Identification of splicing factors signature predicting prognosis risk and the mechanistic roles of novel oncogenes in HNSCC
Head and neck squamous cell carcinoma (HNSCC) is the most frequent subtype of head and neck cancer generally with a poor prognosis and limited treatment options due to its highly heterogeneous malignancy. In this study, we screened functional splicing regulatory RNA binding proteins (RBPs) that are closely related with prognosis of patients with HNSCC and showed significant expression difference between HNSCC tumors and normal tissues. Based on this finding, we have selected six candidate genes (HNRNPC, ZCRB1, RBM12B, SF3A2, SF3B3, and SRSF11) to construct a prognostic prediction model and validated the prognostic model for predicting patient survival. We found that the risk score predicted by our model can serve as an independent prognostic predictor, notably, HNSCC tumors showed enhanced expression of SF3B3, HNRNPC, and ZCRB1, which increases a patient's risk score in the discovered prediction model. The investigation of underlying mechanism validated that knockdown of SF3B3, HNRNPC, and ZCRB1 separately induced a substantial impairment of HNSCC cell survival. Conversely, single overexpression of one of the three genes promoted tumor cellular proliferation. High throughput RNA sequencing analysis and identification revealed that changes in the expression of SF3B3 and HNRNPC remarkably affected the splicing isoforms of genes related to cell cycle regulation, whereas the depletion of ZCRB1 contributed to notable DNA damage. Additionally, the prognostic prediction model's risk score was suggested to be related with immune infiltration score, particularly, SF3B3 has a negative correlation with CD8A expression. Therefore, our findings provide promising prognosis predictors and potential therapeutic targets for better treatment efficacy of HNSCC. Overall design: To investigate the effects of the knockdown or overexpression of SF3B3, HNRNPC, and ZCRB1 genes on hypopharyngeal carcinoma FaDu cells, we established both overexpression and knockdown cell lines based on the FaDu cell line and then performed RNA-seq sequencing analysis.