Proteomic Signatures of Vemurafenib Resistance in Canine Urothelial Carcinoma Harboring the BRAFV595E Mutation.

Naturally occurring canine invasive urothelial carcinoma (InvUC) often harbors a BRAFV595E mutation, analogous to human BRAFV600E found across multiple cancer types, and has been used to investigate the effects of BRAF-targeted therapy. To investigate proteomic and phosphoproteomic changes during therapy, we analyzed 42 samples from 14 dogs with BRAFV595E-positive InvUC treated with vemurafenib. Tumors were collected via cystoscopy before treatment (Pre-Vem), 1 month into treatment (Vem-1-month), and at the time of progressive disease (Vem-PD). We observed consistent early suppression of proteins and phosphosites in tumors after 1 month of vemurafenib treatment in dogs that responded to the treatment, followed by their rebound at the time of progressive disease, highlighting early tumor suppressive events that are later reversed as tumors adapt and develop resistance. Key pathways affected included "positive regulation of telomerase assembly and localization to Cajal body", "positive regulation of protein localization to telomere", and "positive regulation of protein localization to Cajal body". Additionally, consistent "Rho GTPase signaling" changes were observed across both proteomic and phosphoproteomic analyses, underscoring the functional reactivation of this pathway in resistant tumors. In summary, these findings reveal molecular signatures of early response and acquired resistance to vemurafenib and offer a valuable resource for future investigation of BRAF-targeted therapy.