Identification of isoform switching events linked with esophageal adenocarcinoma patient survival informs novel prognostic and therapeutic targets

Esophageal adenocarcinoma (EAC), the dominant subtype of esophageal cancer in developed countries, is a growing health problem, characterized by poor patient prognosis and dismal survival due to ineffective screening tools and a lack of efficacious options targeting the interception or treatment of EAC. Despite molecular advances, molecular targeting of EAC remains elusive, suggesting the need for identifying alternative targets with improved prognostic and therapeutic value. Herein, we performed RNA-sequencing analysis in EAC and Barrett's Esophagus (BE) precursor lesions to identify isoform switching events significantly linked with all-cause and cancer-specific mortality. Patients were stratified based on histopathology alone or in combination with TP53 mutation status, the most commonly mutated gene in EAC. To gain mechanistic insight, we performed isoform-specific siRNA knockdown of two isoforms, TTLL12 and HM13, both linked to patient survival, and investigated mechanisms associated with isoform dysregulation and whether targeting specific isoforms in EAC acts synergistically to improve therapeutic potential. Isoform-specific knockdown of TTLL12 and HM13 significantly decreased the viability of two EAC cell lines, sensitized EAC cell lines to standard-of-care chemotherapy agents (paclitaxel and carboplatin) with synergy, and inhibited EAC cell migratory potential. Knockdown of the TTLL12 isoform led to activation of chaperone-mediated autophagy, which, in turn, decreased expression of CHK1 and TP53; whereas knockdown of the HM13 isoform activated the unfolded protein response and induced endoplasmic reticulum stress-induced autophagy and apoptosis. In addition, HM13 isoform knockdown increased the response to an anti-PD-L1 agent, avelumab, in EAC cells, suggesting a role for isoform switching in immunosuppression. Taken together, study results suggest that isoform switching may provide novel insight for the identification of prognostic markers and inform new potential therapeutic targets for EAC treatment or prevention.