Novel Loci (EIF4A2, ADIPOQ, TPRG1) for Triglyceride / High-density Lipoprotein Cholesterol Ratio Longitudinal Change (ΔTHR) among Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Heart Study (FHS) Offspring Cohort (OS)

Abstract

Aims/hypothesis: Triglyceride (TG) /High density lipoprotein cholesterol (HDL-C) ratio (THR) represents a single surrogate predictor of hyperinsulinemia or insulin resistance that is associated with premature aging processes, risk of diabetes and increased mortality. To identify novel genetic loci for THR change over time (ΔTHR), we conducted genome-wide association study (GWAS) and genome-wide linkage scan (GWLS) among subjects of European ancestry who had complete data from two exams collected about seven years apart from the Long Life Family Study (LLFS, n=1384), a study with familial clustering of exceptional longevity in the US and Denmark.

Methods: Subjects with diabetes or using medications for dyslipidemia were excluded from this analysis. ΔTHR was derived using growth curve modeling, and adjusted for age, sex, field centers, and principal components (PCs). GWAS was conducted using a linear mixed model accounted for familial relatedness. Our linkage scan was built on haplotype-based IBD estimation with 0.5 cM average spacing.

Results: Heritability of ΔTHR was moderate (46%). Our GWAS identified a significant locus at the LPL (p=1.58e-9) for ΔTHR; this gene locus has been reported before influencing baseline THR levels. Our GWLS found evidence for a significant linkage with a logarithm of the odds (LODs) exceeding 3 on 3q28 (LODs=4.1). Using a subset of 25 linkage enriched families (pedigree-specific LODs>0.1), we assessed sequence elements under 3q28 and identified two novel variants (EIF4A2/ADIPOQ-rs114108468, p=5e-6, MAF=1.8%; TPRG1-rs16864075, p=3e-6, MAF=8%; accounted for ~28% and ~29% of the linkage, respectively, and 57% jointly). While the former variant was associated with EIF4A2 (p=7e-5) / ADIPOQ (p=3.49e-2) RNA transcriptional levels, the latter variant was not associated with TPRG1 (p=0.23) RNA transcriptional levels. Replication in FHS OS observed modest effect of these loci on ΔTHR. Of 188 metabolites from 13 compound classes assayed in LLFS, we observed multiple metabolites (e.g., DG.38.5, PE.36.4, TG.58.3) that were significantly associated with the variants (p<3e-4).

Conclusions: our linkage-guided sequence analysis approach permitted our discovery of two novel gene variants EIF4A2/ADIPOQ-rs114108468 and TPRG1-rs16864075 on 3q28 for ΔTHR among subjects without diabetes selected for exceptional survival and healthy aging.

Figure 1.. GWAS results of ΔTHR using whole genome sequenced autosome variants.

A) The Manhantan plot for GWAS results of ΔTHR across 22 chromosomes. P values are two-sided raw P values estimated from a linear additive model. The y-axis depicts the negative log10-transformed P value. The x-axis is genomic coordinates by chromosome number. The blue-colored solid horizontal line denotes the suggestive threshold (p=1e-5). The red-colored solid horizontal line indicates the genome-wide significant cutoff at p=5e-8. B) The LD heatmap of 15 significant SNPs at chromosome 8 that reached genome-wide significance using Haploview. The value displayed is LD r2. C) The Locuszoom plot of ± 200 Kb of lead SNP rs79407615 at chromosome 8. The x-axis is the base pair position in the genome build GRCh38 at chromosome 8. The y-axis is the –log10 of the two-sided P value for each genetic variants. D) The box and whisker plot for the ΔTHR and the LPL residuals across three genotypes of rs79407615. The pairwise comparison P value is estimated using wilcox.test in R.

Figure 2.. Genome-wide linkage analyses of the ΔTHR identified a linkage peak at chromosome 3.

A) The plot of the LOD score across 22 autosomes. The Y-axis is the LOD score estimated with SOLAR. The X-axis is the genomic coordinates by chromosome number. B) The plot of negative log10 transformed p value (Y-axis at right side) and HLOD (Y-axis at left side) vs physical position in Mbp at chromosome 3. C) The association results of rs114108468 and rs16864075 with ΔTHR, ADIPOQ, EIF4A2 and TPRG1.