RNA-seq of human normal mammary gland cells FACS sorted into three populations: ALDH+, ALDH-CD44+CD24-, and ALDH-CD44-CD24+
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB19994 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1883110_1.fastq.gz | Fastqsanger.gz | |||
| ERR1883110_2.fastq.gz | Fastqsanger.gz | |||
| ERR1883111_1.fastq.gz | Fastqsanger.gz | |||
| ERR1883111_2.fastq.gz | Fastqsanger.gz | |||
| ERR1883112_1.fastq.gz | Fastqsanger.gz |
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Project description:The intent of this experiment was to determine the similarities and differences in expression signatures of normal breast cells that express markers associated with an epithelial-like (ALDH+) and mesenchymal-like (CD44+CD24-) stem cells in the normal human breast. Briefly, tissues were collected from women undergoing voluntary reduction mammoplasty. Tissues were dissociated using chemical and enzymatic methods to yield single cells. These cells were sorted by flow cytometry for aldehyde hydrogenase activity (ALDH+), CD44, and CD24, as well as viability, following depletion of hematopoeitc cells, endothelial cells, and fibroblasts.
2018-01-17 | E-MTAB-5585 | biostudies-arrayexpress
Project description:It has been suggested that breast cancers are driven and maintained by a cellular subpopulation with stem cell properties. These breast cancer stem cells (BCSCs) mediate metastasis and by virtue of their resistance to radiation and chemotherapy, contribute to relapse. Although several BCSC markers have been described, it is unclear whether these markers identify the same or independent BCSC populations. Based on established breast cancer cell lines, as well as primary tumor xenografts, we show that BCSCs exist in distinct mesenchymal-like (epithelial-mesenchymal transition, EMT) and epithelial-like (mesenchymal-epithelial transition, MET) states characterized by expression of distinct markers, proliferative capacity and invasive characteristics. The gene expression profiles of mesenchymal-like and epithelial-like BCSCs are remarkably similar across the different molecular subtypes of breast cancer and resemble those of distinct basal and luminal stem cells found in the normal breast. We propose that the plasticity of BCSCs allowing them to transition between EMT- and MET-like states endows these cells with the capacity for tissue invasion, dissemination and growth at metastatic sites. Breast cancer cell lines, primary xenografts and normal breast cells from patient were sorted using flow cytometry to select for cells that were CD24-,CD44+ and ALDH+. Gene expression profiles of CD24-CD44+ cells were compared with non-CD24-CD44+ cells. Gene expression profiles of ALDH+ cells were compared with ALDH- cells.
2013-11-13 | E-GEOD-52262 | biostudies-arrayexpress
Project description:Tumorigenic breast cancer cells characterized by CD44 expression and low or undetectable CD24 levels (CD44+/CD24-/low) may be resistant to chemotherapy and therefore responsible for cancer relapse. Paired breast cancer core biopsies before and after neoadjuvant chemotherapy or lapatinib were obtained and as single cell suspensions stained using antibodies against CD24, CD44, and lineage markers, and then analyzed by flow cytometry. Mammosphere (MS) formation in culture was compared before and after treatment. Global gene expression differences between cancer cells bearing CD44+/CD24-/low cells and all other sorted cells, and between cancer MS and the primary bulk invasive cancers were analyzed. We report that CD44+/CD24-/low tumorigenic breast cancer cells were intrinsically chemoresistant ─ chemotherapy led to increased CD44+/CD24-/low cells, increased self-renewal capacity on MS assays, and enhanced tumorigeneicity in immunocompromised SCID/Beige mice. Conversely, in patients with HER2 overexpressing tumors, the EGFR/HER2 tyrosine kinase inhibitor, lapatinib decreased CD44+/CD24-/low cells, with the majority of these patients after conventional therapy achieving pathologic complete response, a validated surrogate marker for long-term survival. Gene transcription pathways that underlie chemoresistant, MS-forming CD44+/CD24-/low cells involve genes belonging to stem cell self-renewal, Wnt signaling, and early development pathways. Keywords: two group comparison
