Abstract A103: High-throughput genomic and chemical screening in glioblastoma cell lines.
Authors: Ferrer-Luna Ruben , Ramkissoon Shakti , Cheah Jaime , Lamothe Rebecca , Schumacher Steven , Shamji Alykhan , Clemons Paul , Reardon David , Wen Patrick , Schreiber Stuart , Ligon Keith , Beroukhim Rameen 
Published: August 2014

Abstract
Introduction: Glioblastoma is the most malignant and deleterious brain tumor. Average patient survival is less than 14 months and there is no effective cure. Glioma cell lines, grown in serum, have been used to explore new therapeutic approaches, but they are poor representatives of primary tumors. At the genomic level, they exhibit many allelic imbalances and mutations that are likely associated with long-term passages and selective pressure to fit an artificial environment. At the gene expression level, they do not clearly recapitulate expression patterns seen in human glioblastomas. Finally, when these cell lines are injected in animal models tend to form “ball”-like masses rather than infiltrating tumors. Recently, it has been found that “neurosphere” cells derived from glioblastomas cultured in cytokines without serum more closely mirror the phenotype and genotype of primary tumors.
Experimental procedures: We are therefore pursuing a systematic analysis of genetic and non-genetic features that correlate with sensitivity to each of 480 small molecules in 40 neurosphere cell lines grown in the absence of serum. Here we present initial results from 12 neurospheres and nine traditional glioblastoma cell lines. We considered mutations, copy number alterations, and gene expression. In order to determine the representation of cancer stem cells in these populations, we also interrogated the cell surface markers CD44, CD15, and CD133 by flow citometry and the neural stem cell markers Nestin, Olig2, Sox2 and lineage differentiation markers GFAP, Tuj1, and O4 by Western blots.
Summary: We find that copy number profiles of the neurosphere lines resemble glioblastomas more closely than do established cells lines growing in serum. Gene expression profiles denoted that cell lines don't recapitulate accurately molecular signatures previously defined in GBMs. Neurospheres were classified mainly as Proneuronal or Mesenchymal subtypes, in change cell lines growing in serum displayed more heterogeneous profiles being difficult assign to previously defined subtypes. We also find that neurosphere lines are more sensitive to a variety of small molecules than are traditional cell lines. Among the neurospheres, those lines that grow in suspension or as sphereoids tend to exhibit heterogeneity in expression of CD44/CD133/CD15, whereas neurospheres that grow attached to the plate tend to homogenously express CD44 alone. The suspension lines are also more sensitive to a variety of small molecules.
Statement: These results indicate the feasibility of large-scale small molecule screening in neurosphere cell lines, and allowed us correlate with genomic and non-genomic determinants in a more accurate glioblastoma cell line model.
Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A103.
Citation Format: Ruben Ferrer-Luna, Shakti Ramkissoon, Jaime Cheah, Rebecca Lamothe, Steven Schumacher, Alykhan Shamji, Paul Clemons, David Reardon, Patrick Wen, Stuart Schreiber, Keith Ligon, Rameen Beroukhim. High-throughput genomic and chemical screening in glioblastoma cell lines. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A103.