Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk

Abstract

Blood lipid levels are heritable, treatable risk factors for cardiovascular disease. We systematically assessed genome-wide coding variation to identify novel lipid genes, fine-map known lipid loci, and evaluate whether low frequency variants with large effect exist. Using an exome array, we genotyped 80,137 coding variants in 5,643 Norwegians. We followed up 18 variants in 4,666 Norwegians to identify 10 loci with coding variants associated with a lipid trait (P < 5×10−8). One coding variant in TM6SF2 (p.Glu167Lys), residing in a GWAS locus for lipid levels, modifies total cholesterol levels and is associated with myocardial infarction. Transient overexpression and knockdown of TM6SF2 in mouse produces alteration in serum lipid profiles consistent with the association observed in humans, identifying TM6SF2 as the functional gene at a large GWAS locus previously known as NCAN/CILP2/PBX4 or 19p13. This study demonstrates that systematic assessment of coding variation can quickly point to a candidate causal gene.

TM6SF2 is a regulator of liver fat metabolism influencing triglyceride secretion and hepatic lipid droplet content

“…The observed dual role of TM6SF2 in TRL secretion and hepatic TG content is in line with data from population studies demonstrating associations between the 19p12 locus and plasma TG concentration (1-6) and hepatic steatosis (7,8). The clinical importance of this locus is underlined by its relationships to coronary artery disease (5,9,18,19) and type 2 diabetes (10,11). It is expected that further analysis of TM6SF2 will uncover the biological function of TM6SF2 in hepatic lipid metabolism, thereby providing new insights into the complex relationship between liver TG metabolism, coronary artery disease, and type 2 diabetes mellitus.…”

“…The current study extends these reports and demonstrates in human liver cells that TM6SF2 plays a role in both secretion of TRLs and hepatic lipid droplet content. Indeed, it is remarkable that the results from the GWA studies (1-8), the knockdown and overexpression studies in mice (17,18), and the functional analysis of TM6SF2 in human hepatoma cell lines (this study) provide consistent evidence for opposing effects of TM6SF2 on TRL secretion and hepatic lipid droplet content: Reduced expression of TM6SF2 was associated with reduced secretion of TRLs and increased hepatic lipid droplet content, whereas increased expression of TM6SF2 was related to decreased hepatic lipid droplet content. Needless to say, none of these reports resolve the precise functional role of TM6SF2 in these processes.…”

“…These observations are in line with the eQTL data reported here and the results from population studies (7,8) demonstrating that the minor allele of the lead SNP is associated with reduced TM6SF2 mRNA levels and increased hepatic lipid content, suggesting that TM6SF2 plays a role in the development of NAFLD. While this study was under review, it was reported by two different research groups (17,18) that knockdown of Tm6sf2 or transient TM6SF2 overexpression in mice alters serum lipid profiles and influences hepatic TG content. The current study extends these reports and demonstrates in human liver cells that TM6SF2 plays a role in both secretion of TRLs and hepatic lipid droplet content.…”

Non-alcoholic fatty liver disease

“…The TM6SF2 E167K results in lower total cholesterol in humans and expression levels of the variant are lower than the wild-type form. These data indicate that the TM6SF2 E167K variant confers a 'loss-of-function' to the protein that may be both qualitative and quantitative 94 .…”

“…As with PNPLA3, candidate gene studies have shown that the TM6SF2 E167K variant is also associated with progressive NAFLD 93 . Interestingly, evidence has been provided that carriage of the more common TM6SF2 E167K major allele is associated with dyslipidaemia (raised serum LDL cholesterol and triglyceride), increased myocardial infarction and cardiovascular disease risk whereas minor allele carriage is protective 94 . Functional studies suggest that TM6SF2 regulates hepatic lipid efflux, with its deletion or mutation resulting in a reduction in lipoprotein secretion (very low density lipoprotein (VLDL), triglycerides and APOB) leading to increased hepatocellular lipid droplet size and triglyceride accumulation.…”