Variants in the autophagy-related gene IRGM confer susceptibility to non-alcoholic fatty liver disease by modulating lipophagy

Yu-Cheng Lin, Pi-Feng Chang, Hsueh-Fang Lin, Kevin Liu, Mei-Hwei Chang, Yen-Hsuan Ni

Autophagy has been shown to be crucial in the regulation of the intracellular lipid stores in hepatocytes. We hypothesize that immunity-related GTPase family M (IRGM) gene (an autophagy-related gene) variants confer the susceptibility to nonalcoholic fatty liver disease (NAFLD) development. 832 obese children and adolescents aged 6-18 years were recruited. NAFLD was determined by liver ultrasonography. We genotyped PNPLA3 rs738409, GCKR rs780094, TM6SF2rs58542926, sixIRGM single nucleotide polymorphisms (rs13361189, rs9637876, rs72553867, rs10065172, rs1000113, and rs11747270). To understand the molecular mechanism, we examined the effects ofIRGMknockdown and overexpression on autophagic flux and lipid droplet metabolism in human hepatoma cells. 22.8% of recruited obese children and adolescents had NAFLD. Multiple logistic regression analysis revealed that after controlling for the effects of age- and gender-adjusted body mass index, gender, PNPLA3, GCKR, and TM6SF2 polymorphisms, variant IRGM rs10065172 TT genotype independently increased the odds ratio of NAFLD by 2.04 (95% confidence interval 1.22-3.42; P = 0.007), as compared to the CC genotype. The predictive model was validated by means of 10-fold cross-validation. Functional assay revealed that IRGM knockdown inhibited autophagic flux and increased lipid droplet content in HepG2 and PLC/PRF/5 cells, which were reversed by the autophagy inducer rapamycin administration. Similarly, wortmannin (an autophagy inhibitor) increased intra-cellular lipid droplet content. In contrast, overexpression of IRGM caused decreased lipid droplet content in HepG2 cells. Our findings suggest that IRGM may contribute to the development of human NAFLD by altering hepatic lipid metabolism through the autophagy pathway. Autophagy is involved in the process of lipid metabolism in hepatocytes. The mechanism of autophagy regulation by IRGM has just been unveiled. This study demonstrates that genetic variants in IRGM confer risk of human nonalcoholic fatty liver disease. The functional studies reveal how IRGM regulates hepatic lipid droplet content.