Identification of deleterious rare variants in MTTP, PNPLA3, and TM6SF2 in Japanese males and association studies with NAFLD

Supichaya Boonvisut,Kazuhisa Watanabe,Ken Yoshida,Hiroshi Miyashita,Sadahiko Iwamoto,Kazuhiro Nakayama

doi:10.1186/s12944-017-0570-y

Supichaya Boonvisut, Kazuhisa Watanabe + Show 4 more

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https://doi.org/10.1186/s12944-017-0570-y

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Abstract

BackgroundNon-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes without excessive alcohol intake. NAFLD is influenced by genetic factors, and the heritability has been estimated at 0.35 to 0.6 by twin studies. We explored rare variants in known NAFLD-associated genes to investigate whether these rare variants are involved in the susceptibility to NAFLD.MethodsThe target genes for re-sequencing were PNPLA3, TM6SF2, and MTTP. All exons of these three genes were amplified from a discovery panel of 950 Japanese males, and the identified rare variants were further tested for genetic association in 3014 individuals from the Japanese general population and for in vitro functional evaluation.ResultsTarget re-sequencing analysis using next-generation sequencing identified 29 rare variants in 65 Japanese males (6.84%), 12 of which were newly identified base substitutions. A splicing mutation in TM6SF2 that resulted in deletion of 31 amino acids was identified in an NAFLD case. Among eight genotyped rare single-nucleotide polymorphisms (SNPs; minor allele frequency < 0.02), rs143392071 (Tyr220Cys, PNPLA3) significantly increased (odds ratio = 3.52, P = 0.008) and rs756998920 (Val42Ile, MTTP) significantly decreased (odds ratio = 0.03, P = 0.019) the NAFLD risk. Functional assays showed that these two SNPs disrupted protein functions and supported the genetic association.ConclusionCollectively, 1.79% of individuals in our studied population were estimated carriers of rare variants that are potentially associated with NAFLD.

Highlights

Non-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes without excessive alcohol intake
Rare variants of microsomal triglyceride transfer protein (MTTP), patatin like phospholipase domain containing 3 (PNPLA3), and transmembrane 6 superfamily member 2 (TM6SF2) in Japanese adults Twenty-nine rare single-nucleotide variations were identified using GS Junior sequencing in Japanese males in the discovery panel (n = 950) who did not abuse alcohol
To determine whether the identified rare alleles accumulated in NAFLD cases, burden tests of rare variants in the three genes were evaluated by two mutation sets: (A) non-synonymous, splicing disruption, and frame shift variants, and (B) non-synonymous variants that were expected to be damaging as determined by PolyPhen analysis

Summary

Introduction

Non-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes without excessive alcohol intake. Non-alcoholic fatty liver disease (NAFLD) is a disorder characterized by excessive fat deposits in hepatocytes in the absence of excessive alcohol intake. Common variants near neurocan-cartilage intermediate layer protein 2 region (NCAN-CILP2), glucokinase regulator (GCKR), lysophospholipase like 1 (LYPLAL1), and patatin like phospholipase domain containing 3 (PNPLA3) were identified in a GWAS of individuals of European descent [7]. Among these loci, NCANCILP2 and PNPLA3 have been repeatedly identified as being deeply associated with NAFLD in multiple

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