A replication study of GWAS-derived lipid genes in Asian Indians: the chromosomal region 11q23.3 harbors loci contributing to triglycerides

Abstract

Recent genome-wide association scans (GWAS) and meta-analysis studies on European populations have identified many genes previously implicated in lipid regulation. Validation of these loci on different global populations is important in determining their clinical relevance, particularly for development of novel drug targets for treating and preventing diabetic dyslipidemia and coronary artery disease (CAD). In an attempt to replicate GWAS findings on a non-European sample, we examined the role of six of these loci (CELSR2-PSRC1-SORT1 rs599839; CDKN2A-2B rs1333049; BUD13-ZNF259 rs964184; ZNF259 rs12286037; CETP rs3764261; APOE-C1-C4-C2 rs4420638) in our Asian Indian cohort from the Sikh Diabetes Study (SDS) comprising 3,781 individuals (2,902 from Punjab and 879 from the US). Two of the six SNPs examined showed convincing replication in these populations of Asian Indian origin. Our study confirmed a strong association of CETP rs3764261 with high-density lipoprotein cholesterol (HDL-C) (p = 2.03×10(-26)). Our results also showed significant associations of two GWAS SNPs (rs964184 and rs12286037) from BUD13-ZNF259 near the APOA5-A4-C3-A1 genes with triglyceride (TG) levels in this Asian Indian cohort (rs964184: p = 1.74×10(-17); rs12286037: p = 1.58×10(-2)). We further explored 45 SNPs in a ∼195 kb region within the chromosomal region 11q23.3 (encompassing the BUD13-ZNF259, APOA5-A4-C3-A1, and SIK3 genes) in 8,530 Asian Indians from the London Life Sciences Population (LOLIPOP) (UK) and SDS cohorts. Five more SNPs revealed significant associations with TG in both cohorts individually as well as in a joint meta-analysis. However, the strongest signal for TG remained with BUD13-ZNF259 (rs964184: p = 1.06×10(-39)). Future targeted deep sequencing and functional studies should enhance our understanding of the clinical relevance of these genes in dyslipidemia and hypertriglyceridemia (HTG) and, consequently, diabetes and CAD.

Figure 1. Location of genetic markers in chromosomal region (11q23.3) (195 Kb) encompassing BUD13-ZNF259, APOA5-A4-C3-A1, and SIK3 gene cluster.

Exons are shown in black vertical rectangles separated by introns. Significant SNPs (associated with increased triglyceride concentrations) detected in BUD13, ZNF259 and SIK3 are shown in large rectangles on disequilibrium (LD) matrix with their position on the genes indicated by lines. The direction of transcription of genes is shown in arrows. Pair-wise LD between SNPs (D’) is indicated by diamonds shaded in white-grey-black show the range of LD matrix from D’ = 0 in white to D’ = 1 in black. LD block 1 contains 5 most significant SNPs including two top SNPs (rs964184 and rs7350481) of the total 45 analyzed. LD block 2 shows all SNPs from the SIK3 gene and the presence of a strong LD among these SNPs containing two strong signals associated with triglycerides in rs10047459 and rs533556.

Figure 2. Shows the distribution of serum triglyceride levels in Punjabi, US and entire cohort stratified by rs964184 genotypes.

Multiple linear regression analysis was performed using age, BMI and gender in individuals cohorts and age, BMI, gender and place of birth as combined cohorts. P-values in the bars show statistically significant association of ‘G’ risk allele with triglycerides.

Figure 3. Shows the combined effect of risk alleles of for elevating triglyceride levels from BUD13 (rs7350481 rs180326), inter-genic variant from BUD13-ZNF259 (rs964184), and intronic variants from ZNF259 (12286037 and rs618923), and SIK3 (rs100447459, rs533556).

Y axis represents mean triglyceride levels and X axis represents number of risk alleles with the number of participants per risk allele shown in parenthesis below. Rectangles in the plot indicate mean values of triglycerides separated by each risk-allele group and error bars are 95% CI. Note that the the cumulative gene-score of all significant SNPs showed a dose-related increase in TG concentrations ranging from (140.0±6.9 mg/dL with 2–3 risk alleles to 229.2±44.0 mg/dL with 9 risk allele carriers with overall effect increased to 89 mg/dL from 2 to 9 risk alleles (p = 1.62×10⁻⁶ ).