Cardiovascular diseases (CVD), and in particular cerebrovascular and ischemic heart diseases, are leading causes of death globally. 1 Lowering circulating lipids is an important treatment strategy to reduce risk. 2,3 However, some pharmaceutical mechanisms of reducing CVD may increase risk of fatty liver disease or other metabolic disorders. 4,5,6 To identify potential novel therapeutic targets, which may reduce risk of CVD without increasing risk of metabolic disease, we focused on the simultaneous evaluation of quantitative traits related to liver function and CVD. Using a combination of low-coverage (5x) wholegenome sequencing and targeted genotyping, deep genotype imputation based on the TOPMed reference panel 7 , and genome-wide association study (GWAS) meta-analysis, we analyzed 12 liverrelated blood traits (including liver enzymes, blood lipids, and markers of iron metabolism) in up to 203,476 people from three population-based cohorts of different ancestries. We identified 88 likely causal protein-altering variants that were associated with one or more liver-related blood traits. We identified several loss-of-function (LoF) variants reducing low-density lipoprotein cholesterol (LDL-C) or risk of CVD without increased risk of liver disease or diabetes, including variants in known lipid genes (e.g. APOB, LPL). A novel LoF variant, ZNF529:p.K405X, was associated with decreased levels of LDL-C (P=1.3x10 -8 ) but demonstrated no association with liver enzymes or non-fasting blood glucose levels.Silencing of ZNF529 in human hepatocytes resulted in upregulation of LDL receptor (LDLR) and increased LDL-C uptake in the cells, suggesting that inhibition of ZNF529 or its gene product could be used for treating hypercholesterolemia and hence reduce the risk of CVD. Taken together, we demonstrate that simultaneous consideration of multiple phenotypes and a focus on rare protein-altering variants may identify promising therapeutic targets.
MAIN TEXTWe combined several approaches for genomic discovery to identify independent variants associated with 12 liver-related phenotypes (see Supplementary Figure 1 for an overview). The 12 traits we examined were related to: i) blood lipid levels which impact cardiovascular, neurological and eye-related diseases: total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C) and triglyceride (TG) levels; ii) C-reactive protein (CRP; only values <15 mmol/L were included) which is predictive of cardiovascular disease; 8 iii) enzymes which mainly reflect liver function: alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and gamma-glutamyltransferase (GGT); and iv) iron-related phenotypes: serum iron, total iron binding capacity (TIBC), and transferrin saturation percentage (TSP).Using four primary discovery designs, we identified 763 unique variants within 340 genomic regions (i.e. loci) associated with at least one of the 12 quantitative liver-related blood traits. We identified genome-wide ...