MEMA MCF10A Staining Set 3
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ABSTRACT:
PROVIDER: LDS-1447 | LINCS | 2016-11-10
REPOSITORIES: LINCS
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Project description:Basal-like carcinoma is a subtype of breast cancer that is characterized by poor prognosis and high intratumor heterogeneity. Using a basal-like breast epithelial line, we have identified two anti-correlated gene-expression programs that arise among single extracellular matrix (ECM)-attached cells during organotypic 3D culture. The first program contains TGFBR3, a high-affinity receptor for transforming growth factor β (TGFβ) and other related ligands. The second program contains the JUND transcription factor together with the basal-like marker, KRT5. By disrupting the TGFBR3 and JUND programs individually, we reveal an important circuit for 3D morphogenesis that is wired together by four negative-feedback loops. Computational modeling of this circuit showed that it could exhibit damped, antiphase oscillations when excited with small impulses of TGFβ-like ligand. We directly visualize the circuit's spontaneous dynamics in organotypic cultures by using live-cell imaging with engineered pathway reporters. Importantly, we show that the essence of the JUND-TGFBR3 expression circuit holds true in early basal-like tumors that heterogeneously express KRT5. Correlated JUND-KRT5 expression depends critically on contact with stromal ECM and local expression of tenascin C. This work illustrates how complex tumor heterogeneities can be deconstructed into intrinsic single-cell expression circuits that are modulated by the microenvironment. Gene expression analysis of outer ECM-attached vs. inner cells of MCF10A-5E clones grown in organotypic 3D culture at day 6. Total RNA was isolated from ~50 outer ECM-attached cells and ~50 inner cells, each separately microdissected from 8 micron sections of MCF10A structures at day 6 of morphogenesis. Total RNA was amplified in quadruplicate, and hybridized to HumanRef-8 v2.0 Expression BeadChips (Illumina).
2015-06-05 | E-GEOD-41527 | biostudies-arrayexpress
Project description:Basal-like carcinoma is a subtype of breast cancer that is characterized by poor prognosis and high intratumor heterogeneity. Using a basal-like breast epithelial line, we have identified two anti-correlated gene-expression programs that arise among single extracellular matrix (ECM)-attached cells during organotypic 3D culture. The first program contains TGFBR3, a high-affinity receptor for transforming growth factor β (TGFβ) and other related ligands. The second program contains the JUND transcription factor together with the basal-like marker, KRT5. By disrupting the TGFBR3 and JUND programs individually, we reveal an important circuit for 3D morphogenesis that is wired together by four negative-feedback loops. Computational modeling of this circuit showed that it could exhibit damped, antiphase oscillations when excited with small impulses of TGFβ-like ligand. We directly visualize the circuit's spontaneous dynamics in organotypic cultures by using live-cell imaging with engineered pathway reporters. Importantly, we show that the essence of the JUND-TGFBR3 expression circuit holds true in early basal-like tumors that heterogeneously express KRT5. Correlated JUND-KRT5 expression depends critically on contact with stromal ECM and local expression of tenascin C. This work illustrates how complex tumor heterogeneities can be deconstructed into intrinsic single-cell expression circuits that are modulated by the microenvironment. Gene expression analysis of outer ECM-attached vs. inner cells of MCF10A-5E clones grown in organotypic 3D culture at day 6.
2015-06-05 | GSE41527 | GEO
Project description:Recent studies suggest that PDEF is required for secretory cell differentiation in several epithelial tissues. To investigate PDEF in the mammary gland, we examined the effect of this transcription factor on gene expression using microarray based profiling of MCF-10A cells. These cells are non-transformed mammary epithelial cells that express protein and gene expression programs of basal epithelial cells and undetectable levels of endogenous PDEF. Bioinformatics analysis of the genes induced or repressed by PDEF overexpression in MCF10A cells revealed a striking effect on expression of luminal and myoepithelial cell markers.
2014-03-29 | GSE40986 | GEO
Project description:Gene expression data of MCF10A cell subpopulations: luminal, basal and luminal.
2014-06-23 | GSE51397 | GEO
Project description:Recent studies suggest that PDEF is required for secretory cell differentiation in several epithelial tissues. To investigate PDEF in the mammary gland, we examined the effect of this transcription factor on gene expression using microarray based profiling of MCF-10A cells. These cells are non-transformed mammary epithelial cells that express protein and gene expression programs of basal epithelial cells and undetectable levels of endogenous PDEF. Bioinformatics analysis of the genes induced or repressed by PDEF overexpression in MCF10A cells revealed a striking effect on expression of luminal and myoepithelial cell markers. Six samples were harvested 26 hours after retroviral infection with either vector control or PDEF. Each condition was performed in triplicate.
