Genetic associations between serum low LDL-cholesterol levels and variants in LDLR, APOB, PCSK9 and LDLRAP1 in African populations

Abstract

Non-communicable diseases, including cardiovascular diseases (CVDs), are increasing in African populations. High serum low density lipoprotein cholesterol (LDL-cholesterol) levels are a known risk factor for CVDs in European populations, but the link remains poorly understood among Africans. This study investigated the associations between serum LDL-cholesterol levels and selected variants in the low density lipoprotein receptor (LDLR), apolipoprotein B (APOB), proprotein convertase subtilisin/kexin type 9 (PCSK9) and low density lipoprotein receptor adaptor protein 1 (LDLRAP1) genes in some selected African populations. Nineteen SNPs were selected from publicly available African whole genome sequence data based on functional prediction and allele frequency. SNPs were genotyped in 1000 participants from the AWI-Gen, study selected from the extremes of LDL-cholesterol level distribution (500 with LDL-cholesterol>3.5 mmol/L and 500 with LDL-cholesterol<1.1 mmol/L). The minor alleles at five of the six associated SNPs were significantly associated (P<0.05) with lower LDL-cholesterol levels: LDLRAP1 rs12071264 (OR 0.56, 95% CI: 0.39-0.75, P = 2.73x10-4) and rs35910270 (OR 0.78, 95% CI: 0.64-0.94, P = 0.008); APOB rs6752026 (OR 0. 55, 95% CI: 0.41-0.72, P = 2.82x10-5); LDLR: rs72568855 (OR 0.47, 95% CI: 0.27-0.82, P = 0.008); and PCSK9 rs45613943 (OR = 0.72, 95% CI: 0.58-0.88, P = 0.001). The minor allele of the sixth variant was associated with higher LDL-cholesterol levels: APOB rs679899 (OR 1.41, 95% CI: 1.06-1.86, P = 0.016). A replication analysis in the Africa America Diabetes Mellitus (AADM) study found the PCSK9 variant to be significantly associated with low LDL-cholesterol levels (Beta = -0.10). Since Africans generally have lower LDL-cholesterol levels, these LDL-cholesterol associated variants may be involved in adaptation due to unique gene-environment interactions. In conclusion, using a limited number of potentially functional variants in four genes, we identified significant associations with lower LDL-cholesterol levels in sub-Saharan Africans.

Fig 1. Logistic regression of the 14 selected gene variants associated with LDL-cholesterol levels.

The plot shows the odds ratio (OR) for variants after adjusting for covariates (sex and geographic region). Bars represent 95% confidence interval (CI). When OR <1, the minor alleles are associated with low LDL-cholesterol levels. Only one variant is significantly associated with high LDL-cholesterol levels (rs679899) with a significant OR>1.

Fig 2. Genotypes relative to LDL-cholesterol distribution for 6 variants significantly associated with LDL-cholesterol levels after logistic regression.

The 993 AWI-Gen individuals with low and high LDL-cholesterol are included in the plots. A-D: APOB rs6752026, LDLRAP1 rs12071264, PCSK9 rs45613943 and LDLR rs72658855 show how LDL-cholesterol levels decrease with presence of the minor allele. E: LDLRAP1 shows how LDL-cholesterol levels decrease only when both minor alleles are present (deletion). F: APOB rs679899 shows an increase of LDL-cholesterol levels with the presence of the minor allele.

Fig 3. Correlation of the polygenic risk score (PRS) with LDL-cholesterol levels in 993 individuals.

Six LDL-cholesterol associated variants (P<0.05) after adjustment for covariates. Cases include individuals with high LDL-cholesterol levels, and controls with low LDL-cholesterol levels. A: PRS calculated using six variants. Risk score refers to the number of lipid lowering alleles. Plot shows the frequency of cases and controls for each score. The curve of the controls is shifted to the right, indicating that in controls the LDL-cholesterol levels decreases with the addition of alleles associated with lower LDL-cholesterol levels (either common or minor allele). B: Plot of risk score against mean LDL-cholesterol level per risk score. It is apparent that with the addition of each allele associated with lower LDL-cholesterol levels (common or minor allele), the mean LDL-cholesterol level of the participants decreased.