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Comparing 2-dimensional vs. 3-dimensional human prostate cancer transcriptomes uncovers growth-specific gene signatures

ABSTRACT: Prostate cancer research has relied heavily on patient-derived cell lines, which may be used for in vitro (2-dimensional) studies or cultivated as 3-dimensional xenografts in mice. These approaches are likely to have differential impacts on cell differentiation, with implications for research outcomes. Therefore, defining and comparing the transcriptional signatures associated with 2-dimensional and 3-dimensional approaches is essential to adequately plan experiments and interpret research data. In this study, LNCaP, VCaP, and 22Rv1 human prostate cancer cells were either cultivated in monolayers or as xenografts in NOD Scid mice, and their gene transcription profiles were studied and compared using microarray and RT-PCR techniques. This comparison identified gene sets featuring similar expression patterns in all three cancer cell lines and unique transcriptional signatures associated with 3-dimensional versus 2-dimensional growth. Pathway over-representation analysis revealed an enrichment of pathways related to cell-cell interactions, differentiation and the extracellular matrix. Immunohistochemical analyses confirmed that gene up-regulation in xenografts occurred in implanted cancer cells and not mouse stromal cells. Cultivating cells in vitro in the presence of mouse - rather than bovine - serum failed to elicit the gene transcription profile observed in xenografts, further supporting the hypothesis that this profile reflects 3-dimensional growth and enhanced microenvironmental interactions, rather than exposure to mouse-related factors. Overall, these findings define the expression profiles observed in prostate cancer cells cultivated in monolayers and in xenografts, highlighting differentially regulated pathways in each setting and providing essential information for performing and interpreting research in this field.

ORGANISM(S): Homo sapiens

PROVIDER: GSE141545 | GEO | 2020/03/17

REPOSITORIES: GEO

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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 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.

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Comparing 2-dimensional vs. 3-dimensional human prostate cancer transcriptomes uncovers growth-specific gene signatures

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