title: Recapitulation of tumor heterogeneity and molecular signatures in a 3D brain cancer model with decreased sensitivity to histone deacetylase inhibition.
abstract: BACKGROUND
  Physiologically relevant pre-clinical ex vivo models recapitulating CNS tumor micro-environmental complexity will aid development of biologically-targeted agents. We present comprehensive characterization of tumor aggregates generated using the 3D Rotary Cell Culture System (RCCS).
  
  
  METHODS
  CNS cancer cell lines were grown in conventional 2D cultures and the RCCS and comparison with a cohort of 53 pediatric high grade gliomas conducted by genome wide gene expression and microRNA arrays, coupled with immunohistochemistry, ex vivo magnetic resonance spectroscopy and drug sensitivity evaluation using the histone deacetylase inhibitor, Vorinostat.
  
  
  RESULTS
  Macroscopic RCCS aggregates recapitulated the heterogeneous morphology of brain tumors with a distinct proliferating rim, necrotic core and oxygen tension gradient. Gene expression and microRNA analyses revealed significant differences with 3D expression intermediate to 2D cultures and primary brain tumors. Metabolic profiling revealed differential profiles, with an increase in tumor specific metabolites in 3D. To evaluate the potential of the RCCS as a drug testing tool, we determined the efficacy of Vorinostat against aggregates of U87 and KNS42 glioblastoma cells. Both lines demonstrated markedly reduced sensitivity when assaying in 3D culture conditions compared to classical 2D drug screen approaches.
  
  
  CONCLUSIONS
  Our comprehensive characterization demonstrates that 3D RCCS culture of high grade brain tumor cells has profound effects on the genetic, epigenetic and metabolic profiles of cultured cells, with these cells residing as an intermediate phenotype between that of 2D cultures and primary tumors. There is a discrepancy between 2D culture and tumor molecular profiles, and RCCS partially re-capitulates tissue specific features, allowing drug testing in a more relevant ex vivo system.
authors.affiliation: Children's Brain Tumour Research Centre, School of Clinical Sciences, University of Nottingham, Nottingham, United Kingdom.
authors.forename: Stuart J
authors.initials: SJ
authors.lastname: Smith
authors.forename: Martin
authors.initials: M
authors.lastname: Wilson
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Ward
authors.forename: Cheryl V
authors.initials: CV
authors.lastname: Rahman
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Peet
authors.forename: Donald C
authors.initials: DC
authors.lastname: Macarthur
authors.forename: Felicity R A J
authors.initials: FR
authors.lastname: Rose
authors.forename: Richard G
authors.initials: RG
authors.lastname: Grundy
authors.forename: Ruman
authors.initials: R
authors.lastname: Rahman
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology*; D001932:Brain Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*; D045744:Cell Line, Tumor; D049109:Cell Proliferation; D016000:Cluster Analysis; D019008:Drug Resistance, Neoplasm; D005109:Extracellular Matrix / Q000378:metabolism; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D056572:Histone Deacetylase Inhibitors / Q000494:pharmacology*; D006801:Humans; D055442:Metabolome; D010641:Phenotype; D061251:Primary Cell Culture; D018874:Spheroids, Cellular; D014407:Tumor Cells, Cultured; D059016:Tumor Microenvironment
chemical_list: D000970:Antineoplastic Agents; D056572:Histone Deacetylase Inhibitors