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

Heidi G Parker,Brian W Davis,Deborah W Knapp,Deepika Dhawan,Alex C Harris,Jose A Ramos-Vara,Elaine A Ostrander

doi:10.1186/s12885-020-06737-0

Abstract

BackgroundInvasive 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.MethodsWe 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.ResultsWe 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.ConclusionsThese 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.

Highlights

Invasive urothelial carcinoma is highly similar between dogs and humans in terms of pathologic presentation, molecular subtypes, response to treatment and age at onset
Sequencing coverage and QC The complete transcriptomes of seven histologically confirmed canine InvTCC tumors carrying the BRAFV595E mutation (BRAFV595E), four tumors lacking the mutation (BRAFwt), and three matched normal tissues were sequenced to an average of 45.9 million reads per sample
principal component analysis (PCA) and multidimensional scaling (MDS) clustering of both expression datasets separated normal versus tumor samples along the first dimension and tumors carrying the BRAFV595E mutation from the BRAFwt tumors along the second dimension (Fig. 1a)

Summary

Introduction

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. Urothelial carcinoma is the second most common cancer of the urinary tract in humans following prostate cancer [1]. The invasive form of urothelial carcinoma (iUC), which comprises 25–30% of human bladder cancer cases, is the most common urinary bladder tumor of dogs. It accounts for ≥90% of canine bladder tumors, with ≥50,000 dogs predicted to develop the disease yearly in the U.S alone [3, 4]. Distant metastases are present in about 15–20% of dogs at diagnosis, and in ≥50% of dogs at death, with liver, lung, and bone being frequent sites of metastases [3,4,5,6]

Methods

Results

Discussion

Conclusion