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RNAseq-based bladder cancer subtyping and IPA analysis with the xenografts from C57 BL/6J

ABSTRACT: To subtype the Triple gene knockout tumor we generated and assess the similiarities with widely used MB49 cells, TKO cells were injected into bladder wall orthtopically and bladder lumen by catheter intravesically in C57 BL/6J, while MB49 intravesical injection as a control. TKO intravesical tumors, TKO orthotopic tumors and MB49 intravesical tumors were collected and sent for RNA-seq analysis. In results, both intravesical TKO and orthotopic TKO tumors demonstrates transcriptome profiles that closely resembled human basal like muscle invasive bladder cancer using a luminal/basal/neuronal classifier. Principal Component Analysis (PCA) across samples demonstrated that MB49 cells had transcriptome profiles that differed significantly from TKO tumors. Hence, this study suggest that the TKO tumors closely resemble basal like human bladder cancer and MB49 exhibited no expression of urothelial markers.

ORGANISM(S): Mus musculus

PROVIDER: GSE200005 | GEO | 2022/06/01

REPOSITORIES: GEO

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Project description:Full title: Predictive Gene Signatures as Strong Prognostic Indicators of the Effectiveness of Bacillus Calmetteâ??GuÃ©rin (BCG) Immunotherapy in Primary pT1 Bladder Cancers Intravesical BCG immunotherapy is effective in prevention of recurrence and progression in many cases of non-muscle invasive bladder cancer, but many patients fail to respond. This study identified predictive gene signatures in primary pT1 bladder cancer with BCG immunotherapy. Fourty-Eight patients with primary pT1 bladder cancer treated with BCG immunotherapy were used. Microarray gene expression analysis of the 48 primary bladder cancers was carried out. Predictive gene signatures were individually selected based on the recurrence and progression status. Among 43,148 unique genes, 424 and 287 candidate predictive genes that could predict recurrence and progression, respectively, were selected. Time to recurrence or progression was shorter for patients with poor-predictive gene signatures than good-predictive gene signatures (log-rank test, p <0.001, respectively). Validation of predictive gene signatures with RT-PCR was nearly identical to those of microarray (log-rank test, p <0.05, respectively). In multivariate regression analysis, predictive gene signatures were the only independent predictors of recurrence (HR 3.38, p = 0.048) or progression (HR 10.49, p = 0.048) in validation cohorts. Predictive gene signatures have strong diagnostic value for determining the response to intravesical BCG immunotherapy in primary pT1 bladder cancer. Keywords: Gene expression, Bladder cancer, BCG Total RNA, extracted from the fresh frozen tissues of 48 pT1 bladder cancers, was isolated by TRIzol reagent (Life Technologies, NY, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Five-hundred nanograms of total RNA were used for labeling hybridization according to the manufacturerâ??s protocol (Illumina HumanWG-6 BeadChip, version 2, Illumina, Inc., San Diego, CA, USA). Arrays were scanned with an Illumina Bead Array Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc.) according to the manufacturer's instructions. Initial microarray gene expression data were obtained using Bead Studio software with gene expression analysis module (version 3.1.3, Illumina, Inc.).

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RNAseq-based bladder cancer subtyping and IPA analysis with the xenografts from C57 BL/6J

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