet been clarified.

Methods: We performed high-density association mapping based on a single-nucleotide polymorphism (SNP) imputation analysis, using data from a whole-genome sequence reference panel of 1070 Japanese individuals and the previous genome-wide association study (1389 PBC patients, 1508 healthy controls). Among SNPs (P < 5.0 × 10^-7) in the NFKB1/MANBA region, putative primary functional variants and the molecular mechanism for conferring disease susceptibility to PBC were identified by in silico/in vitro functional analysis.

Results: Among the SNPs in the NFKB1/MANBA region, rs17032850 and rs227361, which changed the binding of transcription factors lymphoid enhancer-binding factor 1 (LEF-1) and retinoid X receptor α (RXRα), respectively, were identified as putative primary functional variants that regulate gene expression. In addition, expression-quantitative trait locus data and gene editing using a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system supported the potential role of rs17032850 and rs227361 in regulating NFKB1 and MANBA expression, respectively.

Conclusions: We identified independent putative primary functional variants in NFKB1/MANBA and showed the distinct molecular mechanism by which each putative primary functional variant conferred susceptibility to PBC. Our approach was useful to dissect the pathogenesis not only of PBC, but also other digestive diseases in which NFKB1/MANBA has been reported as a susceptibility locus.

Keywords: CRISPR/Cas9; Disease Susceptibility Gene; GWAS; PBC; e-QTL.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Amino Acid Substitution
Asian People / genetics
Chromosome Segregation / genetics
Gene Expression Regulation
Genetic Loci
Genetic Predisposition to Disease*
Hep G2 Cells
Humans
Jurkat Cells
Linkage Disequilibrium / genetics
Liver Cirrhosis, Biliary / genetics*
NF-kappa B p50 Subunit / genetics*
Polymorphism, Single Nucleotide / genetics*
Risk Factors
Transcription Factors / metabolism
beta-Mannosidase / genetics*

Substances

NF-kappa B p50 Subunit
NFKB1 protein, human
Transcription Factors
beta-Mannosidase