Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

80 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative gene expression analyses identify luminal and basal subtypes of canine invasive urothelial carcinoma that mimic patterns in human invasive bladder cancer

ABSTRACT: Microarrays were used to assay the gene expression profile of canine normal bladder from non-tumor bearing dogs and compared to that of bladder tumor in dogs. Work was conducted to compare gene expression array results between tissue samples from iUC and normal bladder in dogs. Affymetrix canine 2.0 chips were used to conduct the experiment.

ORGANISM(S): Canis lupus familiaris

SUBMITTER: Deborah Knapp

PROVIDER: E-GEOD-66064 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Comparative gene expression analyses identify luminal and basal subtypes of canine invasive urothelial carcinoma that mimic patterns in human invasive bladder cancer

Project description:Microarrays were used to assay the gene expression profile of canine normal bladder from non-tumor bearing dogs and compared to that of bladder tumor in dogs.

2015-08-25 | GSE66064 | GEO

RNA-seq data from naturally-occurring early canine urothelial carcinoma detected through screening of dogs in a high-risk breed (Scottish Terriers)

Project description:Screening for urinary bladder cancer was performed in dogs in a breed (Scottish Terriers) with a very high inherited risk for bladder cancer. Naturally-occurring urothelial carcinoma in dogs serves as a relevant model for muscle invasive bladder cancer in humans. Urothelial carcinoma was detected in dogs with no outward evidence of the cancer. RNAseq data analyses were performed on these "early" tumors, and the sequencing files are included here. RNA-seq data from additional dogs has been deposited in the NCI Integrated Canine Data Commons (ICDC UBC02).

2025-03-23 | GSE199292 | GEO

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

Project description:RNA-seq was used to identify basal and luminal subtypes in canine bladder cancer. In addition to larger gene-sets, a smaller panel of genes was developed to stratify canine samples into either basal or luminal subtype prospectively. Immune signature patterns were queried in basal and luminal subtypes.

2018-08-01 | GSE110661 | GEO

miR-182, miR-221 and miR-222 are potential urinary extracellular vesicle biomarkers for canine urothelial carcinoma

Project description:Urothelial carcinoma (UC) is the most common tumour type in canine bladder cancer. Current diagnostic methods are technically challenging or can lack specificity, hence there is a need for novel biomarkers of UC. To this end, we analysed the microRNA (miRNA) cargo of extracellular vesicles (EVs) from urine samples of dogs with UC to identify miRNAs that could be utilised as biomarkers. Urine was fractionated using ultrafiltration combined with size-exclusion chromatography and small RNA sequencing analysis was performed on both the EV enriched and (EV free) protein fractions. A greater number of candidate miRNA biomarkers were detected in the EV fraction than the protein fraction, and further validation using droplet digital PCR (ddPCR) was performed on the EV enriched fraction of a second cohort of dogs with bladder cancer which validated three miRNAs as candidate biomarkers; miR-182, miR-221 and miR-222 as being significantly overrepresented in dogs with UC when compared with healthy dogs and dogs with urinary tract infections. Pathway analysis confirmed that these three miRNAs are involved in cancer. In addition, their potential downstream gene targets were predicted and PIK3R1, a well-known oncogene is likely to be a shared target between miRNA-182 and miRNA-221/222. In summary, this study highlights the potential of urinary EV-associated miRNAs as a source of biomarkers for the diagnosis of canine UC.

2024-08-08 | GSE256461 | GEO

Association analysis of invasive urinary carcinoma in the Shetland sheepdogs and related breeds.

Project description:Naturally occurring canine invasive urinary carcinoma (iUC) closely resembles human muscle invasive bladder cancer in terms of histopathology, metastases, response to therapy and, low survival rate. The heterogeneous nature of the disease has led to the association of large numbers of risk loci in humans, however most are of small effect. There exists a need for new and accurate animal models of invasive bladder cancer. In dogs, distinct breeds show markedly different rates of iUC, thus presenting an opportunity to identify additional risk factors and overcome the locus heterogeneity encountered in human mapping studies. In the association study presented here, inclusive of 100 Shetland sheepdogs and 58 dogs of other breeds, we identify a homozygous protein altering point mutation within the NIPAL1 gene which increases risk by eight-fold (OR=8.42, CI=3.12-22.71), accounting for nearly 30% of iUC risk in the Shetland sheepdog. Inclusion of six additional loci accounts for the majority of disease risk in the breed and explains nearly 75% of the phenotypes in this study. When combined with sequence data from tumors, we show that variation in the MAPK signaling pathway is an overarching cause of iUC susceptibility in dogs.

