Genetic Links Between Gastrointestinal Disorders and Kidney Stone Disease: Insights from Genome-Wide Cross-Trait Analysis

Yicun Wang; Zhiyi Zhao; Runyi Wang; Xiaopeng Hu

doi:10.34067/KID.0000000689

Genetic Links Between Gastrointestinal Disorders and Kidney Stone Disease: Insights from Genome-Wide Cross-Trait Analysis

Kidney360. 2025 Jan 3. doi: 10.34067/KID.0000000689. Online ahead of print.

Authors

Yicun Wang^{1

2}, Zhiyi Zhao^{1

2}, Runyi Wang^{1

2}, Xiaopeng Hu^{1

2}

Affiliations

¹ Department of Urology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China.
² Institute of Urology, Capital Medical University, Beijing, China.

PMID: 39752564
DOI: 10.34067/KID.0000000689

Abstract

Background: Epidemiological associations between kidney stone disease (KSD) and gastrointestinal disorders have been reported, and intestinal homeostasis plays a critical role in stone formation. However, the underlying intrinsic link is not adequately understood. This study aims to investigate the genetic associations between these two types of diseases.

Methods: We obtained summary statistics from large-scale genome-wide association studies of KSD and gastrointestinal diseases, including gastroesophageal reflux disease (GERD), peptic ulcer disease, inflammatory bowel disease and its subtypes, irritable bowel syndrome (IBS) and diverticular disease (N = 311,254 to 720,199). Their overall genetic correlations were first estimated. We then detected the shared genetic architecture, including pleiotropic single nucleotide polymorphisms (SNPs), loci, genes and biological processes, through cross-trait analyses. In addition, bidirectional Mendelian randomization (MR) analysis was performed to look for their causal relationships.

Results: We found significantly positive genetic correlations between KSD and all five gastrointestinal diseases. The cross-trait analysis identified 3184 potential pleiotropic SNPs, and 33 of which were pleiotropic loci shared by the two disorders. Gene-level analyses revealed 8 pleiotropic causal genes, primarily enriched in biological pathways involving ion homeostasis and response to vitamin D. In the MR analysis, we detected causal effects from GERD, IBS and Crohn's disease to KSD, while no reverse causality was observed.

Conclusions: Our study demonstrated the positive genetic links between KSD and gastrointestinal diseases and reported pleiotropic variants, loci, and genes, implicating potential biological mechanisms in the pathogenesis of stone disease. These findings further support the role of the gut-kidney axis and provide a genetic basis for the prevention, coregulation and treatment of these diseases.