Identification of Key Genes Associated with Endoplasmic Reticulum Stress in Calcium Oxalate Kidney Stones

Previous studies have indicated an association between endoplasmic reticulum stress (ERS) and the formation of kidney stones. To further investigate this mechanism, this research sought to identify key genes linked to ERS in calcium oxalate (CaOx) kidney stones.

Key cells with the highest ERS-related gene (ERSRG) scores were identified through single-cell analysis. These key cells were then categorized into high- and low-score groups based on their average ERSRG scores. To identify key genes, we analyzed the intersection of key ERSRGs and differentially expressed genes (DEGs) within key cells, focusing on genes demonstrating significant expression differences between control and CaOx kidney stone samples. A nomogram was constructed using these key genes to predict the risk of CaOx kidney stones. Gene set enrichment analysis (GSEA) was further performed to explore the functions of these key genes in the disease. Additionally, secondary clustering analysis was conducted on key cells to identify subtypes and evaluate the expression of key genes within these subtypes. Finally, the identified key genes were validated using quantitative real-time PCR (qRT-PCR) and Western blot analysis on cultured HK-2 cells, which were exposed with 2 mM CaOx for 24 h at 37 °C with 5% CO₂ or incubated with regular culture medium.

Endothelial cells were identified as key cells, and nine key genes were pinpointed in CaOx kidney stones: ACSL4, PTK2, DUSP4, MMP7, PHLDB2, TGM2, PPT1, SPARCL1, and LTF. The nomogram developed from these key genes demonstrated robust predictive ability for CaOx kidney stones risk. Additionally, GSEA revealed that olfactory transduction was enriched by key genes except PTK2. Secondary clustering analysis identified four key cell subtypes within endothelial cells, with LTF, MMP7, and SPARCL1 showing significantly differential expression between control and CaOx kidney stones groups across all key cell subtypes. qRT-PCR and Western blot analyses revealed that, compared to the control group, CaOx-exposed HK-2 cells exhibited significantly increased expression of ACSL4, MMP7, TGM2, PPT1, and LTF (p < 0.05), while showing significantly decreased expression of PTK2, DUSP4, SPARCL1, and PHLDB2 (p < 0.05).

This study identified key genes associated with ERS in CaOx kidney stones through single-cell and transcriptomic analysis. The discovery of these genes provides new insights into the treatment of CaOx kidney stones and offers valuable references for subsequent research. Future research should focus on elucidating the precise roles of these candidate genes in CaOx stone pathogenesis to assess their potential for therapeutic intervention.