Computational analysis of bulk and single-cell RNAseq identifies prognostic signature genes in papillary renal cell carcinoma with Y chromosome loss.

Loss of Y chromosome (LOY) is the most commonly occurring somatic event in elderly males, and is associated with poor outcomes in most cancers. However, LOY is shown to be associated with improved survival in papillary renal cell carcinoma(pRCC). The study was designed to analyze the possible molecular mechanism behind this paradoxical event. For this purpose, the transcriptomics dataset of 214 male pRCC patients were retrieved from the TCGA database and the LOY score was calculated based on the expression of the 14 Y chromosome gene set. The LOY score was used to stratify the samples into two groups called Y_high (normal expression of Y chromosome) and Y_low (loss of Y chromosome) by the custom ssGSEA function. LOY-associated transcriptional reprogramming is further elucidated by analyzing differential gene expression analysis, functional enrichment analysis, and tumor immune microenvironment analysis, revealing the enrichment of structural and developmental pathways alongside the downregulation of immunosuppressive mechanisms in Y_low tumors. Leveraging these LOY-associated transcriptional changes, a three-gene prognostic signature (WASF1, MTHFD2, CHMP1A) was derived through LASSO-penalized Cox regression followed by two-step bootstrap stability and multivariate significance filtering, and validated through bootstrap bias correction, time-dependent ROC analysis, calibration curve analysis, and multivariate Cox regression adjusting for age, pathological stage, and metastasis status. Furthermore, single cell transcriptomics analysis and DNA methylation analysis reveals the mosaic nature of the LOY and localized the prognostic gene expression within myeloid cell populations. We conclude that LOY may have less aggressive tumor profile in pRCC, and may provide clinically relevant biomarkers.