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

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

PROVIDER: PRJNA593845 | ENA |

REPOSITORIES: ENA

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

Project description: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.

2020-03-17 | GSE141545 | GEO

High-dimensional transcriptional analyses of UC Colon comparing RNALater to DMSO collection method

Project description:High-dimensional transcriptional analyses of UC Colon comparing RNALater to DMSO collection method

| PRJNA428476 | ENA

Comparing root transcriptomes of cultivated and wild carrots

Project description:Comparing root transcriptomes of cultivated and wild carrots

| PRJEB3356 | ENA

Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice

Project description:Simultaneous single-cell three-dimensional genome and gene expression profiling uncovers dynamic enhancer connectivity underlying olfactory receptor choice

| PRJNA1002315 | ENA

Comparison of spheroid-based 3-dimensional culture to monolayer of larynx carcinoma cell line HLaC78.

Project description:In vitro proliferation and/or invasion tests (such as MTT assay, Boyden Chamber Assay, Scratch assay) using established and well-characterized cell lines can provide easy and reproducible tools to investigate anti-tumour or anti-invasion agents ex vivo. However, in vivo cells in a tissue context interact with neighbouring cells and extracellular matrix components. In 2-dimensional monolayer cultures cells tend to loose tissue-specific properties. 2-D culture models therefore seem unsuitable to mimic the behaviour of cells in a natural, 3-dimensional microenvironment, especially for testing of growth or invasion inhibiting substances. Spheroids on the other hand resemble in many aspects solid, non-vascularized tumour tissue. Within this study the larynx carcinoma cell line HLaC78 was used as a model for comparing overall gene expression in 2D monolayer culture with 72 hrs old HLaC78 multicellular spheroids, providing evidence for extensive restructuring of gene expression in the 3-dimensional context.

2016-03-11 | E-GEOD-67495 | 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

Study differentially expressed genes comparing metastatic sarcomatoid carcinomas vs adenocarcinomas

Project description:Study differentially expressed genes comparing metastatic sarcomatoid carcinomas vs adenocarcinomas

| PRJNA521686 | ENA

Comparing transcriptomes of vegetative and reproductive plants of Selaginella nipponica

Project description:Comparing transcriptomes of vegetative and reproductive plants of Selaginella nipponica

| PRJNA688913 | ENA

Gene expression profiles of colorectal cancer cells under the three dimensional culture

Project description:Colorectal cancer (CRC) shows the high mortality and morbidity. The mortal number of patients and the morbid number of patients with CRC is also increasing. However, the genes which relate to promote tumorigenesis in CRC remain unclear. In order to investigate specific genes and pathways involved in CRC tumorigenesis, we compared genes expressed between three dimensional cultures and control two-dimensional cultures. Total RNA was prepared from the CRC cell lines under the condition of two-dimensional culture and three dimensional culture.

2014-04-12 | E-GEOD-56738 | biostudies-arrayexpress

Transcriptomes of human prostate cells.

Project description:The gene expression profiles of most human tissues have been studied by determining the transcriptome of whole tissue homogenates. Due to the solid composition of tissues it is difficult to study the transcriptomes of individual cell types that compose a tissue. To overcome the problem of heterogeneity we have developed a method to isolate individual cell types from whole tissue that are a source of RNA suitable for transcriptome profiling.Using monoclonal antibodies specific for basal (integrin beta4), luminal secretory (dipeptidyl peptidase IV), stromal fibromuscular (integrin alpha 1), and endothelial (PECAM-1) cells, respectively, we separated the cell types of the prostate with magnetic cell sorting (MACS). Gene expression of MACS-sorted cell populations was assessed with Affymetrix GeneChips. Analysis of the data provided insight into gene expression patterns at the level of individual cell populations in the prostate.In this study, we have determined the transcriptome profile of a solid tissue at the level of individual cell types. Our data will be useful for studying prostate development and cancer progression in the context of single cell populations within the organ.

| S-EPMC1553448 | biostudies-literature

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