Genome-Wide Association Analysis Identifies Variants Associated with Nonalcoholic Fatty Liver Disease That Have Distinct Effects on Metabolic Traits

Abstract

Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (∼26%–27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n = 880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and ∼2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p<5×10−8) in or near PNPLA3, NCAN, and PPP1R3B. We genotype these and 42 other top CT hepatic steatosis-associated SNPs in 592 subjects with biopsy-proven NAFLD from the NASH Clinical Research Network (NASH CRN). In comparisons with 1,405 healthy controls from the Myocardial Genetics Consortium (MIGen), we observe significant associations with histologic NAFLD at variants in or near NCAN, GCKR, LYPLAL1, and PNPLA3, but not PPP1R3B. Variants at these five loci exhibit distinct patterns of association with serum lipids, as well as glycemic and anthropometric traits. We identify common genetic variants influencing CT–assessed steatosis and risk of NAFLD. Hepatic steatosis associated variants are not uniformly associated with NASH/fibrosis or result in abnormalities in serum lipids or glycemic and anthropometric traits, suggesting genetic heterogeneity in the pathways influencing these traits.

Protein phosphatase 1 regulatory subunit 3B gene variation protects against hepatic fat accumulation and fibrosis in individuals at high risk of nonalcoholic fatty liver disease

“…However, we cannot rule out that LOC157273 may directly affect the expression of genes involved in steatosis development and lipid handling. The association with down‐regulation of cholesterol metabolism genes is consistent with the reduced circulating levels of cholesterol in severely obese individuals carrying the A allele, which was also confirmed at the population level both in the United Kingdom Biobank and in previous studies 8. Moreover, differential analysis of gene expression revealed that two genes involved in tumor progression and inflammation26, 27 were significantly down‐regulated in patients who carried the A allele.…”

“…Although the direction of the association is protective and the variant is rarer, the size effect was marked, making it very similar to that of the PNPLA3 I148M variant on these three major outcomes. Despite previous contrasting evidence,8, 9, 10, 11, 12, 13 these novel data lend strong support to the hypothesis that the PPP1R3B variation does protect against hepatic fat accumulation, at least in at‐risk individuals. Furthermore, they support the notion that steatosis is a major driver of liver disease progression to fibrosis7 and HCC18 in individuals with NAFLD.…”

“…Subsequent studies have been consistent with the hypothesis that the rs4240624 variant, which is located 175 kilobase (kb) upstream of the PPP1R3B coding region, associates with reduced fat as estimated by ultrasonography10, 11 and with increased hepatic glycogen content 12. However, when liver fat was directly measured by histology, the association with the PPP1R3B variation was not confirmed 8, 13. Furthermore, Stender et al9 showed that the minor allele of rs4841132, which is in complete linkage disequilibrium with rs4240624, was associated with increased X‐ray attenuation but not with decreased hepatic fat content in population studies.…”

Patatin‐like phospholipase domain containing 3 variants differentially impact metabolic traits in individuals at high risk for cardiovascular events

“…Indeed, there is growing evidence that the PNPLA3 variant is associated with metabolic traits, such as insulin resistance and serum lipid concentrations 12, 13, 14, 15, 22, 23. In particular, the results of our study are in line with a recently published, large, exome‐wide genome‐wide association study showing that the PNPLA3 rs738409 G allele is associated with type 2 diabetes but inversely with LDL, HDL, and triglyceride serum levels 24.…”

“…Although NAFLD can be considered a hepatic manifestation of the metabolic syndrome, the strong association between PNPLA3 rs738409 variants with NAFLD is contrasted by inconsistent results regarding the impact of this variant on other determinants of the metabolic syndrome, such as serum lipid profiles or insulin resistance 12, 13, 14, 15. In the present study, we therefore aimed to further characterize the relationship of PNPLA3 rs738409 variants with metabolic traits in a cohort of individuals who are at high risk of cardiovascular events, i.e., patients undergoing coronary angiography.…”