A genetic variant in the LDLRpromoter is responsible for part of the LDL-cholesterol variability in primary hypercholesterolemia

Abstract

BackgroundGWAS have consistently revealed that LDLR locus variability influences LDL-cholesterol in general population. Severe LDLR mutations are responsible for familial hypercholesterolemia (FH). However, most primary hypercholesterolemias are polygenic diseases. Although Cis-regulatory regions might be the cause of LDL-cholesterol variability; an extensive analysis of the LDLR distal promoter has not yet been performed. We hypothesized that genetic variants in this region are responsible for the LDLR association with LDL-cholesterol found in GWAS.MethodsFour-hundred seventy-seven unrelated subjects with polygenic hypercholesterolemia (PH) and without causative FH-mutations and 525 normolipemic subjects were selected. A 3103 pb from LDLR (-625 to +2468) was sequenced in 125 subjects with PH. All subjects were genotyped for 4 SNPs (rs17242346, rs17242739, rs17248720 and rs17249120) predicted to be potentially involved in transcription regulation by in silico analysis. EMSA and luciferase assays were carried out for the rs17248720 variant. Multivariable linear regression analysis using LDL-cholesterol levels as the dependent variable were done in order to find out the variables that were independently associated with LDL-cholesterol.ResultsThe sequencing of the 125 PH subjects did not show variants with minor allele frequency ≥ 10%. The T-allele from g.3131C > T (rs17248720) had frequencies of 9% (PH) and 16.4% (normolipemic), p < 0.00001. Studies of this variant with EMSA and luciferase assays showed a higher affinity for transcription factors and an increase of 2.5 times in LDLR transcriptional activity (T-allele vs C-allele). At multivariate analysis, this polymorphism with the lipoprotein(a) and age explained ≈ 10% of LDL-cholesterol variability.ConclusionOur results suggest that the T-allele at the g.3131 T > C SNP is associated with LDL-cholesterol levels, and explains part of the LDL-cholesterol variability. As a plausible cause, the T-allele produces an increase in LDLR transcriptional activity and lower LDL-cholesterol levels.

Single nucleotide variations: Biological impact and theoretical interpretation

“…1 For this reason, methods for predicting the impact of SNVs have historically focused on the high-yield category of non-synonymous coding SNVs. The existence of disease-associated synonymous mutations 32,33 and nocoding variations with effects on lincRNA, 34 miRNA, 35,36 and promoters 37,38 has produced interest in other types of mutations as well, but different tools will be needed to analyze these types of variations and such tools are comparatively still new and untested. [39][40][41] Most nsSNVs affect protein function but in distinct ways nsSNVs may affect folding, 42,43 binding affinity, 44,45 expression, 46 post-translational modification, 47,48 and other protein features.…”

“…Future tools will hopefully expand upon this work and may also begin to predict how noncoding SNVs alter methylation patterns and other epigenetic changes. 203,204 With the discovery that SNVs in noncoding regions are sometimes disease associated, [34][35][36][37][38] additional methods to deal with these variants will likely arise over time to tackle this problem.…”

LDLR rs688 TT Genotype and T Allele Are Associated with Increased Susceptibility to Coronary Artery Disease—A Case-Control Study

“…The frequency of genetic polymorphism of LDLR (rs688) across the globe is summarized in Table 1 . The non-coding SNPs in LDLR have also been found to have functions; for instance, rs17248720 in the intergenic region [ 15 ] and in the promoter region c.-139C > G [ 16 ], c.-101T > C, c.-121T > C [ 17 ], and c.-49C > T [ 18 ], are involved in regulation of gene expression and have been reported to cause familial hypercholesterolemia (FH). [ 19 ].…”

Next-generation gene discovery for variants of large impact on lipid traits

“…Furthermore, researchers should not remove highly conserved synonymous SNVs from consideration, a priori , as these SNVs may have a functional role in disease [60]. Similarly, the possibility that a noncoding variant may influence the transcription of nearby genes should be considered [21,61,62]. …”