Lifelong Reduction in LDL (Low-Density Lipoprotein) Cholesterol due to a Gain-of-Function Mutation in LDLR

Abstract

Background - Loss-of-function mutations in the LDL receptor gene ( LDLR ) cause elevated levels of LDL cholesterol and premature cardiovascular disease. To date, a gain-of-function mutation in LDLR with a large effect on LDL cholesterol levels has not been described. Here, we searched for sequence variants in LDLR that have a large effect on LDL cholesterol levels. Methods - We analyzed whole-genome sequence (WGS) data from 43,202 Icelanders. Single-nucleotide polymorphisms and structural variants including deletions, insertions and duplications were genotyped using WGS-based data. LDL cholesterol associations were carried out in a sample of >100,000 Icelanders with genetic information (imputed or WGS). Molecular analyses were performed using RNA sequencing and protein expression assays in Epstein-Barr virus-transformed lymphocytes. Results - We discovered a 2.5 kb deletion (del2.5) overlapping the 3' untranslated region (UTR) of LDLR in seven heterozygous carriers from a single family. Mean level of LDL cholesterol was 74% lower in del2.5 carriers than in 101,851 non-carriers, a difference of 2.48 mmol/L (96 mg/dL) ( P =8.4×10 -8 ). Del2.5 results in production of an alternative mRNA isoform with a truncated 3' UTR. The truncation leads to a loss of target sites for microRNAs known to repress translation of LDLR . In Epstein-Barr virus-transformed lymphocytes derived from del2.5 carriers, expression of alternative mRNA isoform was 1.84-fold higher than the wild-type isoform ( P =0.0013) and there was 1.79-fold higher surface expression of the LDL receptor than in non-carriers ( P =0.0086). We did not find a highly penetrant detrimental impact of lifelong very low levels of LDL cholesterol due to del2.5 on health of the carriers. Conclusions - Del2.5 is the first reported gain-of-function mutation in LDLR causing a large reduction in LDL cholesterol. These data point to a role for alternative polyadenylation of LDLR mRNA as a potent regulator of LDL receptor expression in humans.

Large-Scale Screening for Monogenic and Clinically Defined Familial Hypercholesterolemia in Iceland

“…Individuals were chosen for WGS based on various conditions, including extremes of cholesterol levels. 25 Consequently, the WGS subsample is enriched for individuals with high LDL-C as well as various cardiovascular phenotypes (Table I in the Data Supplement ). We searched for copy-number variants (eg, deletions) in LDLR using several methods based on WGS data (PopDel, 26 DELLY, 27 Graphtyper, 28 and Manta 29 ), single-nucleotide polymorphism genotypes (PennCNV 30 ) and long-read sequences of 3622 Icelanders.…”

Precision Phenomapping of Acute Coronary Syndromes to Improve Patient Outcomes

“…LDL cholesterol associations were carried out in a sample of >100,000 Icelanders with genetic information. A 2.5-kb deletion (del2.5) overlapping the 3' untranslated region of LDLR was discovered in seven heterozygous carriers from a single family [38]. Mean level of LDL cholesterol was 74% lower in del2.5 carriers than in 101,851 noncarriers, a difference of 2.48 mmol/L (96 mg/dL; p = 8.4 × 10 −8 ).…”

“…Whereas loss-of-function mutations in the LDLR are known to cause elevated levels of LDL cholesterol and premature cardiovascular disease, gain-of-function mutations in LDLR with a large effect on LDL cholesterol levels had not been described. Icelandic investigators analysed whole-genome sequencing data from 43,202 Icelanders [38]. Single-nucleotide polymorphisms and structural variants including deletions, insertions and duplications were genotyped using whole-genome sequencing-based data.…”

“…Mean level of LDL cholesterol was 74% lower in del2.5 carriers than in 101,851 noncarriers, a difference of 2.48 mmol/L (96 mg/dL; p = 8.4 × 10 −8 ). Del2.5 resulted in production of an alternative mRNA isoform with a truncated 3' untranslated region [38]. Truncation leads to loss of target sites for microRNAs known to repress translation of LDLR.…”

“…Lifelong very low levels of LDL cholesterol due to del2.5 did not appear to be detrimental to the health of carriers. Del2.5 is the first reported gain-of-function mutation in LDLR causing a large reduction in LDL cholesterol [38].…”