Integrative bulk and single-cell transcriptome analyses reveals manganese metabolism-related prognostic genes in clear cell renal cell carcinoma with experimental validation

Manganese superoxide dismutase (MnSOD) functions as an influencing factor for the progression of clear cell renal cell carcinoma (ccRCC). The MnSOD activity is directly influenced by manganese metabolism. Therefore, our goal was to evaluate the prognostic value of manganese metabolism in ccRCC. Public ccRCC transcriptomic datasets were analyzed. Manganese metabolism-related prognostic genes were identified through univariate Cox regression combined with machine learning approaches. These genes were utilized to develop a risk model, and a nomogram was constructed using independent prognostic factors. Immune microenvironment evaluation revealed differences between risk groups, while single-cell RNA-sequencing (scRNA-seq) characterized key cell populations and prognostic gene expression, validated by RT-qPCR. MPPED2 and PLAU were identified as prognostic genes, with both the risk model and nomogram demonstrating high predictive accuracy. Analysis of 22 immune cell types revealed significant differences in immune infiltration between risk groups, while scRNA-seq data identified epithelial cells as the key cell type involved. RT-qPCR analysis revealed that the ccRCC group demonstrated notably reduced expression levels of MPPED2 and PLAU. This work combined bulk transcriptome and single-cell sequencing to preliminarily pinpoint MPPED2 and PLAU as potential ccRCC prognostic genes, highlight the essential function of epithelial cells, and offer new potential therapeutic targets for ccRCC.