Recapitulation of tumor heterogeneity and molecular signatures in a 3D brain cancer model with decreased sensitivity to histone deacetylase inhibition

PLoS One. 2012;7(12):e52335. doi: 10.1371/journal.pone.0052335. Epub 2012 Dec 18.

Abstract

Introduction: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / pharmacology*
  • Brain Neoplasms / genetics*
  • Brain Neoplasms / metabolism
  • Brain Neoplasms / pathology*
  • Cell Line, Tumor
  • Cell Proliferation
  • Cluster Analysis
  • Drug Resistance, Neoplasm*
  • Extracellular Matrix / metabolism
  • Gene Expression Profiling
  • Gene Expression Regulation, Neoplastic
  • Histone Deacetylase Inhibitors / pharmacology*
  • Humans
  • Metabolome
  • Phenotype
  • Primary Cell Culture
  • Spheroids, Cellular
  • Tumor Cells, Cultured
  • Tumor Microenvironment

Substances

  • Antineoplastic Agents
  • Histone Deacetylase Inhibitors

Grant support

This work was supported by the Samantha Dickson Brain Tumor Trust, the Gentleman’s Night Out Charity and the Joseph Foote Brain Tumour Trust. RR is a Nottingham Advanced Research Fellow and SJS is a National Institute for Health Research/UoN Clinical Fellow. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.