Proteome and transcriptome analysis reveals tubulin isotype switching in paclitaxel-treated esophageal cancer

Background: Despite combination therapies, less than half of patients with resectable esophageal cancer (EC) survive beyond 5 years. Previous studies, primarily using transcriptomics, revealed high plasticity in these cancer cells. In other cancer contexts, such plasticity has been demonstrated to also result in aberrant tubulin expression and resistance to taxanes. Given that taxanes are a cornerstone in EC treatment, we established a multi-omics analysis of neoadjuvantly treated EC cells and tissues with a focus on tubulins. Materials and methods: We applied transcriptomics and proteomics to pretreated EC resection samples and primary cell lines from various treatment settings. RNA-Sequencing and MS-based proteomics data were correlated with clinical outcomes to identify response-associated tubulin genes and proteins. In vitro experiments included lentiviral gene silencing of candidate resistance mediators and pharmacological interventions. Results: In both the transcriptomics and proteomics datasets, tubulin isoforms that are not typically expressed in the esophagus were found to associate with survival outcome. Specifically, we found that beta-tubulin 3 (TUBB3) was associated with unfavorable outcomes. However, TUBB3 silencing in vitro did not render cells sensitive to taxanes, nor did it prevent transitions to resistant cell states. Pharmacological inhibition did not improve the efficacy of chemoradiation. Instead, we found that TUBB3 is highly correlated with mesenchymal cell states, and that its expression is a consequence of such transitions rather than a cause. Conclusions: A neuronal tubulin isoform was found to increase in cells undergoing mesenchymal transition and acquiring resistance. These abundant proteins could serve as biomarkers for acquired therapy resistance in EC.