Genetic inhibition of angiopoietin-like protein-3, lipids, and cardiometabolic risk

Abstract

Background and aims: RNA-based, antibody-based, and genome editing-based therapies are currently under investigation to determine if the inhibition of angiopoietin-like protein-3 (ANGPTL3) could reduce lipoprotein-lipid levels and atherosclerotic cardiovascular disease (ASCVD) risk. Mendelian randomisation (MR) was used to determine whether genetic variations influencing ANGPTL3 liver gene expression, blood levels, and protein structure could causally influence triglyceride and apolipoprotein B (apoB) levels as well as coronary artery disease (CAD), ischaemic stroke (IS), and other cardiometabolic diseases.

Methods: RNA sequencing of 246 explanted liver samples and genome-wide genotyping was performed to identify single-nucleotide polymorphisms (SNPs) associated with liver expression of ANGPTL3. Genome-wide summary statistics of plasma protein levels of ANGPTL3 from the deCODE study (n = 35 359) were used. A total of 647 carriers of ANGPTL3 protein-truncating variants (PTVs) associated with lower plasma triglyceride levels were identified in the UK Biobank. Two-sample MR using SNPs that influence ANGPTL3 liver expression or ANGPTL3 plasma protein levels as exposure and cardiometabolic diseases as outcomes was performed (CAD, IS, heart failure, non-alcoholic fatty liver disease, acute pancreatitis, and type 2 diabetes). The impact of rare PTVs influencing plasma triglyceride levels on apoB levels and CAD was also investigated in the UK Biobank.

Results: In two-sample MR studies, common genetic variants influencing ANGPTL3 hepatic or blood expression levels of ANGPTL3 had a very strong effect on plasma triglyceride levels, a more modest effect on low-density lipoprotein cholesterol, a weaker effect on apoB levels, and no effect on CAD or other cardiometabolic diseases. In the UK Biobank, the carriers of rare ANGPTL3 PTVs providing lifelong reductions in median plasma triglyceride levels [-0.37 (interquartile range 0.41) mmol/L] had slightly lower apoB levels (-0.06 ± 0.32 g/L) and similar CAD event rates compared with non-carriers (10.2% vs. 10.9% in carriers vs. non-carriers, P = .60).

Conclusions: PTVs influencing ANGPTL3 protein structure as well as common genetic variants influencing ANGPTL3 hepatic expression and/or blood protein levels exhibit a strong effect on circulating plasma triglyceride levels, a weak effect on circulating apoB levels, and no effect on ASCVD. Near-complete inhibition of ANGPTL3 function in patients with very elevated apoB levels may be required to reduce ASCVD risk.

Keywords: Angiopoietin-like protein-3; Antibody-based therapies; Atherosclerotic cardiovascular diseases; Cardiometabolic diseases; Gene-editing-based therapies; Lipoprotein-lipid levels; Mendelian randomisation; Protein-truncating variants; RNA-based therapies.

Structured Graphical Abstract

ANGPTL3, angiopoietin-like protein-3; LDL, low-density lipoprotein; RNA, ribonucleic acid; SNP, single-nucleotide polymorphism.

Figure 1

Schematic representation of the Mendelian randomisation study design. ANGPTL3 is a key regulator of blood lipid levels. ANGPTL3 inhibitors are currently under investigation for their impact on metabolic and cardiovascular health. ANGPTL3, angiopoietin-like protein-3; ApoB, apolipoprotein B; ASO, antisense oligonucleotides; eQTL, expression quantitative trait loci; HDL-C, high-density lipoprotein cholesterol; IDL-C, intermediate-density lipoprotein cholesterol; LDL-C, low-density lipoprotein cholesterol; mAb, monoclonal antibody; mRNA, messenger ribonucleic acid; pQTL, protein quantitative trait loci; PTVs, protein-truncating variants; siRNA, small interfering RNA; TG, triglycerides; VLDL-C, very-low-density lipoprotein cholesterol

Figure 2

Impact of genetically predicted liver ANGPTL3 expression on lipoprotein-lipid levels and cardiometabolic diseases. (A) The effects of the strongest SNP (rs11207978) associated with the liver ANGPTL3 expression on lipoprotein-lipid levels and cardiometabolic diseases were obtained using the Wald ratio. Effect sizes (95% CI) are represented by SD or log(OR) change in the outcome per 1-SD increase in liver ANGPTL3 expression. (B) Regional association plots depicting the impact of genetically predicted liver ANGPTL3 expression on lipoprotein-lipid levels and coronary artery disease