2023-08-28 | GSE241367 | GEO

Genome-wide analyses reveals an association between invasive urothelial carcinoma in the Shetland sheepdog, NIPAL1, and the MAPK signaling pathway

Project description:Naturally occurring canine invasive urinary carcinoma (iUC) closely mimics human high grade iUC in terms of age of onset, pathology, cellular and molecular features, metastatic profiles, and treatment response . Shetland sheepdogs (Shelties), the focus of this study, are a small herding breed and popular family pet. Multiple studies demonstrate their extraordinary disease risk, with one survey reporting that of 3359 Shelties, iUC comprised 12% of all Sheltie cancer diagnoses, which is six times the expected rate of 2% for all dogs. In this study we analyze one hundred Shelties and 55 dogs from closely related breeds and identify a single major risk locus associated with iUC, featuring NIPA-like domain containing 1 (NIPAL1), a strong candidate gene, and associated mutations. By segregating samples according to genotype, we identify six additional loci that modify individual disease risk when combined with a putative pathogenic protein altering mutation in NIPAL1. Merging the GWAS loci with tumor sequence identifies the mitogen activated protein kinase (MAPK) signaling pathway as a key component of canine iUC genetic susceptibility.

2024-01-31 | GSE254079 | GEO

Global gene expression of canine bladder K9TCC cells and cancer stem cells after COX-2 inhibition

Project description:Cancer stem cells (CSCs) are fundamental to bladder cancer progression and the cyclooxygenase-2 (COX-2) pathway has a pro-tumorigenic role in CSC function. Naturally occurring bladder cancer in dogs has the potential to be a natural model of the human disease. Here, we used canine specific microarrays to determine changes in global gene expression of canine bladder cancer cells (the K9TCC cell line) and bladder cancer stem cells isolated from the K9TCC cell line after treatment with the selective COX-2 inhibitor mavacoxib or a COX-2 siRNA.

2022-07-20 | GSE183793 | GEO

Expression profile of non-muscle invasive (superficial) bladder carcinoma

Project description:Gene expression profiling of 82 human non-muscle invasive bladder carcinoma and 4 normal bladder samples, for a total of 86 tissues. A Cartes d‚àö‚â†Identite des Tumeurs (CIT) study from the 'Institut Curie' and the french 'Ligue Nationale Contre le Cancer' (http://cit.ligue-cancer.net/).

2015-01-01 | E-MTAB-1940 | biostudies-arrayexpress

Genome-wide screening and identification of long noncoding RNAs and their interaction with protein coding RNAs in bladder urothelial cell carcinoma

Project description:To understand the role of long non-coding RNAs and interaction with coding RNAs in bladder urothelial cell carcinoma (BUCC), we performed genome-wide screening long non-coding RNAs and coding RNAs expression on primary BUCC tissues and normal tissues using long non-coding RNA array (Agilent plateform (GPL13825). By comparing these two groups, significantly differentially expressed lncRNAs and coding RNAs were identified. We further identifed a subset of long noncoding RNAs and their correlation with neighboring coding genes using bioinformatic tools. This analysis provides foundamental understaning of transcriptomic landscape changing during bladder carcinogenesis. 12 BUCC primary tumors and 3 normal tissues were used for long noncoding RNA array experiments which including long non-coding RNAs and coding RNAs. The differential expression of subset of long noncoding RNAs and their interaction with coding RNAs in BUCC compared with normal tissue will be identified with comtational analysis.

2013-12-31 | E-GEOD-51493 | biostudies-arrayexpress

Genomic complexity of urothelial bladder cancer revealed in urinary cfDNA

Project description:Comparison of the genomic profiles of urinary cellular DNA and cell-free DNA (cfDNA) from the urine to matched diagnostic formalin-fixed paraffin embedded (FFPE) tumour DNAs for 23 well-characterised UBC patients.

2015-12-31 | E-MTAB-3841 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data