biostudies-literatureUnknown15Su P<h4>Background</h4>Alternative splicing (AS) of mRNA has emerged as a promising biomarker for various tumors, playing a crucial role throughout nearly all stages of tumor progression and influencing the tumor immune microenvironment (TIME). Our study was designed to develop an AS-based signature for accurate prognosis prediction in lung adenocarcinoma (LUAD) patients, to delineate the associated immune cell landscape, and to pinpoint promising drug targets.<h4>Methods</h4>Prognostic alternative splicing events (PASEs) were identified through univariate Cox regression analysis of RNA-Seq data from The Cancer Genome Atlas (TCGA). These PASEs were incorporated into a least absolute shrinkage and selection operator-Cox proportional hazards model to develop a prognostic signature. Experimental validation was performed using reverse transcription quantitative polymerase chain reaction, immunohistochemistry, and functional assays <i>in vitro</i> and <i>in vivo</i>.<h4>Results</h4>A total of 13 PASEs were selected to form the prognostic signature, which demonstrated excellent predictive power for 1-, 2-, and 3-year overall survival (OS), with area under the receiver operating characteristic curve values of 0.776, 0.751, and 0.767, respectively. High-risk patients, identified by the signature, showed significantly decreased stromal, immune, and combined scores; increased tumor purity (<i>P</i>< 0.001); a reduced prevalence of various immune cell types; diminished immune cell activity; and decreased expression of immune checkpoint genes. Notably, elevated expression of cyclin-dependent kinase inhibitor 2A (CDKN2A), a gene associated with PASEs, correlated with poorer OS and significantly higher infiltration of CD8⁺ T cells, activated memory CD4⁺ T cells, and M1 macrophages compared to patients with lower expression. Further validation studies confirmed increased CDKN2A levels in LUAD tissues, with CDKN2A protein expression inversely correlated with LUAD prognosis (hazard ratio = 2.737; 95% confidence interval, 1.524-4.915; <i>P</i> = 0.0002). CDKN2A was found to promote LUAD progression <i>in vitro</i>. Molecular docking identified YM-201636 and VE-822 (Berzosertib) as potential drugs targeting CDKN2A, both showing promise for LUAD treatment <i>in vivo</i>.<h4>Conclusion</h4>PASEs constitute a comprehensive biomarker for predicting prognosis and monitoring the TIME in LUAD patients. Specifically, CDKN2A stands out as a potential prognostic biomarker and drug target for LUAD.Frontiers in oncology1579017https://www.ebi.ac.uk/biostudies/studies/S-EPMC12669014biostudies-literaturePrognostic alternative mRNA splicing in lung adenocarcinoma.PMC12669014Xu PSu PXu DfalsePrognostic alternative mRNA splicing in lung adenocarcinoma.<h4>Background</h4>Alternative splicing (AS) of mRNA has emerged as a promising biomarker for various tumors, playing a crucial role throughout nearly all stages of tumor progression and influencing the tumor immune microenvironment (TIME). Our study was designed to develop an AS-based signature for accurate prognosis prediction in lung adenocarcinoma (LUAD) patients, to delineate the associated immune cell landscape, and to pinpoint promising drug targets.<h4>Methods</h4>Prognostic alternative splicing events (PASEs) were identified through univariate Cox regression analysis of RNA-Seq data from The Cancer Genome Atlas (TCGA). These PASEs were incorporated into a least absolute shrinkage and selection operator-Cox proportional hazards model to develop a prognostic signature. Experimental validation was performed using reverse transcription quantitative polymerase chain reaction, immunohistochemistry, and functional assays <i>in vitro</i> and <i>in vivo</i>.<h4>Results</h4>A total of 13 PASEs were selected to form the prognostic signature, which demonstrated excellent predictive power for 1-, 2-, and 3-year overall survival (OS), with area under the receiver operating characteristic curve values of 0.776, 0.751, and 0.767, respectively. High-risk patients, identified by the signature, showed significantly decreased stromal, immune, and combined scores; increased tumor purity (<i>P</i>< 0.001); a reduced prevalence of various immune cell types; diminished immune cell activity; and decreased expression of immune checkpoint genes. Notably, elevated expression of cyclin-dependent kinase inhibitor 2A (CDKN2A), a gene associated with PASEs, correlated with poorer OS and significantly higher infiltration of CD8⁺ T cells, activated memory CD4⁺ T cells, and M1 macrophages compared to patients with lower expression. Further validation studies confirmed increased CDKN2A levels in LUAD tissues, with CDKN2A protein expression inversely correlated with LUAD prognosis (hazard ratio = 2.737; 95% confidence interval, 1.524-4.915; <i>P</i> = 0.0002). CDKN2A was found to promote LUAD progression <i>in vitro</i>. Molecular docking identified YM-201636 and VE-822 (Berzosertib) as potential drugs targeting CDKN2A, both showing promise for LUAD treatment <i>in vivo</i>.<h4>Conclusion</h4>PASEs constitute a comprehensive biomarker for predicting prognosis and monitoring the TIME in LUAD patients. Specifically, CDKN2A stands out as a potential prognostic biomarker and drug target for LUAD.2025-01-01T00:00:00Z20252026-06-08T03:17:57.253Z2026-06-08T03:09:05.34ZS-EPMC126690144134138610.3389/fonc.2025.1579017