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RNAseq transcriptomic data of the human mammary cell line MCF10A expressing a shRNA against MME (CD10) or a control shRNA

ABSTRACT: RNAseq transcriptomic data of the human mammary cell line MCF10A expressing a shRNA against MME (CD10) or a control shRNA

PROVIDER: PRJNA775873 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16608905_1.fastq.gz	Fastqsanger.gz
	SRR16608905_2.fastq.gz	Fastqsanger.gz
	SRR16608906_1.fastq.gz	Fastqsanger.gz
	SRR16608906_2.fastq.gz	Fastqsanger.gz
	SRR16608907_1.fastq.gz	Fastqsanger.gz

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RNAseq transcriptomic data of the human mammary cell line MCF10A expressing a shRNA against MME (CD10) or a control shRNA

Project description:The immortalized but not transformed human mammary epithelial stem-like cell line MCF10A was stably transfected with a lentiviral vector expressin a shRNA targeting the MME transcript, coding for the CD10 membrane endopeptidase. This study aims to identify genes regulated by the CD10 modulation.

2023-09-01 | GSE186735 | GEO

Expression data from a model of human mammary stem cells at different stages of transformation, sorted or not on the basis of their CD10 expression

Project description:This study was designed to follow the transcriptome changes during BMP2 mediated transformation of the MCF10A human mammary stem cell model. We found that long-term BMP2/IL6 exposure of MCF10A cells, human immortalized but non-transformed mammary stem cells and progenitors, led to their luminal transformation. MC26 cells correspond to MCF10A cells transformed by BMP2/IL6 long-term exposure and contrarily to their parental cells, are able to engraft in immunodeficient mice and form colonies in soft-agar. M1B26 cells were obtained after BMP2/IL-6 long-term treatment of MCF10A cells sorted for high BMPR1B expression and subsequent isolation and expansion of 3 soft-agar colonies. M1B26 have an increased ability to engraft in mice and form colonies in soft-agar when compared to MC26 cells. As a non-transformed control, MCF10A-CT cells were kept in culture without BMP2/IL6 for the same length of time than MC26 cells. MCF10A-CT, MC26 and M1B26 cells are thus a model allowing to follow the molecular events associated with the initiation of a luminal transformation in mammary stem cells. Expression of the CD10 membrane endopeptidase has been associated with cancer although it can be a marker of both good or poor prognosis depending on the stage of the cancer and on the tissue of origin. In addition, we showed that CD10 was a marker of stem cell containing populations in healthy mammary tissue and that CD10 enzymatic activity was involved in the maintenance of cells immature properties. Having recently shown that CD10 expression was increasing during BMP2 mediated transformation and that CD10 expressing cells were more transformed but that CD10 was not required for transformation, we set out to determine the gene signature associated with CD10 expression.

2023-09-01 | GSE123053 | GEO

Control shRNA- vs. obscurin shRNA-expressing MCF10A cells

Project description:Obscurins (~70-870kDa), encoded by the single OBSCN gene, are cytoskeletal proteins originally identified in striated muscles with structural and regulatory roles. Recently, analysis of 13,023 genes in breast and colorectal cancers identified OBSCN as one of the most frequently mutated genes, implicating it in cancer formation. Herein, we studied the expression profile of obscurins in breast, colon and skin cancer cell lines, and their involvement in cell survival. Immunoblot analysis demonstrated significant reduction of obscurins in cancer cells, resulting from decreased mRNA levels and/or the presence of mutant transcripts. In normal epithelium, obscurins localize in cytoplasmic puncta, the cell membrane and the nucleus. Accordingly, subcellular fractionation demonstrated the presence of two novel nuclear isoforms of ~110 and ~120kDa. Non-tumorigenic MCF10A breast epithelial cells stably transduced with shRNAs targeting giant obscurins exhibited increased viability (~30%) and reduced apoptosis (~20%) following exposure to the DNA damaging agent, etoposide. cDNA microarrays followed by Gene Ontology profiling indicated a substantial number of transcripts related to apoptosis and survival are differentially regulated upon obscurin knock-down. Quantitative RT-PCR further indicated that the anti-apoptotic genes BAG-4 and HAX-1 were up-regulated (1.5 and 1.4 fold, respectively), whereas initiator caspase-9 and death caspase-3 transcripts were down-regulated (0.8 and 0.6 fold, respectively). Our findings are the first to pinpoint critical roles for obscurins in cancer development by contributing to the regulation of cell survival. Two-condition experiment: control shRNA- vs. obscurin shRNA-expressing MCF10A cells exposed to 150 uM etoposide. 3 independent replicates per condition.

