Expression profiles of lncRNAs in 3D cultures.
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ABSTRACT:
PROVIDER: PRJNA852280 | ENA |
REPOSITORIES: ENA
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Project description:Breast cancer cells reprogram the oncogenic lncRNAs/mRNAs co-expression networks in three- dimensional microenvironment To have a more functional approach, organotypic 3D cell cultures that more accurately mimic the characteristics of solid tumors in vivo and the tumor microenvironment are required. In this study, DNA microarrays were employed to deline the changes in lncRNAs expression patterns of breast cancer cells, cultured in 3D and 2D conditions from BT-474 cell line. Furthermore, potential lncRNAs/mRNAs pairs co-expressed in 3D cultures exhibit a high degree of similarity with those found in luminal B breast cancer patients suggesting that they could be adequate pre-clinical tools to identify, not only biomarkers related to endocrine therapy response and PCR, but to understand the biological behavior of cancer cells in 3D microenvironments, which point towards an important contribution of the roles of lncRNAs in organotypic 3D cultures.
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Project description:Expression profiles at the level of miRNAs in 3D cultures.
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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.
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Project description:Expression data from HepG2 cultured in 2D monolayer cultures and 3D Matrigel cultures We performed this study to understand differences in gene expression profiles of 2D and 3D HepG2 cultures
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Project description:Background. Fallopian tube secretory epithelial cells (FTSECs) have been implicated as a cell-of-origin for high-grade serous epithelial ovarian cancer. However, there are relatively few in vitro models of this tissue type available for use in studies of FTSEC biology and malignant transformation. In vitro three-dimensional (3D) cell culture models aim to recreate the architecture and geometry of tissues in vivo and restore the complex network of cell-cell/cell-matrix interactions that occur throughout the surface of the cell membrane. Results. We have established and characterized 3D spheroid culture models of primary FTSECs. FTSEC spheroids contain central cores of hyaline matrix surrounded by mono- or multi-layer epithelial sheets. We found that 3D culturing alters the molecular characteristics of FTSECs compared to 2D cultures of the same cells. Gene expression profiling identified more than a thousand differentially expressed genes between 3D and 2D cultures of the same FTSEC lines. Pathways significantly under-represented in 3D FTSEC cultures were associated with cell cycle progression and DNA replication. This was also reflected in the reduced proliferative indices observed in 3D spheroids stained for the proliferation marker MIB1. Comparisons with gene expression profiles of fresh fallopian tube tissues revealed that 2D FTSEC cultures clustered with follicular phase tubal epithelium, whereas 3D FTSEC cultures clustered with luteal phase samples. Conclusions. This 3D model of fallopian tube secretory epithelial cells will advance our ability to study the underlying biology and etiology of fallopian tube tissues and the pathogenesis of high-grade serous epithelial ovarian cancer. 3 primary FTSEC lines were plated in 2D, or in 3D on polyHEMA coated plates
2013-09-27 | E-GEOD-51220 | biostudies-arrayexpress
Project description:Three-dimensional (3D) organotypic cell cultures more accurately recapitulate the spatial architecture, biological, and epigenetic features of tumors than traditional two-dimensional (2D) monolayer models, thus representing an innovative approach in cancer research. However, the impact of the 3D microenvironment on the reprogramming of non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs in breast cancer cells, remains unexplored. To fill this knowledge gap, we performed RNA sequencing to identify the differential transcriptome of 3D versus 2D cell cultures and novel potential therapeutic targets. Our data showed that the Hs-578T breast cancer cells grew as stellated 3D structures over an extracellular matrix protein- enriched scaffold. Expression profiling data revealed that 88 lncRNAs, 218 microRNAs, and 2,806 mRNAs were modulated in Hs-578T cells under 3D conditions. Regulated protein-encoding genes were found to be associated with cell proliferation, migration, and chemoresistance. Interestingly, coregulatory network analyses reveal a positive regulation of a set of hypoxia-responsive genes related to the lncRNA-SNHG7/miR-486-3p/HIF1A axis in 3D cultures. SNHG7 and HIF1A expression were upregulated, whereas miR-486-3p was downregulated in 3D cultures, correlating with poor overall survival in cancer patients. Functional studies in the 3D environment indicate that the knockdown of SNHG7 abolishes cell proliferation and invasion, while activating apoptosis, thereby sensitizing cancer cells to cisplatin. Furthermore, a significant increase in hypoxic internal regions was found in SNHG7-deficient 3D structures. In conclusion, our data suggested that the 3D architecture of cells reprograms the transcriptional programs of breast cancer cells. Importantly, SNHG7 plays a key role in cancer progression, representing a promising novel therapeutic target for breastcancer.
2026-06-30 | GSE303170 | GEO
Project description:Background: Fallopian tube secretory epithelial cells (FTSECs) have been implicated as a cell-of-origin for high-grade serous epithelial ovarian cancer. However, there are relatively few in vitro models of this tissue type available for use in studies of FTSEC biology and malignant transformation. In vitro three-dimensional (3D) cell culture models aim to recreate the architecture and geometry of tissues in vivo and restore the complex network of cell-cell/cell-matrix interactions that occur throughout the surface of the cell membrane. Results: We have established and characterized 3D spheroid culture models of primary FTSECs. FTSEC spheroids contain central cores of hyaline matrix surrounded by mono- or multi-layer epithelial sheets. We found that 3D culturing alters the molecular characteristics of FTSECs compared to 2D cultures of the same cells. Gene expression profiling identified more than a thousand differentially expressed genes between 3D and 2D cultures of the same FTSEC lines. Pathways significantly under-represented in 3D FTSEC cultures were associated with cell cycle progression and DNA replication. This was also reflected in the reduced proliferative indices observed in 3D spheroids stained for the proliferation marker MIB1. Comparisons with gene expression profiles of fresh fallopian tube tissues revealed that 2D FTSEC cultures clustered with follicular phase tubal epithelium, whereas 3D FTSEC cultures clustered with luteal phase samples. Conclusions: This 3D model of fallopian tube secretory epithelial cells will advance our ability to study the underlying biology and etiology of fallopian tube tissues and the pathogenesis of high-grade serous epithelial ovarian cancer.
2013-09-27 | GSE51220 | GEO
Project description:3D spheroid cultures of primary human hepatocytes (PHH) are used in studies of hepatic drug metabolism and toxicity. However, the 3D spheroids are maintained under different conditions, with possible cofounding results. Here we performed an in-depth analysis of how various culture conditions influence 3D spheroids. Our aim was to find optimal conditions for the maintenance of a normal PHH phenotype.
2022-02-17 | PXD024632 | Pride
Project description:LncRNAs expression profiles in renal tissues from patients with diabetic nephropathy
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