Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity

Abstract

We analyzed genome-wide association studies (GWASs), including data from 71,638 individuals from four ancestries, for estimated glomerular filtration rate (eGFR), a measure of kidney function used to define chronic kidney disease (CKD). We identified 20 loci attaining genome-wide-significant evidence of association (p < 5 × 10(-8)) with kidney function and highlighted that allelic effects on eGFR at lead SNPs are homogeneous across ancestries. We leveraged differences in the pattern of linkage disequilibrium between diverse populations to fine-map the 20 loci through construction of "credible sets" of variants driving eGFR association signals. Credible variants at the 20 eGFR loci were enriched for DNase I hypersensitivity sites (DHSs) in human kidney cells. DHS credible variants were expression quantitative trait loci for NFATC1 and RGS14 (at the SLC34A1 locus) in multiple tissues. Loss-of-function mutations in ancestral orthologs of both genes in Drosophila melanogaster were associated with altered sensitivity to salt stress. Renal mRNA expression of Nfatc1 and Rgs14 in a salt-sensitive mouse model was also reduced after exposure to a high-salt diet or induced CKD. Our study (1) demonstrates the utility of trans-ethnic fine mapping through integration of GWASs involving diverse populations with genomic annotation from relevant tissues to define molecular mechanisms by which association signals exert their effect and (2) suggests that salt sensitivity might be an important marker for biological processes that affect kidney function and CKD in humans.

Figure 1

DNase I Hypersensitivity Sites in Kidney Cells and HDAC8 Binding Sites are Predictive of Posterior Probability of Driving Association Signals at 20 eGFR Loci We tested whether genomic annotations of regulatory chromatin state for 93 cell types, DNase I hypersensitivity sites (DHSs) for 145 cell types, and chromatin immuno-precipitation sequence binding sites for 165 transcription factors were predictive of posterior probability of driving eGFR association signals. Each point corresponds to an annotation, plotted according to the effect size (log-odds ratio for driving association signal) on the x axis and ranked according to the significance of the association on the y axis. Significant association (p < 0.00012, highlighted in red) was defined by Bonferroni correction for 403 tested annotations. The most significant effects included DHSs in kidney cells (RPTECs and HRCEs) and binding sites for HDAC8.

Figure 2

Drosophila RGS14 Heterozygous Mutants Are Resistant to Salt Stress Survival of flies carrying heterozygous loss-of-function mutations in the Drosophila melanogaster RGS14 homolog, loco, was compared to that of controls of the same genetic background. In the isogenic experiment, all genotypes were backcrossed to the control strain. In the heterogenic experiment, controls and loco mutants were crossed with the A.R.R. lab’s wBerlin strain to obtain highly heterozygous progeny. Kaplan-Meier plots demonstrated that flies heterozygous for two independently derived loco mutations, loco^EY-P283 and loco^d06164, were resistant to salt stress across a range of NaCl concentrations when compared to controls. Cox-proportional hazards p values for each mutant, compared to those of controls, are presented and are calculated for each genetic background (isogenic or heterogenic) and NaCl concentration separately. Results are based on 170–200 flies per genotype for each NaCl concentration.

Figure 3

Relative Renal mRNA Expression of Rgs14 and Nfatc1 Expression of Rgs14 is shown in (A) and Nfatc1 in (B). n = 5 or 6 in each group. The empty triangle represents the median. According to the Mann-Whitney test, and compared to the baseline, Rgs14 expression after exposure to a high-salt diet was significantly lower (p = 0.01), and was also lower in CKD (p = 0.06). Nfatc1 expression after exposure to a high-salt diet was also significantly lower (p = 0.03) and trended in the same direction in CKD (p = 0.31).