Impact of Culture Dimensionality and Matrix Composition on Morphology, Phenotype and Drug Response in Pancreatic Cancer Models
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PROVIDER: PRJEB97488 | ENA |
REPOSITORIES: ENA
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2015-12-10 | E-GEOD-75863 | biostudies-arrayexpress
Project description:The traditional method for studying cancer in vitro is to grow immortalized cancer cells in two-dimensional (2D) monolayers on plastic. However, many cellular features are impaired in these unnatural conditions and big alterations in gene expression in comparison to tumors have been reported. Three-dimensional (3D) cell culture models have become increasingly popular and are suggested to be better models than 2D monolayers due to improved cell-to-cell contacts and structures that resemble in vivo architecture. The aim of this study was to develop a simple high-throughput 3D drug screening method and to compare drug responses in JIMT1 breast cancer cells when grown in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. We screened 102 compounds with multiple concentrations and biological replicates for their effects on cell proliferation. The cells were either treated immediately upon plating or they were allowed to grow in 3D for four days prior to the drug treatment. Big variations in drug responses were observed between the models indicating that comparisons of culture model influenced drug sensitivities cannot be made based on effects of a single drug. However, we show with the 63 most prominent drugs that, in general, JIMT1 cells grown on Matrigel were significantly more sensitive to drugs than cells grown in 2D cultures, while responses of cells grown in polyHEMA resembled those of 2D. Furthermore, comparison of gene expression profiles of the cell culture models to xenograft tumors indicated that cells cultured in Matrigel and as xenografts most closely resembled each other. In this study we also suggest that 3D cultures can provide a platform for systematic experimentation of larger compound collections in a high-throughput mode and be used as alternatives for traditional 2D screens towards better comparability to in vivo state.
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2010-05-26 | E-GEOD-5417 | biostudies-arrayexpress
Project description:Mesenchymal stem cells (MSC) are heterogeneous in morphology and transcriptome, resulting in varying therapeutic outcomes. In this study, we found that 3D spheroid culture of heterogeneous MSC, which have undergone conventional 2D monolayer culture for 5-6 passages, synchronized the cells into a uniform cell population with dramatically reduced cell size, and considerably increased levels of immunosuppressive genes and growth factors. Sc-RNA-Seq analysis of the cells revealed that 3D MSC consisted of 2 major cell subpopulations and both expressed high levels of immunosuppressive factors, compared to 6 subpopulations in 2D MSC. In addition, 3D MSC showed a greater suppressive effect on T cells. Moreover, intravenous infusion of a large dose of 3D MSC prior to Imiquimod (IMQ) treatment significantly improved psoriatic lesion. Thus, our results indicate that 3D spheroid culture reprograms heterogeneous mesenchymal stem cells into a uniform immunosuppressive phenotype and promises a novel therapeutic potential for inflammatory diseases.
2024-09-25 | GSE268973 | GEO
Project description:Obvious advantages of 3D cell culture model are the cell morphology better reflecting tissue cell morphology, the formation of zones of i) active proliferation, ii) quiescent viable cell zone and iii) necrotic zone, as well as formation of nutrition, oxygen and drug gradients better reflecting cellular environment in tissue. Nevertheless the 3D cultures are a model still not resembling full complexity of tumor tissue environment in vivo. Few obvious limitations of 3D cell cultures as cancer research model are the lack of vasculature, host immune response and other cell-cell interactions that occur between cancer and stromal cells in tumors. Recognized advantages and limitations of the 3D cell culture models, however do not suggest directly the areas of cancer biology where 3D models could be applied with highest success. Hence detailed analysis at the molecular level of 2D/3D cell cultures and tumors in vivo are needed to unlock the power of 3D cell culture model. In order to elucidate which biological pathways of cancer cells in tumors are best resembled by the 3D cell culture model we have analyzed whole genome gene expression changes in mouse LLC1 cell line when cultured in 2D or laminin rich ECM 3D system.
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Project description:Fibroblasts are the main producers of extracellular matrix (ECM) responsible for ECM maintenance and repair, a process often disrupted in chronic lung diseases. The accompanying mechanical changes adversely affect resident cells and overall lung function. Numerous models have been used to elucidate fibroblast behavior which are now evolving towards complex 3D models incorporating ECM, aiming to replicate the cells’ native environment. Little is known about the cellular changes that occur when moving from 2D to 3D cell culture. This study compared gene expression profiles of primary human lung fibroblasts from 7 subjects with normal lung function, cultured for 24 hours on 2D collagen I-coated tissue culture plastic and in 3D collagen I hydrogels, which are commonly used to mimic ECM in various models, from contraction assays to organ-on-a-chip models. Comparing 3D to 2D cell culture, 6,771 differentially expressed genes (2,896 up, 3,875 down) were found; enriched gene sets within the downregulated genes, identified through Gene Set Enrichment Analysis and Ingenuity pathway analysis, were involved in the initiation of DNA replication which implied downregulation of fibroblast proliferation in 3D. Observation of cells for 72 hours in 2D and 3D environments confirmed the reduced progression through the cell cycle in 3D. A focused analysis examining the Hippo pathway and ECM-associated genes, showed differential patterns of gene expression in the 3D versus 2D culture. Altogether, the transcriptional response of fibroblasts cultured in 3D indicated inhibition of proliferation, and alterations in Hippo and ECM pathways indicating a complete switch from proliferation to ECM remodeling.
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Project description:2D culture as a model for drug testing often turns to be clinically futile. Therefore, 3D cultures (3Ds) show potential to better model responses to drugs observed in vivo. In preliminary studies, using melanoma (B16F10) and renal (RenCa) cancer, we confirmed that 3Ds better mimics the tumor microenvironment. Here, we evaluate how the proposed 3D mode of culture affects tumor cell susceptibility to anti-cancer drugs, which have distinct mechanisms of action (everolimus, doxorubicin, cisplatin). Melanoma spheroids show higher resistance to all used drugs, as compared to 2D. In RCC model, such modulation was only observed for doxorubicin treatment. As drug distribution was not affected by the 3D shape, we assessed the expression of MDR1 and mTor. Upregulation of MDR1 in RCC spheroids was observed, in contrast to melanoma. In both models mTor expression was not affected by the 3D cultures. By NGS, 10 genes related with metabolism of xenobiotics by cytochrome p450 were deregulated in renal cancer spheroids; 9 of them were later confirmed in melanoma model. The differences between 3D models and classical 2D cultures point to the potential to uncover new non canonical mechanisms to explain drug resistance set by the tumor in its microenvironment.
2022-01-20 | GSE190296 | GEO