2009-08-15 | GSE7513 | GEO
Project description:Tumorigenic breast cancer cells characterized by CD44 expression and low or undetectable CD24 levels (CD44+/CD24-/low) may be resistant to chemotherapy and therefore responsible for cancer relapse. Paired breast cancer core biopsies before and after neoadjuvant chemotherapy or lapatinib were obtained and as single cell suspensions stained using antibodies against CD24, CD44, and lineage markers, and then analyzed by flow cytometry. Mammosphere (MS) formation in culture was compared before and after treatment. Global gene expression differences between cancer cells bearing CD44+/CD24-/low cells and all other sorted cells, and between cancer MS and the primary bulk invasive cancers were analyzed. We report that CD44+/CD24-/low tumorigenic breast cancer cells were intrinsically chemoresistant â chemotherapy led to increased CD44+/CD24-/low cells, increased self-renewal capacity on MS assays, and enhanced tumorigeneicity in immunocompromised SCID/Beige mice. Conversely, in patients with HER2 overexpressing tumors, the EGFR/HER2 tyrosine kinase inhibitor, lapatinib decreased CD44+/CD24-/low cells, with the majority of these patients after conventional therapy achieving pathologic complete response, a validated surrogate marker for long-term survival. Gene transcription pathways that underlie chemoresistant, MS-forming CD44+/CD24-/low cells involve genes belonging to stem cell self-renewal, Wnt signaling, and early development pathways. Experiment Overall Design: Human breast tumor samples were sorted using flow cytometry to select for cells that were CD44+ and CD24-. Gene expression profiles of these cells were compared with profiles of the other sorted cells (CD24+ and CD44-/CD24-). Experiment Overall Design: Core biopsies of primary breast tumors were taken and placed immediately in cold RPMI-1640 supplemented with 10% heat-inactivated newborn calf serum (HINCS, Invitrogen, Carlsbad, CA). Within an hour, the samples were minced and then digested in 10-15 mL of MEGM with 250-300 units/mL collagenase at 370C. The samples were filtered, washed, and then subjected to hypotonic shock to lyse red blood cells. About 106 single cells were re-suspended, incubated for 15 min at 40C with anti-CD44 (APC), anti-CD24 (FITC), and anti-lineage cocktail antibodies (PE-conjugated anti-CD2, CD3, CD10, CD16, CD18, CD31 and CD 140B) (Pharmingen, San Diego, CA) using the manufacturerâs suggested concentrations. The cells were then washed twice, re-suspended with the viability dye propidium iodide, and analyzed using Dako MoFlo flow cytometry. Side- and forward- scatter were used to eliminate debris and cell doublets, and the Lin- cells were further analyzed by CD44 and CD24 markers.
2009-08-22 | E-GEOD-7513 | biostudies-arrayexpress
Project description:CD44+/CD24- subpopulation of normal and cancerous breast epithelial cells are suggested to have stem cell properties. The goal of this study was to identify gene expression differences between CD44+/CD24- and CD44-/CD24+ subpopulation of cells from a same cell lines. We selected MCF-10A cells, which are immortalized derived from a fibrocystic breast disease. These cells are immortalized but not transformed and express basal cell markers. Cells were from a single sort but plated into four 100 mm plates. RNA was prepared from each plate separately for the analysis. Comparison of gene expression between 2 groups ( CD44+/CD24- and CD44-/CD24+) 4 replicates each.
2010-03-07 | E-GEOD-15192 | biostudies-arrayexpress
Project description:To understand the role of p53 in regulating stem cell population (CD24-CD44+) and stemness-associated miRNAs, we first compared miRNA expression profiles between human mammary epithelical cells knocked-down p53 and control cells. We then cross-referenced p53-regulated miRNAs with stemness-associated miRNAs analyzed from expression profiling of sorted CD24-CD44+ and non-CD24-CD44+ cell populations. Further biological experiments were performed with the miRNAs that are altered in CD24-CD44+ stem cell populations and also regulated by p53. Total RNAs, including miRNAs, extracted from CD24-CD44+ cells (labeled in Hy3) and non-CD24-CD44+ cells (labeled in Hy5) were hybridized on Exiqon miRCURY LNA arrays according to the manufacturer's protocol.
