RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma

Abstract

Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans and between the two species there are similarities in histology and biologic behavior. Due to these similarities, dogs have been proposed as models for meningioma pathobiology. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, studies are lacking that utilize RNAseq to characterize gene expression in clinical cases of canine meningioma. The primary objective of this study was to develop a technique for which high quality RNA can be extracted from formalin-fixed, paraffin embedded tissue and then used for transcriptome analysis to determine patterns of gene expression. RNA was extracted from thirteen canine meningiomas–eleven from formalin fixed and two flash-frozen. These represented six grade I and seven grade II meningiomas based on the World Health Organization classification system for human meningioma. RNA was also extracted from fresh frozen leptomeninges from three control dogs for comparison. RNAseq libraries made from formalin fixed tissue were of sufficient quality to successfully identify 125 significantly differentially expressed genes, the majority of which were related to oncogenic processes. Twelve genes (AQP1, BMPER, FBLN2, FRZB, MEDAG, MYC, PAMR1, PDGFRL, PDPN, PECAM1, PERP, ZC2HC1C) were validated using qPCR. Among the differentially expressed 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 canine meningioma samples to provide biologically relevant transcriptome analyses using a next-generation sequencing technique, such as RNA-seq.

Canine Primary Intracranial Cancer: A Clinicopathologic and Comparative Review of Glioma, Meningioma, and Choroid Plexus Tumors

“…Human-telomerase reverse transcriptase expression has been described in a number of canine meningioma subtypes; however, has not been evaluated in a prognostic setting (138). Somatostatin receptor-2 expression has recently been described in a variety of canine meningioma subtypes, a finding that is supported by RNAseq data analysis of canine meningioma that revealed increased expression of somatostatin receptors (126, 139). The significance of this finding is unclear; however, similar findings have been noted in a number of human tumors, including meningioma.…”

“…Canine meningiomas are widely infiltrated by inflammatory cells including an abundance of neutrophils, either associated with or unassociated with areas of necrosis, large numbers of macrophages and an abundance of lymphocyte subtypes (124). Initial immunohistochemical analysis for interleukin 6 and 8 expression failed to yield significant expression levels; however, RNA transcriptome analysis of canine meningioma revealed overexpression in a number of immunomodulatory genes (125, 126). Chondroid and osseous metaplasia are sporadically seen in various subtypes, although they are most commonly seen in the optic nerve-associated meningiomas.…”

Identification of Key Genes and Pathways Associated with Mast Cells Resting in Meningioma

“…Moreover, survival analysis (Survival package with logrank test; threshold value of P value < 0.05) of key genes related to resting mast cells showed that the risk model constructed based on 9 key genes (CXCL8, MYC, CXCL2, CXCL3, TNFAIP3, FOSL1, HIST1H2BN, BCL2A1 and SLC2A3) could predict the prognosis of patients with meningioma. A previous study reported that MYC expression is dysregulated in human meningioma, indicating its potential role in oncogenic processes [37]. Cai et al [38] found that c-MYC in meningioma is targeted by RIZ1 to negatively regulate the ubiquitin-binding enzyme E2C/UbcH1.…”

Inhibitory effect of AQP1 silencing on adhesion and angiogenesis in ectopic endometrial cells of mice with endometriosis through activating the Wnt signaling pathway

“…AQP1 gene expression was up-regulated in endometriosis (Figure 1(b)). AQP1 was then predicted to interact with topoisomerase 2-beta (TOP2B) by PPI (Figure 1 (c)), which was correlated to the Wnt/β-catenin signaling pathway [12,26,27]. All in all, AQP1 gene is highly expressed in endometriosis and is related to Wnt signaling pathway in silico.…”