Figure 2

Impact of genetically predicted liver ANGPTL3 expression on lipoprotein-lipid levels and cardiometabolic diseases. (A) The effects of the strongest SNP (rs11207978) associated with the liver ANGPTL3 expression on lipoprotein-lipid levels and cardiometabolic diseases were obtained using the Wald ratio. Effect sizes (95% CI) are represented by SD or log(OR) change in the outcome per 1-SD increase in liver ANGPTL3 expression. (B) Regional association plots depicting the impact of genetically predicted liver ANGPTL3 expression on lipoprotein-lipid levels and coronary artery disease

Figure 3

Impact of genetically predicted plasma ANGPTL3 levels on lipoprotein-lipid levels and cardiometabolic diseases. (A) The effects of the strongest SNP (rs10889352) associated with the plasma ANGPTL3 levels on lipoprotein-lipid levels and cardiometabolic diseases were obtained using the Wald ratio. Effect sizes (95% CI) are represented by SD or log(OR) change in the outcome per 1-SD increase in plasma ANGPTL3 levels. (B) Regional association plots depicting the impact of genetically predicted plasma ANGPTL3 levels on lipoprotein-lipid levels and coronary artery disease

Figure 3

Impact of genetically predicted plasma ANGPTL3 levels on lipoprotein-lipid levels and cardiometabolic diseases. (A) The effects of the strongest SNP (rs10889352) associated with the plasma ANGPTL3 levels on lipoprotein-lipid levels and cardiometabolic diseases were obtained using the Wald ratio. Effect sizes (95% CI) are represented by SD or log(OR) change in the outcome per 1-SD increase in plasma ANGPTL3 levels. (B) Regional association plots depicting the impact of genetically predicted plasma ANGPTL3 levels on lipoprotein-lipid levels and coronary artery disease

Figure 4

Genome-wide association studies of circulating angiopoietin-like protein-3 levels. Manhattan plot representing the results of the genome-wide association studies of circulating angiopoietin-like protein-3 levels in the (A) deCODE and (B) Fenland cohorts. (C) The effects of single-nucleotide polymorphisms associated with circulating ANGPTL3 levels on lipoprotein-lipid levels and cardiometabolic diseases were obtained using inverse-variance-weighted Mendelian randomisation. Effect sizes (95% CI) are represented by SD or log(OR) change in the outcome per 1-SD increase in circulating ANGPTL3 levels

Figure 4

Genome-wide association studies of circulating angiopoietin-like protein-3 levels. Manhattan plot representing the results of the genome-wide association studies of circulating angiopoietin-like protein-3 levels in the (A) deCODE and (B) Fenland cohorts. (C) The effects of single-nucleotide polymorphisms associated with circulating ANGPTL3 levels on lipoprotein-lipid levels and cardiometabolic diseases were obtained using inverse-variance-weighted Mendelian randomisation. Effect sizes (95% CI) are represented by SD or log(OR) change in the outcome per 1-SD increase in circulating ANGPTL3 levels

Figure 5

Impact of genetic variation at ANGPTL3 on triglyceride and apolipoprotein B levels. (A) Inverse-variance-weighted Mendelian randomisation scatterplot depicting the causal impact of triglyceride-reducing SNPs on apolipoprotein B (apoB) levels. The top liver eQTL-SNP (rs11207978) influencing ANGPTL3 hepatic gene expression levels and the top plasma pQTL-SNP (rs10889352) influencing ANGPTL3 levels are highlighted. (B) Impact of rare and common genetic variants at the ANGPTL3 locus on triglyceride and apoB reductions

Figure 6

Impact of ANGPTL3 protein-truncating variants on coronary artery disease rates in the participants of the UK Biobank. (A) Carriers of at least one ANGPTL3 protein-truncating variant (PTV) associated with lower plasma triglyceride levels had a comparable coronary artery disease (CAD) event rate than non-carriers. (B) Carriers of at least one PCSK9 PTV associated with lower plasma apolipoprotein B levels had a lower CAD event rate than non-carriers