The combination of transcriptome and Mendelian randomization reveals clinical and immuno-functional biomarkers of alternative splicing regulation associated with planar cell polarity signaling pathways in pan-cancer

Abstract

Background The intricate interplay between alternative splicing (AS) events and the planar cell polarity (PCP) signaling pathway is known to play a crucial role in cancer initiation and progression. Understanding the prognostic implications and immunological features of PCP-related AS events can unveil novel biological markers and potential targets for immunotherapy. Methods We sourced genes associated with the PCP signaling pathway from diverse databases and extracted RNA-seq, clinical records, and AS profiles from TCGA and TCGA SpliceSeq databases. Employing the least absolute shrinkage and selection operator (LASSO), we identified prognostically significant AS events and developed risk scoring models and nomograms. Immune distinctions within risk subgroups were assessed using the ESTIMATE algorithm, CIBERSORT analysis, and single-sample gene set enrichment analysis (ssGSEA). Furthermore, we analyzed selected differentially expressed AS genes for their relevance to prognosis and immunity. A regulatory network connecting AS and splicing factors (SFs) was delineated using Cytoscape. Mendelian randomization (MR) and Bayesian weighted MR (BWMR) were employed to validate causal links among AS genes identified in multivariable Cox regression analysis. Results Analysis of 115 AS events across 9812 pan-cancer-related genes revealed 80 AS events significantly associated with prognosis. A risk score model based on 12 carefully selected AS events effectively predicted overall survival (OS) in tumor patients and correlated with clinical parameters. The risk score also showed associations with the tumor microenvironment, immune cell infiltration, and immune checkpoint genes. Notably, PRICKLE3, PSMA4, and AP2S1 AS genes were identified as influential in immune characteristics and prognosis across various cancers. A correlation network between AS events and SF genes provided insights into potential biomarkers. MR analysis identified NPHP3 and UBA52 as protective factors against cancer occurrence. Conclusion This study elucidates the role of AS events in cancer prognosis and tumor immunology, providing risk-scoring models and nomogram prognostic tools for the PCP signaling pathway in pan-cancer patients. Furthermore, the causal relationship between PCP-related AS genes and cancer was confirmed using genetic approaches, underscoring the potential for targeted therapeutic interventions.