Laser capture microdissection-based transcriptomic analysis of neoplastic mast cells reveals novel molecular alterations across canine cutaneous mast cell tumor grades

Mast cell tumors (MCTs) are one of the most common skin neoplasms in dogs, yet their biological behaviour and the underlying molecular mechanisms remain poorly understood. In this study, neoplastic mast cells (MCs) were isolated from formalin-fixed paraffin-embedded (FFPE) canine MCT biopsies using laser capture microdissection (LCM), followed by RNA sequencing of these cells. In this way, MC-specific mechanisms were investigated in high- versus low-grade canine MCTs. To this end, 32 canine cutaneous MCTs were analysed, of which 18 were graded as low- and 14 as high-grade tumors based on histopathology. A total of 74 differentially expressed genes were identified including MOB3B , EXOC6B , BAIAP2 , and TRMO , which have established associations with several human cancers. Gene Set Enrichment Analysis revealed significant enrichment of tumorigenic pathways, including KIT signalling, Ras signalling, ubiquitin-mediated proteolysis, and neurotrophin signalling in high-grade MCTs. Additionally, immune-related pathways, including IL-2 signalling, natural killer cell-mediated cytotoxicity, and leukocyte transendothelial migration, underscored the role of immune interactions in high-grade MCTs. This is the first study to focus on gene expression patterns derived from LCM-isolated neoplastic MCs and their role in the molecular mechanisms driving MC malignancies.