A pan-cancer analysis of the core pre-mRNA 3′ end processing factors, and their association with prognosis, tumor microenvironment, and potential targets

Abstract Alternative polyadenylation (APA) is a crucial mechanism for regulating gene expression during pre-mRNA 3′ processing. Pre-mRNA 3′ end processing factors is the main factor involved in this process. However, pre-mRNA 3′ end processing factors in different cancer expression profiles and the relationship between pre-mRNA 3′ end processing factors and tumor microenvironment and the prognosis of the same patient is still unclear. In this study, we conducted a comprehensive exploration of the core pre-mRNA 3′ end processing factors across various cancer types by utilizing common cancer database, and revealing a robust correlation between the expression of these core factors and tumor characteristics. Leveraging advanced bioinformatics databases, we evaluated the expression levels and prognostic relevance of pre-mRNA 3′ end processing factors across pan-cancer tissues. Our extensive pan-cancer analysis revealed unique expression patterns of pre-mRNA 3′ end processing factors in both tumor and adjacent non-tumorous tissues. Notably, we found a significant correlation between the expression levels of pre-mRNA 3′ end processing factors and patient prognosis. Furthermore, we identified strong associations between pre-mRNA 3′ end processing factors expression and various factors, such as stromal, immune, RNA stemness, and DNA stemness scores across pan-cancer tissues. Our data also highlighted a link between the expression of pre-mRNA 3′ end processing factors and sensitivity to specific drugs, including pyrazoloacndine, amonaflide, and chelerythrinede, among others. We found four key pre-mRNA 3′ end processing factors that play a crucial role in mRNA preprocessing. Our study illuminates the potential promotion and inhibition role of pre-mRNA 3′ end processing regulators in the progression of cancer, CPSF2, CPSF3, CSTF2, SYMPK offering valuable insights for future research investigations on these regulators as diagnostic markers and therapeutic targets across pan-cancer.