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

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.

非酒精性脂肪性肝病（NAFLD）呈家族聚集性，但目前已知的唯一影响其发病风险的常见遗传变异仅定位于PNPLA3基因邻近区域。本研究借助大型人群队列中计算机断层扫描（CT）测得的肝脏脂肪变性——一种非侵入性的NAFLD评估手段——开展全基因组关联（GWA）分析，旨在识别更多影响NAFLD发病风险的遗传变异。本研究采用方差组分分析方法，证实基于家系的阿米什人群研究、家庭心脏研究及弗雷明汉心脏研究（样本量880~3070例）中，CT评估的肝脏脂肪变性具有约26%~27%的遗传力。本研究整合了来自旧秩序阿米什人群、年龄、基因/环境易感性-雷克雅未克研究（AGES）、家庭心脏研究及弗雷明汉心脏研究的7176名个体的数据，对CT肝脏脂肪变性与约240万个经插补或基因分型的单核苷酸多态性（SNPs，single nucleotide polymorphism的复数形式）的全基因组关联分析结果开展固定效应meta分析，最终鉴定出PNPLA3、NCAN及PPP1R3B基因内或其邻近区域存在达到全基因组显著性水平（p<5×10^-8）的关联变异。本研究对来自非酒精性脂肪性肝炎（NASH）临床研究网络（NASH CRN）的592例经活检证实为NAFLD的受试者，对上述关联变异及另外42个排名靠前的CT肝脏脂肪变性关联SNPs进行了基因分型。与来自心肌遗传学联盟（MIGen）的1405名健康对照相比，本研究观察到NCAN、GCKR、LYPLAL1及PNPLA3基因内或其邻近区域的变异与组织学确诊的NAFLD存在显著关联，但PPP1R3B基因区域的变异未呈现此类关联。上述五个基因位点的变异与血清脂质、血糖及人体测量学特征呈现各异的关联模式。本研究鉴定出了影响CT评估的肝脏脂肪变性及NAFLD发病风险的常见遗传变异。与肝脏脂肪变性相关的遗传变异并非均与NASH/肝纤维化相关，也并非均会导致血清脂质、血糖及人体测量学指标异常，这提示调控上述性状的通路存在遗传异质性。