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TGF-beta-mediated microRNA expression in breast cancer cells

ABSTRACT: We utilized 3D-organotypic cultures whose physical properties were altered by inclusiong of type I collagen to create biomechanically rigid microenvironments that approximated those typically observed in primary mammary tumors. Compliant 3D-organotypic cultures were also generated to recapitulate the biomechanical properties of pulmonary microenvironments typically encountered by disseminated breast carcioma cells. The murine 4T1 progression series represents an established model of triple negative breast cancer development and metastasis and consists of isogenically-derived nonmetastatic 67NR, systemically invasive 4TO7, and highly metastatic 4T1 cells that were propagated for 6 days in the absense or presense of TGF-beta in either rigid or compliant 3D-cultures. Afterward, total RNA was extracted and subjected to miRNA profiling.

ORGANISM(S): Mus musculus

PROVIDER: GSE41274 | GEO | 2012/10/31

SECONDARY ACCESSION(S): PRJNA176422

REPOSITORIES: GEO

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TGF-beta-mediated microRNA expression in breast cancer cells

Project description:We utilized 3D-organotypic cultures whose physical properties were altered by inclusiong of type I collagen to create biomechanically rigid microenvironments that approximated those typically observed in primary mammary tumors. Compliant 3D-organotypic cultures were also generated to recapitulate the biomechanical properties of pulmonary microenvironments typically encountered by disseminated breast carcioma cells. The murine 4T1 progression series represents an established model of triple negative breast cancer development and metastasis and consists of isogenically-derived nonmetastatic 67NR, systemically invasive 4TO7, and highly metastatic 4T1 cells that were propagated for 6 days in the absense or presense of TGF-beta in either rigid or compliant 3D-cultures. Afterward, total RNA was extracted and subjected to miRNA profiling. two replicates of each growth and treatment condition for each cell line.

2012-10-31 | E-GEOD-41274 | biostudies-arrayexpress

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Quantification of regenerative potential in primary human mammary epithelial cells

Project description:We present an organoid regeneration assay in which freshly dissociated human mammary epithelial cells from healthy donors are grown in adherent/rigid or floating/compliant collagen I gels. In both conditions, luminal progenitors (CD49f+EpCAM+) form spheres, whereas basal cells (CD49fhiEpCAM-) generate branched ductal structures. However, in compliant but not rigid collagen gels, branching ducts form alveoli at their tips, express basal and luminal markers at correct positions and display contractility, which is required for alveologenesis. Thereby, branched structures generated in compliant collagen gels resemble terminal ductal-lobular units (TDLUs), the functional units of the mammary gland. Moreover, the membrane metallo-endopeptidase CD10 as an additional surface marker enriches for TDLU-formation and reveals the presence of stromal cells within the CD49fhiEpCAM- population. In summary, we describe a defined in vitro assay system to quantify cells with regenerative potential and systematically investigate their interaction with the physical environment at distinct steps of morphogenesis. Comparison of three cell populations derived from FACS-sorted primary human mammary epithelial cells: luminal progenitors, CD10+ basal cells and CD10- basal cells.

2015-07-02 | E-GEOD-64248 | biostudies-arrayexpress

Quantification of regenerative potential in primary human mammary epithelial cells

2015-07-02 | GSE64248 | GEO

Expression profiles at the level of miRNAs in 3D cultures.

Project description:Three-Dimensional Organotypic Cultures Reshape the microRNAs Transcriptional Program in Breast Cancer Cells Three-dimensional (3D) cell cultures have several advantages over conventional monolayer two-dimensional (2D) cultures as they can better mimic tumor biology. This study delineated the changes in microRNA (miRNA) expression patterns of breast cancer cells cultured in 3D and 2D conditions. 3D organotypic cultures showed morphological changes such as cell–cell and cell–extracellular matrix interactions associated with a loss of polarity and reorganization on bulk structures in both basal Hs578T and luminal T47D breast cancer cells. Data indicate that down-regulated miRNAs in Hs578T 3D cultures, relative to the 2D condition, contribute to a positive regulation of biological processes such as response to hypoxia and focal adhesion, whereas over-expressed miRNAs were related to negative regulation of the cell cycle. Remarkably, the repro-gramming of miRNAs’ transcriptional profiles was accompanied by changes in the expression of key miRNA/mRNA coregulation networks, such as miR-935/HIF-1A, which correlated with the expression found in clinical breast tumors and predicted poor patient outcomes. These data have implications in our understanding of cancer biology and impact the miRNA/mRNA regulatory axes of cells grown in 3D cultures. Our data represent a guide for novel miRNA candidates for functional analysis, including the response to therapy and biomarker discovery in breast cancer.

