Genetic variants of calcium and vitamin D metabolism in kidney stone disease

Nat Commun. 2019 Nov 15;10(1):5175. doi: 10.1038/s41467-019-13145-x.

Abstract

Kidney stone disease (nephrolithiasis) is a major clinical and economic health burden with a heritability of ~45-60%. We present genome-wide association studies in British and Japanese populations and a trans-ethnic meta-analysis that include 12,123 cases and 417,378 controls, and identify 20 nephrolithiasis-associated loci, seven of which are previously unreported. A CYP24A1 locus is predicted to affect vitamin D metabolism and five loci, DGKD, DGKH, WDR72, GPIC1, and BCR, are predicted to influence calcium-sensing receptor (CaSR) signaling. In a validation cohort of only nephrolithiasis patients, the CYP24A1-associated locus correlates with serum calcium concentration and a number of nephrolithiasis episodes while the DGKD-associated locus correlates with urinary calcium excretion. In vitro, DGKD knockdown impairs CaSR-signal transduction, an effect rectified with the calcimimetic cinacalcet. Our findings indicate that studies of genotype-guided precision-medicine approaches, including withholding vitamin D supplementation and targeting vitamin D activation or CaSR-signaling pathways in patients with recurrent kidney stones, are warranted.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Asian People / genetics
  • Calcium / metabolism*
  • Diacylglycerol Kinase / genetics
  • Diacylglycerol Kinase / metabolism
  • Female
  • Genetic Variation
  • Genome-Wide Association Study
  • Genotype
  • Humans
  • Japan
  • Kidney Calculi / genetics*
  • Kidney Calculi / metabolism
  • Male
  • Middle Aged
  • Polymorphism, Single Nucleotide
  • Prospective Studies
  • Proteins / genetics
  • Proteins / metabolism
  • Receptors, Calcium-Sensing / genetics
  • Receptors, Calcium-Sensing / metabolism
  • United Kingdom
  • Vitamin D / metabolism*
  • White People / genetics

Substances

  • Proteins
  • Receptors, Calcium-Sensing
  • WDR72 protein, human
  • Vitamin D
  • DGKD protein, human
  • Diacylglycerol Kinase
  • Calcium