Fine-Mapping the NCAN Locus: Using Genetic Variations to Understand Non-Alcoholic Fatty Liver Disease

Abstract

To extend the findings of the GOLD Consortium GWAS meta-analysis, we studied a large population of bariatric surgery patients with intra-operatively obtained liver biopsies. Single nucleotide polymorphism rs2228603 in NCAN was associated with liver steatosis, hepatocyte ballooning and inflammation. Because NCAN is not highly expressed in liver, the rs2228603 in NCAN is likely marking the involvement of a nearby gene. Therefore, to determine if expression of any of the genes in the NCAN locus varies based on liver steatosis and SNP rs2228603 genotype, patients with extremes of hepatic steatosis who had been grouped based on NCAN SNP rs2228603 genotype were compared. For two of the genes in the NCAN locus, GATAD2A and TM6SF2, lower mRNA levels were associated with liver steatosis in patients with the NCAN rs2228603 CC genotype while higher levels were associated with liver steatosis in patients with the CT genotype. These findings suggest that NCAN SNP rs2228603 may affect the way in which levels of the nearby genes GATAD2A and TM6SF2 are associated with liver steatosis. To further evaluate the role of TM6SF2, a gene of unknown function, we performed gene silencing with morpholino oligonucleotides in the zebrafish model to demonstrate that knockdown of Tm6sf2 reproduced the liver steatosis phenotype and simultaneously increased hepatic expression of Fabp6.