Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer

Abstract

There is growing evidence that molecular subtypes (e.g. luminal and basal subtypes) affect the prognosis and treatment response in patients with muscle invasive urinary bladder cancer (invasive urothelial carcinoma, iUC). Modeling these subtypes in pre-clinical animal studies is essential, but it is challenging to produce these subtypes, along with other critical host and tumor features, in experimentally-induced animal models. This study was conducted to determine if luminal and basal molecular subtypes are present in naturally-occurring canine iUC, a cancer that mimics the human condition in other key aspects. RNA sequencing was performed on 29 canine treatment naive iUC tissue samples and on four normal canine bladder mucosal samples. Data were aligned to CanFam 3.1, and differentially expressed genes were identified. Unsupervised hierarchical clustering of these genes revealed two distinct groups (n = 13, n = 16). When genes that distinguish basal and luminal subtypes in human cancer (n = 2015) were used to probe genes differentially expressed between normal canine bladder and iUC, 829 enriched signature genes were identified. Unsupervised hierarchical clustering of these genes revealed two distinct groups comprised of 18 luminal subtype tumors and 11 basal subtype tumors. The enriched genes included MMP9, SERPINE2, CAV1, KRT14, and RASA3 in basal tumors, and PPARG, LY6E, CTSE, CDK3, and TBX2 in luminal tumors. In supervised clustering, additional genes of importance in human iUC were identified in canine iUC associated with claudin-low and infiltrated tumors. A smaller panel of genes (n = 60) was identified that distinguished canine luminal and basal iUC with overall 93.1% accuracy. Immune signature patterns similar to those in human iUC were also identified with the greatest enrichment of immune genes being in the basal subtype tumors. These findings provide additional compelling evidence that naturally-occurring canine iUC is a highly relevant and much needed model of human iUC for translational research.

A comparative meta andin silicoanalysis of differentially expressed genes and proteins in canine and human bladder cancer

“…In our meta-analysis, we identified five previous studies containing transcriptome data and in the most recent study (Parker et al, 2020), they cross validated their finding with other three published manuscripts (Dhawan et al, 2018, Maeda et al 2018, Dhawan et al, 2015). Thus, we opted to analyze the transcriptome data from these five previous studies and cross validate with TCGA data.…”

“…We selected three previous studies that evaluated the transcriptome (RNA-seq) of canine bladder carcinoma, with the data sets available online at NCBI short-read archive (SRA) under BioProject ID PRJNA559406 (Parker et al, 2020), GEO database (ref: GSE24152) (Dhawan et al, 2018) or available at the DDBJ Sequenced Read Archive repository (http://trace.ddbj.nig.ac.jp/dra/index_e.html) with accession number DRA005844). Besides that, we also included one manuscript evaluating the transcriptome of canine bladder cancer using microarray data (Dhawan et al, 2015) and one manuscript that performed both mRNA-seq and exome-seq (Ramsey et al 2017).…”

“…Transitional cell carcinoma (TCC), also called urothelial carcinoma, is the most common bladder cancer in both humans and dogs, sharing clinical, pathological and molecular alterations (Dhawan et al, 2018, Maeda et al, 2018, Ramsey et al, 2017). In the United States, it is expected 81.400 new cases and 17.980 bladder cancer-related deaths (Siegel et al, 2020).…”

“…Thus, in the human literature, the muscle invasive bladder carcinoma is focus of recent studies. In dogs, the infiltration is not standardized, since in several cases tissue samples comes from cystoscopy (Dhawan et al 2018, Dhawan et al 2015).…”

“…In dogs, some recent studies performing transcriptome analysis revealed several important molecular findings, such as differentiation of canine bladder cancer in molecular subtypes according to BRAFV595E somatic mutation ( BRAFV600E in humans) (Parker et al 2020), identification therapeutic targets ( PTGER2, ERBB2, CCND1, VEGF , and EGFR ) and separation in basal and luminal subtypes, as for human bladder cancers, in order to compare their different muscular invasive potential (Dhawan et al, 2018). Therefore, studies performing comparative molecular comparisons between human and canine bladder carcinomas can provide a unique opportunity to study this cancer subtype in both species.…”