Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA206202 | ENA |
REPOSITORIES: ENA
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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 compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures. Gene expression analysis of MCF7 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.
2013-10-30 | E-GEOD-47583 | 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 compare gene expression patterns of MCF7 breast cancer cells when grown as xenografts, in 2D, in polyHEMA coated anchorage independent 3D models and in Matrigel on-top 3D cell culture models. Surprisingly small variations in gene expression patterns were observed between the models indicating that 3D and xenograft are not always that different from 2D cell cultures.
2013-10-30 | GSE47583 | GEO
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. Gene expression analysis of JIMT1 breast cancer cells cultured as xenografts for 43 days, in two dimensional cultures for seven days (2D7d), in polyHEMA three dimensional cell culture models for four and seven days (PH7d and PH7d), and in Matrigel three dimensional cultures for four and seven days (MG4d and MG7d). Two biological replicates was included for each sample.
2013-10-30 | E-GEOD-42529 | 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.
2013-10-30 | GSE42529 | GEO
Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001. Gene microarrays were used to observe the global gene expression in A549 cells cultured in multi-well plate with or without FP001 and identified distinct classes of up or down-regulated genes. A549 cells were cultured for 5 days in normal attachment plate with normal medium (as control) or normal attachment plate with FP001 containing medium. Each sample was collected three times.
2015-07-31 | E-GEOD-69577 | biostudies-arrayexpress
Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001. Gene microarrays were used to observe the global gene expression in A549 cells cultured in multi-well plate with or without FP001 and identified distinct classes of up or down-regulated genes.
2015-07-31 | GSE69577 | GEO
Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed a novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001, a bacteria-derived polysaccharide. Gene microarrays were used to observe the global gene expression in SKOV3 cells cultured with adhesion condition (2D, control) or with low adhesion condition (FP001) and identified distinct classes of up or down-regulated genes. SKOV3 cells were cultured for 11 days in normal attachment plates with normal medium (as control) or low-attachment plates with FP001 containing medium. Each sample was collected three times.
2015-07-31 | E-GEOD-69523 | biostudies-arrayexpress
Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001. Gene microarrays were used to observe the global gene expression in A549 cells cultured with normal adhesion plate (2D, control) or with low adhesion plate (+FP001) and identified distinct classes of up or down-regulated genes. A549 cells were cultured for 5 days in three different conditions as follows. (1) Normal attachment plates with normal medium (as control), (2) low-attachment plates with normal medium, (3) low-attachment plates with FP001 containing medium. Each sample was collected three times.
2015-07-31 | E-GEOD-69477 | biostudies-arrayexpress
Project description:We used splicing-sensitive microarrays to detect differences in alternative splicing between two breast cancer cell lines MCF7 (estrogen receptor positive) and MDA-MB-231 (estrogen receptor negative), as well as cultured human mammary epithelial cells (HMEC). Several splicing alterations in genes, including CD44, FAS, RBM9, HnRNPA/B, APLP2, and MYL6, were detected by the microarray, and verified by RT-PCR. We also compared splicing in these breast cancer cells cultured in either two-dimensional flat dishes (2-D) or in three-dimensional Matrigel (3-D) conditions. Only a subset of the splicing differences that distinguish MCF7 cells from MDA-MB-231 cells under 2-D culture condition is retained under 3-D conditions, suggesting that alternative splicing events are influenced by the geometry of the culture conditions of these cells. Keywords: Splicing-sensitive microarray
2005-12-30 | GSE3042 | GEO
Project description:Preclinical cancer drug discovery efforts have employed two-dimensional (2D)-cell-based assay models, which fail to forecast in vivo efficacy and contribute to a lower success rates of clinical approval. Three-dimensional (3D) cell culture models are recently expected to bridge the gap between 2D and in vivo models. We have developed a novel 3D culture method that improves the growth of spheroid-forming cancer cells under anchorage-independent condition by leveraging a feature of FP001, a bacteria-derived polysaccharide. Gene microarrays were used to observe the global gene expression in SKOV3 cells cultured with adhesion condition (2D, control) or with low adhesion condition (FP001) and identified distinct classes of up or down-regulated genes.
2015-07-31 | GSE69523 | GEO