2014-03-29 | E-GEOD-40986 | biostudies-arrayexpress
Project description:The overall goal of this study is to identify the genomic binding of RUNX1 in MCF10A cells. We used ChIPseq (chromatin immunoprecipitation assay followed by deep sequencing) to identify the binding sites of RUNX1 in MCF10A cells. We performed ChIPseq of RUNX1 using parental MCF10A cells and did not identify high confident binding sites. To overcome this hurdle, we first generated a RUNX1 deleted MCF10A cell line using CRISPR-Cas9. We then transduced this RUNX1 KO MCF10A cells with lentiviruses that inducibly expresses RUNX1. After treating RUNX1 inducible MCF10A cells with 1 ug/ml doxycycline for 24 hours, we performed ChIPseq of RUNX1.
2019-04-18 | GSE129314 | GEO
Project description:Gene expression data of MCF10A cell subpopulations: luminal, basal and luminal. Three samples were analized. Expression of 105 selected genes was evaluated, including 5 HK genes.
2014-06-23 | E-GEOD-51397 | biostudies-arrayexpress
Project description:Using basal‐like untransformed cells, MCF10A, as a model system, data from our laboratory showed that both mRNAs and microRNAs exhibit dynamic changes in expression following EGF stimulation (Amit et al, 2007; Avraham et al, 2010; Kostler et al, 2013). We further demonstrated that the inducible mRNAs and microRNAs are embedded into regulatory subnetworks, which are deregulated in diverse tumor types. Considering the emerging roles for long noncoding RNAs (lncRNAs) in metastasis of breast cancer (Serviss et al, 2014), we raised the possibility that some EGF‐inducible lncRNAs might play a role in basal‐like breast cancer. Thus, MCF10A cells were stimulated with EGF (10 ng/ml) for 0, 20, 40, 60, 120, 240 and 480 minutes. RNA was then extracted from cells and expression of lncRNAs was measured using Agilent SurePrint microarrays.
2017-07-27 | E-MTAB-4822 | biostudies-arrayexpress
Project description:Breast tumors expressing lower levels of Estrogen Receptor (ER) represent a distinct subset of breast cancer characterized by the emergence of basal-like characteristics within tumors that are traditionally considered luminal-like. Lineage tracing of these low-ER tumors in the MMTV-PyMT mouse mammary tumor model revealed that the basal-like tumor cells within these tumors arose from normal luminal epithelial cells, suggesting that luminal-to-basal plasticity is responsible for the evolution and emergence of basal-like characteristics within these tumors. This study aims to identify the potential drivers of this plasticity by using single-cell RNA sequencing to identify populations of lineage-restricted luminal cells and luminal-derived basal cells within the tumor, and comparing their gene expression profiles.
2023-03-01 | GSE214815 | GEO
Project description:The mechanisms regulating breast cancer differentiation state are poorly understood. Of particular interest are molecular regulators controlling the highly aggressive and poorly differentiated traits of basal-like breast carcinomas. Here we show that the Polycomb factor EZH2 maintains the differentiation state of basal-like breast cancer cells, and promotes the expression of progenitor-associated and basal-lineage genes. Specifically, EZH2 regulates the composition of basal-like breast cancer cell populations by promoting a M-bM-^@M-^\bi-lineageM-bM-^@M-^] differentiation state, in which cells co-express basal- and luminal-lineage markers. We show that human basal-like breast cancers contain a subpopulation of bi-lineage cells, and that EZH2-deficient cells give rise to tumors with a decreased proportion of such cells. Bi-lineage cells express genes that are active in normal luminal progenitors, and possess increased colony formation capacity, consistent with a primitive differentiation state. We found that GATA3, a driver of luminal differentiation, performs a function opposite to EZH2, acting to suppress bi-lineage identity and luminal progenitor gene expression. GATA3 levels increase upon EZH2 silencing, leading to the observed decrease in bi-lineage cell numbers. Our findings reveal a novel role for EZH2 in controlling basal-like breast cancer differentiation state and intra-tumoral cell composition. Total of four treatments (HCC70 cells stably expressing shEZH2, shEED, or EZH2 cDNA, and MDA-MB-468 cells stably expressing shEZH2) were done in duplicates, each with its own control.
2012-09-21 | E-GEOD-36939 | biostudies-arrayexpress