Gene expression perturbation in vitro—A growing case for three-dimensional (3D) culture systems

• Published in: Seminars in cancer biology Vol. 15; no. 5; pp. 405 - 412
• Main Authors: Birgersdotter, Anna, Sandberg, Rickard, Ernberg, Ingemar
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.10.2005
• Subjects: 3-D cell culture; Cancer cell lines; Cell Adhesion; Cell Line; Cell Line, Tumor; Cell Proliferation; Coculture Techniques; DNA - metabolism; Down-Regulation; Gene Expression Regulation, Neoplastic; Global gene expression; Humans; Medicin och hälsovetenskap; Neoplasm Metastasis; Neoplasms - metabolism; Oligonucleotide Array Sequence Analysis; Phenotype; Transcription, Genetic; Transcriptome; Tumor stroma; Up-Regulation; Global gene expression; Cancer cell lines; Tumor stroma; Transcriptome; 3-D cell culture
• ISSN: 1044-579X; 1096-3650
• DOI: 10.1016/j.semcancer.2005.06.009

Cells grown in vitro are dramatically perturbed by their new microenvironment. Analyses of genome-wide gene expression levels offer a first glance at which genes and pathways are affected in cell lines as compared to their tissues of origins. We have summarized available gene expression data and review how cell lines adapt to in vitro environments, to what degree they express markers of their tissues of origins and discuss how cells grown in three-dimensional (3D) cultures may have more physiological interactions with neighbouring cells and extracellular matrix. We will also discuss the interplay between malignant cells and stroma present in tumours but lacking in cell lines and how these differences might affect gene expression comparisons of cell lines to tumours. A model simulating impact of stromal cells on gene expression profiles is presented. Understanding the transcriptomes of cells grown in 2D and 3D cultures and how they compare to those of in vivo cells are important for improving cell line model systems and for the reconstituting of tissues in vitro.