Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from SP and non-SP sorted anti-EpCAM treated A2C12 cells

ABSTRACT: Targeted therapies against cancer stem cells which are enriched in side populations (SP) involves interruption of Wnt-signalling. Furthermore, EpCAM is a SP marker and modulator of Wnt-signalling. Therefore, the effects of an anti-EpCAM treatment on SP-cells and WNT/M-NM-2-catenin signalling was studied. SP of the murine lung adenocarcinoma cell line A2C12 was obtained by fluorescence activated cell sorting and whole genome scans helped to define their molecular phenotype after anti-EpCAM antibody treatment. Anti-EpCAM treated and untreated A2C12 cells were subjected to Hoechst 33342 dye exclusion assay and sorted to SP and non-SP fractions by FACS. Three biological replicates.

ORGANISM(S): Mus musculus

SUBMITTER: Thomas KrM-CM-<wel

PROVIDER: E-GEOD-31246 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Intratumoral heterogeneity is a major barrier against effective cancer therapy. Human malignant mesothelioma (HMM) that is closely associated with asbestos exposure is extremely heterogeneous in morphology and molecular phenotype. Contrast to genetic mutations, the role of epigenetic modifications in the generation and maintenance of heterogeneous populations in cancers remains largely undetermined. The present study was performed to investigate underlying molecular mechanisms for the emergence of intratumoral heterogeneity by identifying the global microRNA expression profile of distinct subpopulations of MS1 cell line, a HMM cell line. More aggressive cancer cells could be enriched by side population (SP) assay in HMM [20]. The sorted SP and NSP subpopulations were subjected to the microarray analysis of miRNA expression to investigate differentially altered miRNA genes defining tumor heterogeneity in HMM. Total RNAs were isolated from the sorted subpopulations of HMM cells, SP and non-SP fractions. The expression profile of miRNAs was evaluated using Affymetrix GeneChip miRNA Arrays. After data extraction and normalization, the microRNAs defining the cell subpopulations were determined using bioinformatics softwares. A total of 95 miRNAs including 42 up-regulated and 53 down-regulated were identified based on the criteria of 2 fold difference and a p-value < 0.05. Functional ontology of the dysregulated miRNAs revealed that a large number of target genes were categorized into the regulation of various cellular processes, including cell proliferation, programmed cell death, cell migration, cellular response to stress, and stem cell maintenance. The data show that microRNAs are significantly involved in the generation and maintenance of intratumoral heterogeneity and their regulation could be an effective strategy to eradicate a more aggressive cancer cell subpopulation. This is the first to report the profile of miRNA expression in CSCs in HMM by using side population assay assisted with flow cytometry. It will be valuable to understand the regulatory function of HMM CSC miRNAs in generation and maintenance of intratumoral heterogeneity. Total RNAs were isolated from the sorted subpopulations of HMM cells, SP and non-SP fractions. (no replicates)

Project description:The side population (SP), recently identified in several normal tissues and in a variety of tumors, may comprise cells endowed with stem cell features. In this study, we investigated the presence of SP in epithelial ovarian cancer (EOC) and found it in 4 out of 6 primary cultures from xenotransplants, as well as in 9 out of 25 clinical samples analyzed. SP cells from one xenograft bearing a large SP fraction were characterized in detail and they were capable of recreate the full repertoire of cancer cell populations observed in the parent tumor. Moreover, SP cells had higher proliferation rates, were much less apoptotic compared to non-SP cells, and generated tumors more rapidly than non-SP cells. We also investigated the effects of interferon-alfa (IFN-alpha), a cytokine which has been widely used to treat solid tumors, on EOC cells and observed that IFN-alpha exerts marked anti-proliferative and pro-apoptotic effects on primary cultures containing SP cells. IFN-alfa-treatment invariably caused a dramatic reduction in SP size in tumor cell lines of different origin and in normal bone-marrow SP cells, associated with a distinctive transcriptional profile. Gene therapy with human IFN-alpha resulted in regression of established tumors bearing a large SP fraction, which was not observed when tumors bearing low SP levels were treated. These findings could have relevant clinical implications since they imply that tumors bearing large SP numbers - albeit rare - could be sensitive to IFN-alpha treatment. Experiment Overall Design: 4 Affymetrix microarrays: Experiment Overall Design: 2 technical replicates: Ovarian cancer, untreated Side Population, rep1 Experiment Overall Design: Ovarian cancer, untreated Side Population, rep2 Experiment Overall Design: + Experiment Overall Design: 2 technical replicates: Ovarian cancer, IFN-alpha treated Side Population, rep1 Experiment Overall Design: Ovarian cancer, IFN-alpha treated Side Population, rep2

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Expression data from SP and non-SP sorted anti-EpCAM treated A2C12 cells

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