The identification of RNA splicing aberrations and their potential regulatory network in Chinese non-small cell lung cancer

Alternative splicing contributes to the carcinogenic process of non-small cell lung cancer. Although extensive efforts have characterized cancer-associated alternative splicing events, the upstream regulators governing these aberrant splicing events remain poorly understood. Here, we integrated multi-omics data from 22 lung adenocarcinoma, 13 lung squamous cell carcinoma and matched adjacent normal tissues of Chinese patients. We aimed to identify cancer-associated splicing events, construct regulatory networks of RBP, miRNA and DNA methylation on them and dissect carcinogenic pathways at integrated multi-omics layers in lung adenocarcinoma and squamous cell carcinoma, respectively. We identified that immune-suppression pathways and oxidative phosphorylation specifically promote the progression of adenocarcinoma and squamous cell carcinoma, respectively. ATP5F1C exon 9 inclusion in adenocarcinoma and LTBP3 exon 25 exclusion in squamous cell carcinoma, involved in proliferation, invasion and metastasis, are key splicing events with therapeutic potential. Furthermore, we proposed miR-4521-PABPC5-ATP5F1C, miR-4423-3p-IGF2BP3/miR-944-RBMS3-LTBP3 as upstream regulatory axes potentially driving these events. Notably, genome-wide CpG methylation exhibited widespread association with distant splicing events, potentially playing a trans-regulatory role by disrupting splice factor (BCL11B, RUNX1, RUNX2) binding near CpG sites and inhibiting RBMS3 transcription. Our findings shed light on the potential functional impact and multi-layer regulation of cancer-associated splicing events, offering novel insights for splicing-switching therapies to improve non-small cell lung cancer treatment and prognosis.