Genome-Wide Association Studies of Metabolites in Patients with CKD Identify Multiple Loci and Illuminate Tubular Transport Mechanisms

Abstract

<b>Background</b> The kidneys have a central role in the generation, turnover, transport, and excretion of metabolites, and these functions can be altered in CKD. Genetic studies of metabolite concentrations can identify proteins performing these functions.<b>Methods</b> We conducted genome-wide association studies and aggregate rare variant tests of the concentrations of 139 serum metabolites and 41 urine metabolites, as well as their pairwise ratios and fractional excretions in up to 1168 patients with CKD.<b>Results</b> After correction for multiple testing, genome-wide significant associations were detected for 25 serum metabolites, two urine metabolites, and 259 serum and 14 urinary metabolite ratios. These included associations already known from population-based studies. Additional findings included an association for the uremic toxin putrescine and variants upstream of an enzyme catalyzing the oxidative deamination of polyamines (<i>AOC1</i>, <i>P</i>-min=2.4×10^-12), a relatively high carrier frequency (2%) for rare deleterious missense variants in <i>ACADM</i> that are collectively associated with serum ratios of medium-chain acylcarnitines (<i>P</i>-burden=6.6×10^-16), and associations of a common variant in <i>SLC7A9</i> with several ratios of lysine to neutral amino acids in urine, including the lysine/glutamine ratio (<i>P</i>=2.2×10^-23). The associations of this <i>SLC7A9</i> variant with ratios of lysine to specific neutral amino acids were much stronger than the association with lysine concentration alone. This finding is consistent with <i>SLC7A9</i> functioning as an exchanger of urinary cationic amino acids against specific intracellular neutral amino acids at the apical membrane of proximal tubular cells.<b>Conclusions</b> Metabolomic indices of specific kidney functions in genetic studies may provide insight into human renal physiology.