2011-02-01 | E-GEOD-25036 | biostudies-arrayexpress
Project description:To understand the role of p53 in regulating stem cell population (CD24-CD44+) and stemness-associated miRNAs, we first compared miRNA expression profiles between human mammary epithelical cells knocked-down p53 and control cells. We then cross-referenced p53-regulated miRNAs with stemness-associated miRNAs analyzed from expression profiling of sorted CD24-CD44+ and non-CD24-CD44+ cell populations. Further biological experiments were performed with the miRNAs that are altered in CD24-CD44+ stem cell populations and also regulated by p53.
2011-02-01 | GSE25036 | GEO
Project description:CD44+/CD24- subpopulation of normal and cancerous breast epithelial cells are suggested to have stem cell properties. The goal of this study was to identify gene expression differences between CD44+/CD24- and CD44-/CD24+ subpopulation of cells from a same cell lines. We selected MCF-10A cells, which are immortalized derived from a fibrocystic breast disease. These cells are immortalized but not transformed and express basal cell markers. Cells were from a single sort but plated into four 100 mm plates. RNA was prepared from each plate separately for the analysis.
2010-03-01 | GSE15192 | GEO
Project description:All the regulated lncRNAs in breast cancer stem cells (BCSCs, CD44+CD24- sorted)MCF-7 cells compared to non-BCSCs (non-CD44+CD24- sorted) MCF-7 cells
| PRJNA517151 | ENA
Project description:TSV40ER and hTERT immortalized mammospheres undergo transformation in culture to generate breast cancer stem cells The stem cell hypothesis of cancer predicts that cancers arise from the transformation of normal stem/progenitor cells present within adult tissues. However, the molecular mechanisms that lead to the transformation of these cells remain largely unknown, mainly owing to the lack of suitable model systems. In this study, we have generated an immortalized breast epithelial cell line, NBLE, by over-expressing the SV40 Early Region and the catalytic domain of human telomerase into mammosphere-derived cells that are enriched in breast stem/progenitor cells. While primary mammospheres fail to grow beyond four passages in suspension culture, NBLE cells propagated continuously generating spheres at a high frequency of 35%. These cells also expressed stemness-related genes, and differentiated into both luminal and myoepithelial lineages. Interestingly, after around 135 population doublings in culture, the late passage cells exhibited a mesenchymal morphology and contained >90% of CD44+/CD24Low/- cells resembling breast cancer stem cells. When injected subcutaneously into nude mice, the late passage NBLEs formed invasive tumors closely resembling breast adenocarcinomas, the most common type of breast cancer. The transformed NBLE cells showed hyperactivation of Wnt, Hh and TGFbeta pathways, suggesting that the deregulation of these self-renewal pathways may have in part contributed to tumorigenesis. Gene expression analysis further revealed a high degree of similarity with breast cancer stem cells. Thus, our study provides a unique model system to study signaling pathways involved in self-renewal, differentiation, and transformation of breast stem/progenitor cells. Additionally, the NBLE cells can be utilized for screening drugs specifically targeting breast cancer stem cells. NBLE cells were generated by over-expressing SV40ER and hTERT into mammosphere-derived cells. These cells harnored CD44+/CD24- fraction that resembled breast cancer stem cells. To understand the unique gene expression of this fraction we performed microarray on CD44+/CD24- versus rest fractions from NBLE cells (Rep 1 and Rep 2). To see if this gene profile has any similarity with breast cancer stem cells, we performed CD44+/CD24- versus rest microarray on two primary breast tumors (CB272 and CB258-Rep1 andRep2).
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