title: Tissue elasticity regulated tumor gene expression: implication for diagnostic biomarkers of primitive neuroectodermal tumor.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  Our results suggest that tissue elasticity plays important roles in miRNA expression, which, in turn, regulate tumor growth or tumorigenicity.
authors.affiliation: Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave., Orange, CA, 92868, United States of America; Department of Biological Science, California State University, Fullerton, CA, 92834, United States of America.
authors.forename: Long T
authors.initials: LT
authors.lastname: Vu
authors.affiliation: Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave., Orange, CA, 92868, United States of America.
authors.forename: Vic
authors.initials: V
authors.lastname: Keschrumrus
authors.affiliation: Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States of America.
authors.forename: Xi
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, United States of America.
authors.forename: Jiang F
authors.initials: JF
authors.lastname: Zhong
authors.affiliation: Bioengineering Research Center, School of Medicine, Shenzhen University, Shenzhen, 518057, Guangdong, China.
authors.forename: Qingning
authors.initials: Q
authors.lastname: Su
authors.affiliation: Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave., Orange, CA, 92868, United States of America; Department of Pediatric Surgery, CHOC Children's Hospital, 1201 West La Veta Ave., Orange, CA, 92868, United States of America; Department of Surgery, University of California Irvine School of Medicine, 333 City Blvd. West, Suite 700, Orange, CA 92868, United States of America.
authors.forename: Mustafa H
authors.initials: MH
authors.lastname: Kabeer
authors.affiliation: Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave., Orange, CA, 92868, United States of America; Department of Neurological Surgery, Saint Joseph Hospital, Orange, CA, 92868, United States of America; Department of Neurological Surgery, University of California Irvine School of Medicine, Orange, CA, 92862, United States of America.
authors.forename: William G
authors.initials: WG
authors.lastname: Loudon
authors.affiliation: Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Hospital Research Institute, University of California Irvine, 1201 West La Veta Ave., Orange, CA, 92868, United States of America; Department of Neurology, University of California Irvine School of Medicine, Orange, CA, 92697-4292, United States of America; Department of Biological Science, California State University, Fullerton, CA, 92834, United States of America.
authors.forename: Shengwen Calvin
authors.initials: SC
authors.lastname: Li
mesh_terms: D020413:3' Untranslated Regions; D000180:Acrylic Resins / Q000494:pharmacology; D014408:Biomarkers, Tumor / Q000235:genetics / Q000378:metabolism*; D002478:Cells, Cultured; D002648:Child; D053487:DEAD-box RNA Helicases / Q000235:genetics / Q000378:metabolism; D004548:Elasticity; D016326:Extracellular Matrix Proteins / Q000235:genetics / Q000378:metabolism; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate / Q000737:chemistry / Q000494:pharmacology; D007438:Introns; D014411:Neoplastic Stem Cells / Q000187:drug effects / Q000378:metabolism*; D018242:Neuroectodermal Tumors, Primitive / Q000378:metabolism*; D026723:Polyadenylation; D011137:Polystyrenes / Q000494:pharmacology; D034622:RNA Interference; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic; D053781:Transforming Growth Factor beta2 / Q000235:genetics / Q000378:metabolism; D014409:Tumor Necrosis Factor-alpha / Q000235:genetics / Q000378:metabolism; D000099166:Polyacrylamides
chemical_list: D020413:3' Untranslated Regions; D000180:Acrylic Resins; D014408:Biomarkers, Tumor; D053487:DEAD-box RNA Helicases; D016326:Extracellular Matrix Proteins; D020136:Hydrogel, Polyethylene Glycol Dimethacrylate; D011137:Polystyrenes; D043244:Ribonuclease III; D053781:Transforming Growth Factor beta2; D014409:Tumor Necrosis Factor-alpha; D000099166:Polyacrylamides; C408087:DICER1 protein, human