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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

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

Salmonella Typhimurium: Immobilized growth vs. Planktonic growth

Project description:Transcriptional profiling of four growth phases S. Typhimurium comparing immobilised growth with planktonic growth.

2011-11-01 | GSE32995 | GEO

Whole-transcriptome sequencing uncovers core regulatory modules and gene signatures of human fetal growth restriction.

Project description: Not available

| S-EPMC6987274 | biostudies-literature

Three-dimensional tumor cell growth stimulates autophagic flux and recapitulates chemotherapy resistance

Project description:Current preclinical models in tumor biology are limited in their ability to recapitulate relevant (patho-) physiological processes, including autophagy. Three-dimensional (3D) growth cultures have frequently been proposed to overcome the lack of correlation between two-dimensional (2D) monolayer cell cultures and human tumors in preclinical drug testing. Besides 3D growth, it is also advantageous to simulate shear stress, compound flux and removal of metabolites, e.g. via bioreactor systems, through which culture medium is constantly pumped at a flow rate reflecting physiological conditions. Here, we show that both Staticic 3D growth and 3D growth within a bioreactor system modulate key hallmarks of cancer cells, including proliferation and cell death as well as macroautophagy, a recycling pathway often activated by highly proliferative tumors to cope with metabolic stress. The autophagy-related gene expression profiles of 2D- and 3D-grown cells are substantially different, with the 3D-grown cells exhibiting an expression profile closely resembling the (patho-) physiological Statice of a tumor. Underscoring the importance of this pathway, autophagy-controlling transcription factors, such as TFEB and FOXO3, are upregulated in tumors, and 3D-grown cells have increased expression compared with cells grown in 2D conditions. Three-dimensional cultures depleted of the autophagy mediators BECN1, ATG5 or ATG7 or the transcription factor FOXO3, are more sensitive to cytotoxic treatment. Accordingly, combining cytotoxic treatment with compounds affecting late autophagic flux, such as chloroquine, renders the 3D-grown cells more susceptible to therapy and increases intracellular doxorubicin concentration to the level of 2D-grown cells. Altogether, 3D cultures are a valuable tool to study drug response of tumor cells, as these models recapitulate (patho-) physiologically relevant pathways, such as autophagy.

2017-07-04 | GSE100020 | GEO

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

Study differentially expressed genes comparing metastatic sarcomatoid carcinomas vs adenocarcinomas

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

| PRJNA521686 | ENA

The differences in miRNA expression with miRNA microarrays of two-dimensional (2D)- and three-dimensional (3D)-SNP cells

Project description:Canine mammary gland tumors can be used as predictive models for human breast cancer. There are several types of microRNAs common in human breast cancer and canine mammary gland tumors. The functions of microRNAs in canine mammary gland tumors are not well understood. In the present study, we compared the characterization of microRNA expression in two-dimensional and three-dimensional canine mammary gland tumor cell models. The expression of microRNA-210 in the three-dimensional-SNP cells was 10.19 times higher than that in the two-dimensional-SNP cells.

2022-07-07 | GSE203410 | GEO

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