Whole-exome sequencing identifies novel protein-altering variants associated with serum apolipoprotein and lipid concentrations

Abstract

Background Dyslipidemia is a major risk factor for cardiovascular disease, and diabetes impacts the lipid metabolism through multiple pathways. In addition to the standard lipid measurements, apolipoprotein concentrations provide added awareness of the burden of circulating lipoproteins. While common genetic variants modestly affect the serum lipid concentrations, rare genetic mutations can cause monogenic forms of hypercholesterolemia and other genetic disorders of lipid metabolism. We aimed to identify low-frequency protein-altering variants (PAVs) affecting lipoprotein and lipid traits. Methods We analyzed whole-exome (WES) and whole-genome sequencing (WGS) data of 481 and 474 individuals with type 1 diabetes, respectively. The phenotypic data consisted of 79 serum lipid and apolipoprotein phenotypes obtained with clinical laboratory measurements and nuclear magnetic resonance spectroscopy. Results The single-variant analysis identified an association between the LIPC p.Thr405Met (rs113298164) and serum apolipoprotein A1 concentrations (p=7.8×10−8). The burden of PAVs was significantly associated with lipid phenotypes in LIPC, RBM47, TRMT5, GTF3C5, MARCHF10, and RYR3 (p<2.9×10−6). The RBM47 gene is required for apolipoprotein B post-translational modifications, and in our data, the association between RBM47 and apolipoprotein C-III concentrations was due to a rare 21 base pair p.Ala496-Ala502 deletion; in replication, the burden of rare deleterious variants in RBM47 was associated with lower triglyceride concentrations in WES of >170,000 individuals from multiple ancestries (p=0.0013). Two PAVs in GTF3C5 were highly enriched in the Finnish population and associated with cardiovascular phenotypes in the general population. In the previously known APOB gene, we identified novel associations at two protein-truncating variants resulting in lower serum non-HDL cholesterol (p=4.8×10−4), apolipoprotein B (p=5.6×10−4), and LDL cholesterol (p=9.5×10−4) concentrations. Conclusions We identified lipid and apolipoprotein-associated variants in the previously known LIPC and APOB genes, as well as PAVs in GTF3C5 associated with LDLC, and in RBM47 associated with apolipoprotein C-III concentrations, implicated as an independent CVD risk factor. Identification of rare loss-of-function variants has previously revealed genes that can be targeted to prevent CVD, such as the LDL cholesterol-lowering loss-of-function variants in the PCSK9 gene. Thus, this study suggests novel putative therapeutic targets for the prevention of CVD.

Whole-genome sequencing identifies variants in ANK1, LRRN1, HAS1, and other genes and regulatory regions for stroke in type 1 diabetes

“…Patients in WGS and WES were non-overlapping. The patient selection for both data sets were originally designed for DKD, such that half of the individuals had severe DKD, and half had no DKD (i.e., normal albumin excretion rate) despite a long duration of T1D 21 , 43 . Importantly, this resulted in stroke cases being younger and having shorter diabetes duration than controls, contradictory to presumption.…”

“…Rare variants can be reliably studied with next-generation sequencing-based techniques such as whole-genome sequencing (WGS) and whole-exome sequencing (WES). We have previously used WES to identify protein coding variants associated with lipid and apolipoprotein traits in T1D 21 . In the general population, novel stroke risk loci have been identified with WGS 22 .…”

Whole-exome and Whole-genome Sequencing of 1097 Individuals with Type 1 Diabetes Reveals Novel Genes for Diabetic Kidney Disease

“…Variants and genes were replicated with FinnDiane GWAS data ( Supplementary Methods , [28]). Altogether 6,449 individuals and 15.21M variants with imputation quality r 2 > 0.7 passed the QC.…”

Whole-genome sequencing identifies variants inANK1,LRRN1,HAS1,and other genes and regulatory regions for stroke in type 1 diabetes

“…Rare variants can be reliably studied with nextgeneration sequencing-based techniques such as whole-genome sequencing (WGS) and whole-exome sequencing (WES). We have previously used WES to study low frequency variants for DKD 27 , and identified protein coding variants associated in lipid and apolipoprotein traits in T1D 28 . In the general population, novel stroke risk loci have been identified with WGS 29 , although Jurgens et al (2022) analyzed WES in the UK Biobank for cardiometabolic traits and did not discover exome-wide significant stroke risk genes 30 .…”

“…Rare variants can be reliably studied with next-generation sequencing-based techniques such as whole-genome sequencing (WGS) and whole-exome sequencing (WES). We have previously used WES to identify protein coding variants associated in lipid and apolipoprotein traits in T1D 20 . In the general population, novel stroke risk loci have been identified with WGS 21 .…”