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Expression of FRY-targeting shRNA in MCF10A cells

Project description:We identified the predicted FRY gene as a candidate mammary carcinoma susceptibility gene. This gene has not been characterized in mammals, so for part of our analysis we conducted microarray experiments to look at the changes in gene expression which occur when FRY-targeting shRNA is expressed in the nontumorigenic MCF10A mammary epithelial cell line (a cell line which we identified as having higher FRY mRNA expression than breast cancer cell lines). We used microarrays to identify the FRY interactome and identified that FRY affects the expression of gene networks that maintain normal cellular and tissue architecture, organization, differentiation of epithelial cells.

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Expression analysis of the effect of overexpression of Cebpb shRNA in mouse 4T1 mammary tumor cells

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Cbl family proteins are required to maintain the proteome homeostasis in mammary epithelial cells

Project description:EGFR degradation is delayed in Cbl, Cbl-b double-deficient MCF10A but EGF stimulation does not enhance their growth. We performed a transcriptome analysis to gain insights into biological consequences of Cbl, Cbl-b loss in mammary epithelial cells. We compared the transcriptome of MCF10A cells expressing shRNA against Cbl and Cbl-b with control shRNA-expressing cells using Affymetrix U133 Plus 2.0. Each sample was prepared in duplicates. Data were analyzed by GSEA.

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MCF10A cells expressing HER2 and HER3 and grown in three-dimensional cultures

Project description:The tyrosine kinase receptors HER2 and HER3 play an important role in breast cancer. The HER2/HER3 heterodimer is a critical oncogenic unit associated with reduced relapse-free and decreased overall survival. We provide gene expression profile of the mammary epithelial cells MCF10A expressing HER2, HER3 or HER2/HER3 and grown in three-dimensional cultures for 15 days in the presence of heregulin, a known HER3-ligand that stabilizes and activates the HER2/HER3 heterodimer. The mammary epithelial cells MCF10A were transduced with retroviral vectors expressing HER2, HER3 or both. Cells from each group were grown for 15 days in three-dimensional cultures. At the end of the experiment, RNA was extracted for gene expression analysis.

2012-09-01 | E-GEOD-37009 | biostudies-arrayexpress

RNA-seq of MCF10A cells stably expressing empty vector, GFP, miR-105, or MYC

Project description:To identify gene expression changes associated with overexpression of miR-105 or MYC in MCF10A non-cancerous human mammary epithelial cells, we analyzed RNA isolated from engineered MCF10A cell lines that stably express empty vector, GFP, miR-105, or MYC by RNA-seq. Gene expression in cells overexpressing miR-105 or MYC was compared to cells expressing the empty vector or GFP, both of which served as controls in this experiment.

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Expression analysis of the effect of overexpression of Cebpb shRNA in mouse 4T1 mammary tumor cells

Project description:Investigation of whole genome gene expression level changes in mouse 4T1 mammary tumors expressing Cebpb shRNA, compared to 4T1 tumors expressing control shRNA. Analysis of mouse 4T1 mammary tumors expressing Cebpb shRNA compared to control shRNA are further described in Johansson & Berg et al 2012. A 10 chip study using total RNA recovered from five separate 4T1 tumors expressing Cebpb shRNA and five separate 4T1 tumors expressing control shRNA. All tumors were surgically removed after subcutaneous implantation in syngeneic BALB/c mice two weeks earlier. Each chip measures the expression level of 44,170 genes from Mus Musculus with fourteen 24-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.

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MCF10A cells expressing HER2 and HER3 and grown in three-dimensional cultures

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