RNAseq expression patterns of canine invasive urothelial carcinoma reveal two distinct tumor clusters and shared regions of dysregulation with human bladder tumors

Abstract

Background: Invasive urothelial carcinoma (iUC) is highly similar between dogs and humans in terms of pathologic presentation, molecular subtypes, response to treatment and age at onset. Thus, the dog is an established and relevant model for testing and development of targeted drugs benefiting both canine and human patients. We sought to identify gene expression patterns associated with two primary types of canine iUC tumors: those that express a common somatic mutation in the BRAF gene, and those that do not. Methods: We performed RNAseq on tumor and normal tissues from pet dogs. Analysis of differential expression and clustering, and positional and individual expression was used to develop gene set enrichment profiles distinguishing iUC tumors with and without BRAFV595E mutations, as well as genomic regions harboring excessive numbers of dysregulated genes. Results: We identified two expression clusters that are defined by the presence/absence of a BRAFV595E (BRAFV600E in humans) somatic mutation. BRAFV595E tumors shared significantly more dysregulated genes than BRAF wild-type tumors, and vice versa, with 398 genes differentiating the two clusters. Key genes fall into clades of limited function: tissue development, cell cycle regulation, immune response, and membrane transport. The genomic site with highest number of dysregulated genes overall lies in a locus corresponding to human chromosome 8q24, a region frequently amplified in human urothelial cancers. Conclusions: These data identify critical sets of genes that are differently regulated in association with an activating mutation in the MAPK/ERK pathway in canine iUC tumors. The experiments also highlight the value of the canine system in identifying expression patterns associated with a common, shared cancer.

Multi-omics approach identifies germline regulatory variants associated with hematopoietic malignancies in retriever dog breeds

“…The nearest gene to the CFA5 critical interval, NLRP1 , was 1.7Mb upstream, suggesting the risk locus may have distal effects ( S5 Table ). When comparing gene expression levels in individual samples to the average expression across controls (see Methods, [ 22 ]), seven genes and one lncRNA demonstrated significant individual expression (z-score≥|2.5|) among cases. After excluding one heterozygous dog who received chemotherapy one week prior to the blood draw, comparison of the four dogs homozygous for the CFA5 risk haplotype to the remaining six heterozygous dogs revealed an additional 17 genes or non-coding RNAs with significant differential and individual expression ( S5 Table ).…”

A Comparative Meta-Analysis and in silico Analysis of Differentially Expressed Genes and Proteins in Canine and Human Bladder Cancer

“…We selected three previous studies that evaluated the transcriptome (RNA-seq) of canine bladder carcinoma, with the datasets available online via the NCBI short-read archive (SRA) under BioProject ID PRJNA559406 ( 18 ), GEO database (ref: GSE24152) ( 1 ), and DDBJ Sequenced Read Archive repository ( http://trace.ddbj.nig.ac.jp/dra/index_e.html ) with accession number DRA005844. In addition, we also included one manuscript evaluating the transcriptome of canine bladder cancer using microarray data ( 13 ) and one manuscript that performed both mRNA-seq and exome-seq ( 3 ).…”

“…In our meta-analysis, we identified five previous studies containing transcriptome data, and in the most recent study (18), the authors cross-validated their findings with three other published manuscripts (1,2,13). Thus, we opted to analyze the transcriptome data from these five previous studies and cross-validate them with TCGA data.…”

“…In dogs, some recent studies performing transcriptome analysis revealed several important molecular findings, such as different differentiation degrees of canine bladder cancer in molecular subtypes categorized according to the BRAFV595E somatic mutation ( BRAFV600E in humans) ( 18 , 19 ), the identification of therapeutic targets ( PTGER2, ERBB2, CCND1, VEGF , and EGFR ), and categories based on basal and luminal subtypes, as for human bladder cancers, enabling the comparison of muscular invasion potential between dogs and humans ( 1 ). Therefore, studies performing molecular comparisons between human and canine bladder carcinomas can provide a unique opportunity to study this cancer subtype in both species.…”

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“…with the datasets available online via the NCBI short-read archive (SRA) under BioProject ID PRJNA559406 (18), GEO database (ref: GSE24152) (1), and DDBJ Sequenced Read Archive repository (http://trace.ddbj.nig.ac.jp/dra/index_e. html) with accession number DRA005844.…”