Unraveling immune heterogeneity across pan-cancer and deep insights in lung adenocarcinoma based on alternative splicing.

Abstract

Alternative splicing (AS) participates in tumor development and tumor microenvironment formation. However, the landscape of immune-infiltrating AS events in pan-cancer and mechanisms of AS in lung adenocarcinoma (LUAD) have not been comprehensively characterized. We systematically profiled the immune-infiltrating AS event landscape of pan-cancer using data from The Cancer Genome Atlas, analyzing both commonalities and specific characteristics among different cancer types. We found that AS events tend to occur specifically in one cancer type rather than in multiple cancer types. AS events were used to classify 512 LUAD samples into 2 subtypes by unsupervised clustering: the aberrant splicing subtype and the immune-infiltrating subtype. The 2 subtypes showed significant differences in clinicopathology, prognosis, transcriptomics, genomics, and immune microenvironment. We constructed a classification signature comprising 10 genes involved in 14 AS events using logistic regression. The robustness of the signature was validated in 3 independent datasets using survival analysis. To explore AS mechanisms in LUAD, we constructed subtype-specific coexpression networks using Pearson correlation analysis. AS event of AKT3 regulated by splicing factor ENOX1 was associated with poor prognosis in LUAD. Overall, we outline AS events associated with immune infiltration in pan-cancer, and this study provides insights into AS mechanisms in LUAD patient classification.