451. isoform switching events may provide new insight for the identification of prognostic and therapeutic targets in esophageal adenocarcinoma

Abstract Background Esophageal adenocarcinoma (EAC) represents a growing health problem characterized by rising incidence and poor prognosis due to late-stage diagnosis coupled with treatment resistance. Although EAC is a cancer with a high mutational burden, it lacks highly prevalent oncogenic drivers that can be therapeutically targeted. Herein, we investigated whether isoform switching events, defined as a change of the dominant gene isoform, may offer prognostic or therapeutic value in EAC. Methods We conducted RNA-sequencing on RNA isolated from patients undergoing esophagectomy following a diagnosis of EAC or Barrett’s with high-grade dysplasia (BE.HGD). Isoform switching events between Barrett’s low-grade dysplasia (BE.LGD) and BE.HGD + EAC alone or in combination with TP53 mutation were identified using IsoformSwitchAnalyzeR. Patients were stratified into tertiles based on isoform expression level, followed by cancer-free survival analysis using the log-rank test. To evaluate whether mortality-linked isoforms influence cancer cell growth, viability, migration and response to standard chemotherapy (Paclitaxel and Carboplatin), isoform-specific siRNA knockdown experiments targeting TTLL12 and HM13 were performed in OE19 and OE33 EAC cell lines. Results Isoform switching events were identified in 71 genes comparing BE.LGD with BE.HGD + EAC, with 10 isoforms significantly associated with cancer-specific patient mortality. With the inclusion of TP53 mutation status, 67 genes were isoform-switched and 16 isoforms were significantly linked with cancer-specific mortality. Knockdown of TTLL12 and HM13 isoforms, two survival-linked isoforms, led to significant inhibition of cell viability and inhibition of cell migration in EAC cell lines. Moreover, combination treatment of isoform-specific siRNA and chemotherapeutic agents further decreased cell viability with synergistic effects observed in both cell lines suggesting a role for specific isoform switches in therapeutic sensitization. Conclusions Our research identified specific isoform switching events significantly linked to increased cancer mortality among EAC patients. Gene knockdown studies of two identified isoforms led to significant inhibition of EAC cell migration and viability with synergy observed when cells were treated with both siRNA and standard chemotherapeutic agents. In conclusion, identification of isoform switching events may provide fresh insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC treatment or prevention.