Large-Scale Proteomics Data Reveal Integrated Prognosis-Related Protein Signatures and Role of SMAD4 and RAD50 in Prognosis and Immune Infiltrations of Prostate Cancer Microenvironment.

UNLABELLED: As prostate cancer (PCa) is one of the most commonly diagnosed cancer worldwide, identifying potential prognostic biomarkers is crucial. In this study, the survival information, gene expression, and protein expression data of 344 PCa cases were collected from the Cancer Proteome Atlas (TCPA) and the Cancer Genome Atlas (TCGA) to investigate the potential prognostic biomarkers. The integrated prognosis-related proteins (IPRPs) model was constructed based on the risk score of each patients using machine-learning algorithm. IPRPs model suggested that Elevated RAD50 expression ( p  = 0.016) and down-regulated SMAD4 expression ( p  = 0.017) were significantly correlated with unfavorable outcomes for PCa patients. Immunohistochemical (IHC) staining and western blot (WB) analysis revealed significant differential expression of SMAD4 and RAD50 protein between tumor and normal tissues in validation cohort. According to the overall IHC score, patients with low SMAD4 ( p  < 0.0001) expression and high RAD50 expression ( p  = 0.0001) were significantly correlated with poor outcomes. Besides, expression of SMAD4 showed significantly negative correlation with most immune checkpoint molecules, and the low SMAD4 expression group exhibited significantly high levels of LAG3 ( p  < 0.05), TGFβ ( p  < 0.001), and PD-L1 ( p  < 0.05) compared with the high SMAD4 expression group in the validation cohort. Patients with low SMAD4 expression had significantly higher infiltration of memory B cells ( p  = 0.002), CD8 + T cells ( p  < 0.001), regulatory T cells ( p  = 0.006), M2-type macrophages ( p  < 0.001), and significantly lower infiltration of naïve B cells ( p  = 0.002), plasma cells ( p  < 0.001), resting memory CD4 + T cells ( p  < 0.001) and eosinophils ( p  = 0.045). Candidate proteins were mainly involved in antigen processing and presentation, stem cell differentiation, and type I interferon pathways.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-022-00070-1.