Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease

Abstract

Nonalcoholic fatty liver disease (NAFLD) is a burgeoning health problem of unknown etiology that varies in prevalence among ancestry groups. To identify genetic variants contributing to differences in hepatic fat content, we carried out a genome-wide association scan of nonsynonymous sequence variations (n = 9,229) in a population comprising Hispanic, African American and European American individuals. An allele in PNPLA3 (rs738409[G], encoding I148M) was strongly associated with increased hepatic fat levels (P = 5.9 x 10(-10)) and with hepatic inflammation (P = 3.7 x 10(-4)). The allele was most common in Hispanics, the group most susceptible to NAFLD; hepatic fat content was more than twofold higher in PNPLA3 rs738409[G] homozygotes than in noncarriers. Resequencing revealed another allele of PNPLA3 (rs6006460[T], encoding S453I) that was associated with lower hepatic fat content in African Americans, the group at lowest risk of NAFLD. Thus, variation in PNPLA3 contributes to ancestry-related and inter-individual differences in hepatic fat content and susceptibility to NAFLD.

Figure 1

Whole-genome scan of liver triglyceride content measured by proton magnetic resonance imaging in the Dallas Heart Study (n=2,111). (a) Quantile-quantile plot of P-values. (b) Scatter plot of P-values. The dashed line denotes the Bonferroni corrected significance threshold (P=5.4×10⁻⁶).

Figure 2

Association between a sequence variant in PNPLA3 (I148M) and hepatic triglyceride (TG) content. (a) PNPLA3 is a 481 residue protein that contains a patatin-like domain at the N terminus (residues 10-179, UniProt http://pir.uniprot.org/uniprot/) with consensus sequences for a Ser-Asp catalytic dyad (Gly-X-Ser-X-Gly and Asp-X-Gly/Ala). The I148M substitution (rs738409) is located between the consensus sequences for the catalytic dyad and is highly conserved. (b) Median hepatic TG content, body mass index (BMI), homeostatic model assessment of insulin resistance (HOMA-IR) and plasma TG levels in the Dallas Heart Study. Values for hepatic fat content were compared using ANOVA. Age, gender, BMI, diabetes status, ethanol use and global ancestry were included as covariates in the model. (c) Median hepatic fat contents and PNPLA3-I148M genotypes in European-Americans, African-Americans and Hispanics in the Dallas Heart Study. Associations between hepatic fat content and PNPLA3-I148M genotypes were tested using ANOVA with age, local ancestry, gender, diabetes status, ethanol intake and BMI as covariates.

Figure 3

Identification of a PNPLA3 allele (S453I) associated with lower hepatic fat content in African-Americans in the Dallas Heart Study. (a) Exons and flanking introns of PNPLA3 were sequenced in the 32 European-American and African-American men and women and in the 16 Hispanic men and women with the lowest and highest hepatic triglyceride content determined using proton magnetic resonance imaging. The NS variations identified in individuals in only the high, only the low and in both the high and low groups are shown. All the variants not found in both groups were present in only a single subject unless otherwise indicated. The rs numbers for polymorphisms and the oligonucleotides used for PCR-sequencing of the coding regions and are provided in Supplementary Tables 3 online and Supplementary Table 4 online. (b) Median hepatic TG content in African-Americans carrying the wild-type or PNPLA3-453I allele. (c) Number of individuals with PNPLA3-453I in the upper and lower deciles of hepatic fat content.