Expression analysis of epithelial membrane protein 1 (EMP1) gene in kidney stone patients

Calcium oxalate (CaOx) nephrolithiasis is a recurrent urological disorder, and Randall’s plaque (RP) of the renal papilla is widely accepted as an early site of stone nucleation. Although immune activation, epithelial injury, and extracellular matrix (ECM) remodeling have been reported in RP, the cell-type-specific transcriptional features of Epithelial Membrane Protein 1 (EMP1) in this tissue context remain undefined.

A secondary, hypothesis-generating analysis of a publicly available single-cell RNA sequencing (scRNA-seq) dataset (NCBI GEO accession GSE176155; BioProject PRJNA735197) comprising renal papillary tissue from patients undergoing percutaneous nephrolithotomy for CaOx nephrolithiasis (RP samples) and matched normal renal papilla samples was performed. Raw FASTQ data were processed through Cell Ranger (v6.0.1) aligned to GRCh38, followed by quality control, normalization, dimensionality reduction (PCA, UMAP), graph-based clustering, and cell-type annotation in Seurat (v4.0.5) using canonical markers cross-checked against the Kidney Cell Atlas. Differential expression at the single-cell level was assessed by the Wilcoxon rank-sum test with Bonferroni correction. Coexpression, functional enrichment (GO, KEGG), and weighted gene coexpression network analysis (WGCNA) were used to characterise EMP1-associated transcriptional modules. Pseudobulk-style ANOVA and linear regression were performed as exploratory sensitivity checks at the sample level.

At the single-cell level, EMP1 was significantly downregulated in RP-derived epithelial and stromal clusters compared with normal renal papilla (adjusted p < 0.01, log2FC ≤ –0.30). EMP1 was co-expressed with C3, RNASE1, NRG1, IFI16, S100A10, HSPA6, and FN1, and the EMP1-correlated module identified by WGCNA was negatively correlated with the RP phenotype (r = –0.72, p < 0.001). GO and KEGG enrichment showed associations with cell adhesion, integrin and heparin binding, leukocyte migration, neutrophil extracellular trap formation, and focal adhesion. Sample-level pseudobulk ANOVA and regression analyses did not reach statistical significance for most genes, consistent with the limited number of donors and the loss of cell-type resolution after pseudobulk aggregation; these results are presented as exploratory.

This study reports an associative, hypothesis-generating link between reduced EMP1 expression in renal papillary epithelial and stromal populations and the molecular landscape of Randall’s plaque. Independent transcriptomic, spatial, and functional validation will be required before EMP1 can be considered a candidate biomarker or therapeutic target in CaOx nephrolithiasis.