RNA-seq of adherent MDA-MB-231 cells, and their 16hour and 5day mammospheres and siRNA treatment
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE136190 | GEO | 2021/02/23
REPOSITORIES: GEO
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Project description:In the past few years, mammary cancer initiating cells (CICs) have been identified in mouse and human as a subpopulation of tumor cells that selectively posses tumor initiation and self-renewal capacity and the ability to give rise to bulk populations of non-tumorigenic cancer cells progeny through differentiation. They could also be responsible for tumor progression, metastasis, resistance to therapy and recurrence. Thus, the understanding of the pathways regulating CIC self-renewal, differentiation and tumorigenicity represents an important task in the development of effective anticancer therapies. To detect the set of genes associated to CIC in our mouse breast cancer model we analysed three prototypic situations: TUBO cells grown in DMEM under adherent conditions (called TDA in GSE26517 and epithelial bulk in GSE21451), TUBO cells grown in mammosphere medium under adherent conditions (called TMA in GSE26517), TUBO cells grown in mammosphere medium under low-attachment conditions (called mammospheres p1 in GSE21451), i.e. the conditions used to support the formation of mammospheres. This analysis led to the identification of growth factors and immune system-related genes, including toll-like receptor 2 (TLR2). The inhibition of TLR2 signaling pathway strongly impaired mammosphere generation, demonstrating the involvement of TLR2 in CSC self-renewal. We profiled on MouseWG?6 v2.0 Illumina beadchips two independent experiments: ADHERENT (GSE26517) made by the comparison between TDA and TMA and SOSPENSION (part of GSE21451) made by the comparison between epithelial bulk and mammospheres p1. Mammosphere medium contains epidermal growth factor (EGF), insulin and basic fibroblast growth factor (bFGF) that may influence transcript expression in a way not necessarily related to the assembly of mammospheres. Therefore, following normalization and removal of those transcripts not expressed and not changing, we used the Integrative Correlation coefficient (IC, Parmigiani et al. Clin Cancer Res 2004, 10:2922–2927) as filter to remove genes only associate to growth factors present in the mammosphere medium under adherent growth conditions, i.e IC > 0.1. Differential gene expression was then assessed by regularized t?test (Smyth GK. Stat Appl Genet Mol Biol 2004, 3:Article3) comparing mammospheres p1 with respect to epithelial bulk, using an uncorrected p-value ? 0.05, together with an absolute log2 fold change threshold ?1.
2013-11-30 | E-GEOD-26527 | 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. Experiment Overall Design: Cells from human breast tumors were grown as mammospheres (MS). Experiment Overall Design: Isolated single cell suspensions from primary breast cancers were plated onto non-adherent (polyhema-coated) plastic, counted with a hematocytometer, and 20,000 cells were then seeded into a 6-well ultra-low attachment plate supplemented with 2mL MEGM, with the addition of 2 mL of freshly unfrozen MEGM every 3-4 days. Gene expression profiles were taken of both MS and primary bulk tumors and compared with each other.
2009-08-22 | E-GEOD-7515 | biostudies-arrayexpress
Project description:In the past few years, mammary cancer initiating cells (CICs) have been identified in mouse and human as a subpopulation of tumor cells that selectively posses tumor initiation and self-renewal capacity and the ability to give rise to bulk populations of non-tumorigenic cancer cells progeny through differentiation. They could also be responsible for tumor progression, metastasis, resistance to therapy and recurrence. Thus, the understanding of the pathways regulating CIC self-renewal, differentiation and tumorigenicity represents an important task in the development of effective anticancer therapies. To detect the set of genes associated to CIC in our mouse breast cancer model we analysed three prototypic situations: TUBO cells grown in DMEM under adherent conditions (called TDA in GSE26517 and epithelial bulk in GSE21451), TUBO cells grown in mammosphere medium under adherent conditions (called TMA in GSE26517), TUBO cells grown in mammosphere medium under low-attachment conditions (called mammospheres p1 in GSE21451), i.e. the conditions used to support the formation of mammospheres. This analysis led to the identification of growth factors and immune system-related genes, including toll-like receptor 2 (TLR2). The inhibition of TLR2 signaling pathway strongly impaired mammosphere generation, demonstrating the involvement of TLR2 in CSC self-renewal.
2013-11-30 | GSE26527 | GEO
Project description:Tumorpsheres and mammospheres were used to propagate mouse breast tumor-initiating cells and their normal stem/progenitor counterparts, respectively. Mammospheres induced to differentiate were used to model the more differentiated cells of the mouse mammary gland. We used microarrays to find differentrially expressed genes between tumorspheres, mammospheres, and mammospheres induced to differentiate
2012-01-30 | GSE32463 | GEO
Project description:Cancer stem cells (CSCs) comprise a small subpopulation of undifferentiated cancer cells with the ability to self-renew and give rise to the heterogeneous cancer cell lineages that form tumorous masses. Thus, tumor eradication may be greatly improved by specifically targeting CSCs, as they exhibit resistance to conventional therapy. To gain insight into the unique biology of CSCs, we developed patient-derived xenograft (PDX) tumors from ER-negative breast cancer patient tissue from which we isolated mammospheres, a method known to enrich for cells with CSC-properties. An unbiased, comparative global proteomic analysis using label-free mass spectrometry was performed on the patient tumor tissues and corresponding PDX tumors and mammospheres. Good concordance between the proteome profiles of patient tumor tissue and corresponding PDX tumors was observed. However, lower abundance of immune- and extracellular matrix-related proteins and higher abundance of proteins associated with cell-to-cell adhesion including desmosome proteins and β-catenin were observed in PDX versus patient tumors. Interestingly, analysis of proteins elevated in mammospheres vs. PDX tumors identified an enrichment of proteins associated with de novo cholesterol synthesis. The clinical relevance of increased cholesterol biosynthesis protein expression was verified in a large gene expression data set of clinical breast cancers showing correlation with shorter relapse-free survival. RNA interference and chemical inhibition of the cholesterol biosynthesis pathway reduced mammosphere formation and growth of CSCs derived from PDX tumors and cancer cell lines. Our findings identify the cholesterol biosynthesis pathway as central for CSC growth and a potential therapeutic target for CSC as well as providing an additional mechanistic explanation for the observed benefit of statins in breast cancer treatment.
