Identification of a prognostic alternative splicing signature in oral squamous cell carcinoma.

Shuting Zhang, Xiang Wu, Pengfei Diao, Chenxing Wang, Dongmiao Wang, Sheng Li, Yanling Wang, Jie Cheng

Journal of cellular physiology 2020 May

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Alternative splicing (AS) is critically associated with tumorigenesis and patient's prognosis. Here, we systematically analyzed survival-associated AS signatures in oral squamous cell carcinoma (OSCC) and evaluated their prognostic predictive values. Survival-related AS events were identified by univariate and multivariate Cox regression analyses using OSCC data from the TCGA head neck squamous cell carcinoma data set. The Percent Spliced In calculated by SpliceSeq from 0 to 1 was used to quantify seven types of AS events. A predictive model based on AS events was constructed by least absolute shrinkage and selection operator Cox regression assay and further validated using a training-testing cohort design. Patient survival was estimated using the Kaplan-Meier method and compared with Log-rank test. The receiver operating characteristics curve area under the curves was used to evaluate the predictive abilities of these predictive models. Furthermore, gene-gene interaction networks and the splicing factors (SFs)-AS regulatory network was generated by Cytoscape. A total of 825 survival-related AS events within 719 genes were identified in OSCC samples. The integrative predictive model was better at predicting outcomes of patients as compared to those models built with the individual AS event. The predictive model based on three AS-related genes also effectively predicted patients' survival. Moreover, seven survival-related SFs were detected in OSCC including RBM4, HNRNPD, and HNRNPC, which have been linked to tumorigenesis. The SF-AS network revealed a significant correlation between survival-related AS genes and these SFs. Our findings revealed a systemic portrait of survival-associated AS events and the splicing network in OSCC, suggesting that AS events might serve as novel prognostic biomarkers and therapeutic targets for OSCC. © 2019 Wiley Periodicals, Inc.

Citation

Shuting Zhang, Xiang Wu, Pengfei Diao, Chenxing Wang, Dongmiao Wang, Sheng Li, Yanling Wang, Jie Cheng. Identification of a prognostic alternative splicing signature in oral squamous cell carcinoma. Journal of cellular physiology. 2020 May;235(5):4804-4813