Prognostic alternative splicing signatures in esophageal cancer reveal SF3A3 as a key oncogenic splicing factor

Esophageal cancer (ESCA) is a highly lethal malignancy with limited therapeutic options, largely due to late-stage diagnosis and molecular complexity. Dysregulated alternative splicing (AS) contributes to ESCA progression, but its prognostic and mechanistic roles remain poorly characterized. The aim of this study is to investigate the role of AS in ESCA progression and to elucidate its potential as a prognostic factor.

The percent spliced in (PSI) values for seven subtypes of AS events, RNA-seq and clinical information of ESCA cohorts were retrieved from The Cancer Genome Atlas (TCGA) database. Survival-related AS events were identified through Cox regression analysis. The AS events were integrated to formulate the prognostic signature both for overall survival (OS) and progression-free interval (PFI). ESCA patients were categorized into high- or low-risk groups using the median risk score of the signature. Kaplan-Meier analysis, receiver operating characteristic (ROC) analyses, and Cox regression were performed to evaluate the prognostic efficacy of this signature. Cell proliferation was measured with Cell Counting Kit-8 (CCK8) and colony formation. Tumor xenograft experiment was performed to evaluate the tumor growth of ESCA cells in vivo.

We identified 27,611 AS events in 162 ESCA patients from TCGA, with exon skipping, alternate promoter, and alternate terminator as the most common types. A prognostic signature integrating all seven AS types accurately predicted OS and PFI in ESCA. Patients with a high-risk score demonstrated a poor prognosis. The splicing factor SF3A3 was found to promote esophageal squamous cell carcinoma (ESCC) cell proliferation and tumor growth by regulating the AS of LGALS9.

This study identified survival-associated AS signatures, potentially improving the prediction of survival outcomes in ESCA patients. Moreover, the splicing factor SF3A3 was shown to promote tumor progression by regulating AS of LGALS9, suggesting it as a promising therapeutic target.