Defining the somatic mutational spectrum of canine oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is the most common oral malignancy of epithelial origin in dogs, representing ~6% of all cancers in this species. Current standard of care consists of wide-margin surgical excision in eligible patients according to stage of disease. Although long-term remission can be achieved, surgery is invasive and results in varying degrees of dysfunction. We have previously shown that the MAPK pathway is hyperactivated in canine OSCC, and that oral administration of the small-molecule inhibitor trametinib can significantly reduce local tumor burden in some patients and represents a clinically applicable neoadjuvant strategy. However, not all tumors are sensitive to trametinib, and the response appears to be at least partially dependent on the presence of specific underlying somatic variants including the well-known MAPK pathway-activating BRAF V595E mutation. These observations suggest that tumors that carry wild-type BRAF alleles likely harbor oncogenic mutations in genes that dysregulate other pathways not inhibited by trametinib, or that confer tumor cells the ability to evade MAPK-pathway inhibition. However, the mutational landscape of OSCC has not been thoroughly investigated, and it remains unknown whether other somatic mutations underlie the apparent oncogenic signaling heterogeneity. In this study, we investigated the somatic mutational landscape of canine OSCC by performing high-coverage whole-genome sequencing of OSCC tumor tissues compared with matched blood-derived germline DNA from 15 dogs known to be sensitive (n=6) or resistant (n=9) to trametinib. Results confirmed the presence of BRAF V595E alleles in most responders, and showed that canine OSCC is genetically heterogeneous, that non-responder dogs have a higher somatic mutational burden compared to responders, and that somatic mutations predicted to have a deleterious effect are relatively common in genes such as TP53, CDH10, HRAS, and FAT2, among others. A larger cohort tied to clinical outcomes, complemented with transcriptional and functional data, will help identify other molecular vulnerabilities and ways to more robustly stratify dogs considered potential candidates for targeted interventions.