RNA-seq transcriptome analysis OF formalin-fixed paraffin-embedded canine meningioma

Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans. Canine meningiomas closely resemble human meningiomas in histological appearance as well as biological behavior. Because of the similarities between canine and human meningiomas, dogs have been proposed as models and surrogates for studying and treating human cancers including meningioma. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, there is a paucity of suitable fresh material available for studies of differential expression (DE) of genes in cases of veterinary neoplasia. We report here the use of formalin-fixed paraffin embedded (FFPE) specimens as much as a decade old, to provide RNA suitable for transcriptome analysis using next-generation sequencing (NGS). RNA was extracted from 13 canine meningiomas – 12 from (FFPE) and one flash-frozen. These represented 6 grade I and 7 grade II/III. RNA was also collected from flash-frozen meningeal tissue (arachnoid) from 3 control dogs. RNA from FFPE was of sufficient quality to successfully identify 125 significantly DE genes, the majority of which were related to oncogenic processes. 12 genes (AQP1, BMPER, FBLN2, FRZB, MEDAG, MYC, PAMR1, PDGFRL, PDPN, PECAM1, PERP, ZC2HC1Cc) were validated using qPCR. Among the DE genes were oncogenes, tumor suppressors, transcription factors, VEGF-related genes, and members of the WNT pathway. Our work demonstrates that RNA of sufficient quality can be extracted from FFPE samples to provide biologically relevant transcriptome analyses using a NGS technique, such as RNA-seq. Overall design: RNAseq was performed on 13 meningioma samples (FFPE) and 3 normal controls.