2019-07-02 | PXD011222 | Pride
Project description:Tumorpsheres and mammospheres were used to propagate mouse breast tumor-initiating cells and their normal stem/progenitor counterparts, respectively. Mammospheres induced to differentiate were used to model the more differentiated cells of the mouse mammary gland. We used microarrays to find differentrially expressed genes between tumorspheres, mammospheres, and mammospheres induced to differentiate Primary cells were isolate from either mouse mammary glands (FVB/N) or mouse mammary tumors and placed in stem cell media (MMTV-Neu [N2O2]. Spheres were passaged every 7 days for 3-5 passages and harvested for RNA isolation
2012-01-30 | E-GEOD-32463 | biostudies-arrayexpress
Project description:Purpose: The goals of this study is to compare and examine the transcriptional profile in the secondary mammospheres of control versus CIC-deficient T47D cells by mRNA sequencing and to understand the molecular basis of the CIC regulation of CSC-like properties in luminal type of breast cancer cells. Methods: DNA library for mRNA sequencing of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells was prepared using a TruSeq Stranded Total RNA LT Sample Prep Kit (Gold) and their libraries sequenced on the NovaSeq sequencer accompanying the NovaSeq 6000 S4 Reagent Kit. The trimmed reads that passed quality filters were mapped to reference genome with HISAT2, followed by assembly of transcript with StringTie. Results: A total of 20377 genes were differentially expressed (10438 upregulated and 9939 downregulated) in the CIC-deficient T47D mammospheres when compared with control mammospheres. Approximately 5% of the transcripts showed differential expression between the control and CIC-deficient secondary mammospheres, with a fold change ≥1.2 and p value <0.05. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analyses revealed that CIC-deficient mammospheres differentially expressed genes that are involved in processes associated with cancer progression such as cell cycle, cell proliferation, cell growth, and apoptotic process, as well as autoimmunity. Conclusions: Our results show the first comparative analysis of secondary mammospheres derived from control and CIC-deficient T47D breast cancer cells. The data reported here should also provide reference for expression profiles of CSC-like cells in ER+/PR+/HER2- luminal breast cancer cells. We conclude that CIC deficiency promotes CSC-like properties and thus breast cancer progression through controlling CSC-related pathways including focal adhesion and extracellular matrix (ECM)-receptor interactions, and may also regulate cell cycle, cell proliferation, and apoptosis.
2019-12-18 | GSE142171 | GEO
Project description:Despite anti-estrogen therapy, almost 30% of estrogen receptor positive (ER+) breast cancer patients relapse. Amino acids (AAs) in the tumor microenvironment may affect the metastatic capacity of breast cancer cells. Essential AAs (EAAs) cannot be produced by human cells and might therefore be targetable as therapeutics. By using liquid chromatography-mass spectrometry we identified the ribophorin-2 (RPN2) and the splicing factor U2AF 35 kDa subunit (U2AF1) as the most significantly affected proteins after lysine and estradiol (E2) exposure in T47D and MCF-7 mammospheres, respectively. RPN2 and U2AF1 were identified as prognostic factors for patient survival in breast cancer databases.
2020-11-25 | PXD022008 | Pride
Project description:Mammosphere medium (Grange et al. Neoplasia 2008;10(12):1433-43) contains epidermal growth factor (EGF), insulin and basic fibroblast growth factor (bFGF) that may influence transcript expression in a way not necessarily related to the assembly of mammspheres. To identify the set of genes associated mammosphere cell growth medium we analyzed two prototypic situations in triplicate experiments: TUBO cells (a mouse breast cancer cell line derived by Balb-neuT mice) grown in DMEM under adherent conditions (TDA), TUBO cells grown in Mammosphere medium under adherent conditions (TMA). Two prototypic situations in triplicate experiments were analysed: TUBO cells (Rovero et al. Gene Ther 2001;8(6):447-52) grown in DMEM under adherent conditions (TDA), TUBO cells grown in Mammosphere medium under adherent conditions (TMA).
2013-11-30 | E-GEOD-26517 | biostudies-arrayexpress
Project description:Mammosphere medium (Grange et al. Neoplasia 2008;10(12):1433-43) contains epidermal growth factor (EGF), insulin and basic fibroblast growth factor (bFGF) that may influence transcript expression in a way not necessarily related to the assembly of mammspheres. To identify the set of genes associated mammosphere cell growth medium we analyzed two prototypic situations in triplicate experiments: TUBO cells (a mouse breast cancer cell line derived by Balb-neuT mice) grown in DMEM under adherent conditions (TDA), TUBO cells grown in Mammosphere medium under adherent conditions (TMA).
2013-11-30 | GSE26517 | GEO