2022-05-16 | GSE203045 | GEO

Comparison of gene expression profiles of normal human bronchial epithelial cells in 2D and 3D cultural conditions

Project description:The experiment is part of a project to study DNA repair process after ionizing radiation in organotypic 3-dimentional human bronchial epithlial cell culture. Human bronchial epithelial cells were grown in tissue culture flask (2D) or in matrics gel (3D). Three independent cultures were done for each condition.

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Project description:We have developed a robust methodology for the derivation of kidney organoids from human pluripotent stem cells further vascularized taking advantage of several in vivo approaches. Our methodology suffices for the generation of kidney derivatives transcriptomically comparable with 22 weeks of gestation kidney tissues and highlight the use of longer periods of exposure to 3D in order to promote renal differentiation in a time frame of 15 days. In order to ascertain the impact of extracellular matrix microenvironment in renal differentiation undifferentiated human pluripotent stem cells were further cultured in compliant substrates mirroring embryo-ECM microenvironment (1kPa) in order to promote renal differentiation and compared these conditions in front of rigid substrates (60 kPa) mimicking hard substrates normally used when differentiating human pluripotent stem cells

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Organotypic three-dimensional cancer cell cultures mirror drug responses in vivo: Lessons learned from the inhibition of EGFR signaling

Project description:Complex three-dimensional (3D) in vitro model systems that recapitulate human tumor biology are essential to better understand the pathophysiology of the disease and to aid in the discovery of novel anti-cancer therapies. 3D organotypic cultures exhibit intercellula communication, nutrient and oxygen gradients, and cell polarity that is lacking in traditional two-dimensional (2D) monolayer cultures. In the present study, we could demonstrate that 2D and 3D cancer models exhibit different drug sensitivities towards both targeted inhibitors of EGFR signaling and broad acting cytotoxic agents. Changes in the kinase activities of Erb family members and differential expression of apoptosis- and survival-associated genes before and after drug treatment may account for the differential drug sensitivities. Importantly, EGFR oncoprotein addiction was evident only in the 3D cultures mirroring the effect of EGFR inhibition in the clinic. Furthermore, targeted drug efficacy was strongly increased when incorporating cancer-associated fibroblasts into the 3D cultures. Taken together, we could provide conclusive evidence that complex 3D cultures are more predictive of the clinical outcome than their 2D counterparts. In the future, 3D cultures will be instrumental for understanding the mode of action of drugs, identifying genotype-drug response relationships and developing patient-specific and personalized cancer treatments.

2017-11-30 | GSE102722 | GEO

Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression

Project description:Commonly used monolayer cell cultures lack the capacity to provide a physiologically relevant environment for cell culture in terms of cell-cell architecture, extracellular matrix composition, and spatiotemporal delivery of key growth factors and small molecules, such as oxygen. Here, we describe a three-dimensional (3D) approach to cell culture in vitro, utilizing a bioreactor system designed to control oxygenation of 3D cancer cell cultures, in order to better mimic tumor microenvironments observed in vivo. We found transcriptomic differences in breast and ovarian cancer cell cultures grown in traditional monolayer cultures as compared to cultures grown in a Matrigel three-dimensional matrix. We also investigated the transcriptomes of 3D cultures grown in 21% O2, 3% O2, and a gradient of 3% O2 to 0% O2 using our bioreactor system. By controlling oxygen delivery, we observed differences in cell growth morphology and transcriptome regulation under the three conditions.

2019-04-02 | GSE129111 | GEO

3D Biocomposite Culture Enhances Differentiation of Dopamine-like Neurons from SH-SY5Y cells: A Model for Studying Parkinson’s Disease Phenotypes

Project description:Studies of underlying neurodegenerative processes in Parkinson’s Disease (PD) have traditionally utilized cell cultures grown on two-dimensional (2D) surfaces. Biomimetic three-dimensional (3D) cell culture platforms have been developed to better emulate features of the brain’s natural microenvironment. We here use our bioengineered brain-like tissue model, composed of a silk-hydrogel composite, to study the 3D microenvironment’s contributions on the development and performance of dopaminergic-like neurons (DLNs). Compared with 2D culture, SH-SY5Y cells differentiated in 3D microenvironments were enriched for DLNs concomitant with a reduction in proliferative capacity during the neurodevelopmental process. Additionally, the 3D DLN cultures were more sensitive to oxidative stresses elicited by the PD-related neurotoxin 1-methyl-4-phenylpyridinium (MPP). MPP induced transcriptomic profile changes specific to 3D-differentiated DLN cultures, replicating the dysfunction of neuronal signaling pathways and mitochondrial dynamics implicated in PD. Overall, this physiologically-relevant 3D platform resembles a useful tool for studying dopamine neuron biology and interrogating molecular mechanisms underlying neurodegeneration in PD.

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