Tissue elasticity regulated tumor gene expression: implication for diagnostic biomarkers of primitive neuroectodermal tumor

• Published in: PloS one 2015-03, Vol.10 (3), p.e0120336-e0120336
• Main Authors: Vu, Long T, Keschrumrus, Vic, Zhang, Xi, Zhong, Jiang F, Su, Qingning, Kabeer, Mustafa H, Loudon, William G, Li, Shengwen Calvin
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; Acids; Acrylic Resins - pharmacology; Binding sites; Bioinformatics; Biomarkers; Biomarkers, Tumor - genetics; Biomarkers, Tumor - metabolism; Brain; Brain cancer; Brain research; Cancer therapies; Cell culture; Cells, Cultured; Child; Children & youth; Comparative analysis; Cytokines; DEAD-box RNA Helicases - genetics; DEAD-box RNA Helicases - metabolism; Diagnostic systems; DNA microarrays; Elasticity; Extracellular matrix; Extracellular Matrix Proteins - genetics; Extracellular Matrix Proteins - metabolism; Female; Gene expression; Gene Expression Regulation, Neoplastic; Genes; Genomes; Genomics; Humans; Hydrogel, Polyethylene Glycol Dimethacrylate - chemistry; Hydrogel, Polyethylene Glycol Dimethacrylate - pharmacology; Hydrogels; Introns; Kinases; Laboratories; Medical diagnosis; Medical research; Medicine; MicroRNA; MicroRNAs; miRNA; Neoplastic Stem Cells - drug effects; Neoplastic Stem Cells - metabolism; Nervous system diseases; Neuroectodermal Tumors, Primitive - metabolism; Neurosciences; Oncology; Physical characteristics; Physical properties; Polyacrylamide; Polyadenylation; Polystyrene; Polystyrene resins; Polystyrenes - pharmacology; Proteins; Ribonuclease III - genetics; Ribonuclease III - metabolism; Ribonucleic acid; RNA; RNA Interference; RNA polymerase; Signaling; Stem cells; Substrates; Surgery; Tissue culture; Transcription; Transcription, Genetic; Transforming Growth Factor beta2 - genetics; Transforming Growth Factor beta2 - metabolism; Transforming growth factors; Tumor cells; Tumor Necrosis Factor-alpha - genetics; Tumor Necrosis Factor-alpha - metabolism; Tumor necrosis factor-α; Tumorigenicity; Tumors
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0120336

The tumor microenvironment consists of both physical and chemical factors. Tissue elasticity is one physical factor contributing to the microenvironment of tumor cells. To test the importance of tissue elasticity in cell culture, primitive neuroectodermal tumor (PNET) stem cells were cultured on soft polyacrylamide (PAA) hydrogel plates that mimics the elasticity of brain tissue compared with PNET on standard polystyrene (PS) plates. We report the molecular profiles of PNET grown on either PAA or PS. A whole-genome microarray profile of transcriptional expression between the two culture conditions was performed as a way to probe effects of substrate on cell behavior in culture. The results showed more genes downregulated on PAA compared to PS. This led us to propose microRNA (miRNA) silencing as a potential mechanism for downregulation. Bioinformatic analysis predicted a greater number of miRNA binding sites from the 3' UTR of downregulated genes and identified as specific miRNA binding sites that were enriched when cells were grown on PAA-this supports the hypothesis that tissue elasticity plays a role in influencing miRNA expression. Thus, Dicer was examined to determine if miRNA processing was affected by tissue elasticity. Dicer genes were downregulated on PAA and had multiple predicted miRNA binding sites in its 3' UTR that matched the miRNA binding sites found enriched on PAA. Many differentially regulated genes were found to be present on PS but downregulated on PAA were mapped onto intron sequences. This suggests expression of alternative polyadenylation sites within intron regions that provide alternative 3' UTRs and alternative miRNA binding sites. This results in tissue specific transcriptional downregulation of mRNA in humans by miRNA. We propose a mechanism, driven by the physical characteristics of the microenvironment by which downregulation of genes occur. We found that tissue elasticity-mediated cytokines (TGFβ2 and TNFα) signaling affect expression of ECM proteins. Our results suggest that tissue elasticity plays important roles in miRNA expression, which, in turn, regulate tumor growth or tumorigenicity.