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Micro-engineered perfusable 3D-bioprinted glioblastoma model for in-vivo mimicry of tumor microenvironment

ABSTRACT: We aimed to evaluated the effect of the cells growth conditions on the genetic profile of the cells. More specifically, we wanted to evaluate whether our 3D cancer model better reflects the in vivo scenario than 2D culture methods . Therfore, we performed RNA-seq of glioblastoma tumors grown in mice and compared it to a "penta-culture" comprised of GL261 murine GB cells, primary astrocytes, microglia, pericytes, and endothelial cells, grown in 2D or in 3D-bioink

ORGANISM(S): Mus musculus

PROVIDER: GSE178371 | GEO | 2021/08/18

REPOSITORIES: GEO

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Madin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.

Project description:In order to gain insight into epithelial morphogenesis and the influence of culture geometry on gene expression patterns, Madin Darby Canine Kidney (MDCK) epithelial cells where grown in 2-dimensional (2D) culture or 3-dimensional (3D) culture . MDCK cells cultured in 2D were plated atop a pre-solidified type I collagen gel. Cells cultured under these conditions grew as flat monolayer sheets. In 3D culture, cells are embedded within type I collagen gel. Cells grown under these conditions form large spherical cysts with hollow central lumens. We anticipate, therefore, that these results provide insight into the mechanisms that regulate epithelial cystogenesis. Cells grown in the 2D or 3D geometries were collected from digested type I collagen gels on day 8. The 2D MDCK cells were treated as the control condition and there gene expression patterns were compared to those of 3D grown cells, which served as the experimental condition.

2013-06-03 | E-GEOD-28381 | biostudies-arrayexpress

FRT thyroid cells: 2D monolayers vs. 3D follicles

Project description:Transcriptional profiling of the Fischer Rat Thyroid (FRT) cells comparing polarizing cells grown as a confluent two-dimensional monolayer (2D culture system) with cells grown in matrigel where they acquire a three-dimensional follicular structure (3D culture system).The goal was to identify regulators of 3D epithelial thyroid polarization and follicle formation.

2016-11-24 | GSE71259 | GEO

Madin-Darby Canine Kidney (MDCK) cells grown in 2-dimensional and 3-dimensional type I collagen culture.

2013-06-03 | GSE28381 | GEO

Gene expression analysis in TGFbeta/TNFalpha treated A549 spheroid cultures

Project description:TGFbeta/TNFalpha treated spheroid A549 cultures are a model of the epithelial-mesenchymal transition (EMT). These experiments capture the changes in global gene expression that result from cells being induced to undergo EMT (3D control vs 3D treated), but also the differences in gene expression when A549 is grown in spheroid cultures (2D control vs 3D untreated). EMT is efficiently induced only in the spheroid culture model. A total of 8 samples are analyzed, corresponding to 4 conditions (2D control, 2D treated, 3D control, 3D treated) and 2 biological replicates.

2013-09-12 | E-GEOD-42373 | biostudies-arrayexpress

Gene expression profile of Skov3 cells cultured with DMSO (Control) or GA-017 in 3D condition

Project description:3D cell culture models are recognized for representing the physiological microenvironment and exhibiting higher concordance with in vivo conditions, when compared to a conventional 2D cell culture model. However, cells grown in 3D cultures are likely to exhibit slower growth than those in 2D cultures. We found that addition of a novel small molecule named GA-017 to culture media promotes the cell proliferation particularly under 3D conditions. Gene microarrays were used to observe the global gene expression in Skov3 cells cultured under 3D condition with DMSO or GA-017 and identified distinct classes of up or down-regulated genes.

2021-04-01 | GSE145538 | GEO

High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells.

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.

2013-10-30 | GSE42529 | GEO

Characterization of HT-29 cells cultured in NanoCulture plates

Project description:To characterize cells cultured in 3D culture system using NanoCulture plates (NCPs) (Scivax) and in 2D culture, we examined gene expression in HT-29 cells on day 1 or day 7 on NCPs or 2D monolayer culture, using DNA microarrays. From our study, tumour cells grown on NCPs were morphologically different from cells in 2D monolayers, and the cells on NCPs actively migrated and aggregated to form multicellular spheroids (MCSs). To characterize this cell migration and intercellular adhesion, we compared gene expression in HT-29 cells on day 1 on NCPs and 2D monolayer culture using DNA microarrays. We could not find any significant difference in gene expression related to cell migration or cell-cell adhesion between cells grown on NCPs and as 2D monolayers on day 1, showing that cells on NCPs migrated and aggregated without any changes in gene expression (3D Day1 vs 2D Day1 2Fold change.xls). We next characterized mature 3D MCSs on NanoCulture plates, by comparing the gene expression profile of MCSs on day 7 and day 1 (3D Day7 vs 3D Day 1 2Fold change.xls). On day 7, we found a statistically significant increase in the expression of genes related to multicellular organization, intercellular signalling and the response to hypoxia. DNA microarray analysis also showed that the expression of genes that have been reported to be target genes for the transcription factor hypoxia-inducible factor 1 (HIF-1) (Ke, Q. & Costa, M. Hypoxia-inducible factor-1 (HIF-1). Mol Pharmacol 70, 1469-1480 (2006); Semenza, G.L. Defining the role of hypoxia-inducible factor 1 in cancer biology and therapeutics. Oncogene 29, 625-634.) was increased on day 7. When compared day 7 with 2D culture cells, the same tendency was observed (3D Day7 vs 2D Day 7 2Fold change.xls).

2010-08-25 | GSE23773 | GEO

Lung cell lines grown in 2D and 3D

Project description:Comparison of gene expression data between cell lines grown on 2D tissue culture plastic or 3D matrigel A427, A549, H23, H358, H460, H661, H1437, and H1703 cells were compared

2020-09-26 | GSE158597 | GEO

Genome wide expression data and chromatin changes data of murine cardiac fibroblasts in different topological states

Project description:cardiac fibroblasts in 2D, 3D or 3D-2D or 3D-2D-3D , 2D-5days, 3D-5 days or cardiac fibroblasts grown in different stiffness of 0.5, 8 and 64 lkPA were harvested for gene expression analysis or chromatin changes analysis.

2018-04-20 | GSE113277 | GEO

Transcription profiling of 25 breast cancer cell lines grown in 2D and 3D tissue culture conditions

Project description:A comparison of gene expression profiles for 25 breast cancer cell lines grown in 2D and 3D tissue culture conditions

2007-05-02 | E-TABM-244 | biostudies-arrayexpress