title: Three-dimensional culture of melanoma cells profoundly affects gene expression profile: a high density oligonucleotide array study.
abstract: Growth in three-dimensional (3D) architectures has been suggested to play an important role in tumor expansion and in the resistance of cancers to treatment with drugs or cytokines or irradiation. To obtain an insight into underlying molecular mechanisms, we addressed gene expression profiles of NA8 melanoma cells cultured in bidimensional monolayers (2D) or in 3D multicellular tumor spheroids (MCTS). MCTS containing 10-30,000 cells were generated upon overnight culture in poly-Hydroxyethylmethacrylate (polyHEMA) coated plates. Kinetics of cell proliferation in MCTS was significantly slower than in monolayer cultures. Following long-term culture (>10 days), however, MCTS showed highly compact and organised cell growth in outer layers, with necrotic cores. Oligonucleotide microarray analysis of the expression of over 20,000 genes was performed on cells cultured in standard 2D, in the presence of collagen as model of extracellular matrix (ECM), or in MCTS. Gene expression profiles of cells cultured in 2D in the presence or absence of ECM were highly similar, with >/=threefold differences limited to five genes. In contrast, culture in MCTS resulted in the significant, >/=threefold, upregulation of the expression of >100 transcripts while 73 were >/=threefold downregulated. In particular, genes encoding CXCL1, 2, and 3 (GRO-alpha, -beta, and gamma), IL-8, CCL20 (MIP-3alpha), and Angiopoietin-like 4 were significantly upregulated, whereas basic FGF and CD49d encoding genes were significantly downregulated. Oligonucleotide chip data were validated at the gene and protein level by quantitative real-time PCR, ELISA, and cell surface staining assays. Taken together, our data indicate that structural modifications of the architecture of tumor cell cultures result in a significant upregulation of the expression of a number of genes previously shown to play a role in melanoma progression and metastatic process.
authors.affiliation: Institut für Chirurgische Forschung und Spitalmanagement (ICFS) and Departement Forschung, University of Basel, Basel, Switzerland.
authors.forename: Sourabh
authors.initials: S
authors.lastname: Ghosh
authors.forename: Giulio C
authors.initials: GC
authors.lastname: Spagnoli
authors.forename: Ivan
authors.initials: I
authors.lastname: Martin
authors.forename: Sabine
authors.initials: S
authors.lastname: Ploegert
authors.forename: Philippe
authors.initials: P
authors.lastname: Demougin
authors.forename: Michael
authors.initials: M
authors.lastname: Heberer
authors.forename: Anca
authors.initials: A
authors.lastname: Reschner
mesh_terms: D002455:Cell Division; D015536:Down-Regulation; D004797:Enzyme-Linked Immunosorbent Assay; D020869:Gene Expression Profiling; D006801:Humans; D008545:Melanoma / Q000235:genetics / Q000378:metabolism* / Q000473:pathology*; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D018874:Spheroids, Cellular; D013194:Staining and Labeling; D014407:Tumor Cells, Cultured; D015854:Up-Regulation