Glioma cells on the run – the migratory transcriptome of 10 human glioma cell lines

Tim Demuth^*¹ , Jessica L Rennert^*¹ , Dominique B Hoelzinger¹ , Linsey B Reavie¹ , Mitsutoshi Nakada¹^,2 , Christian Beaudry¹ , Satoko Nakada¹^,3 , Eric M Anderson¹ , Amanda N Henrichs¹ , Wendy S McDonough¹ , David Holz¹ , Anna Joy¹ , Richard Lin⁴ , Kuang H Pan⁴ , Chih J Lih⁴ , Stan N Cohen⁴ and Michael E Berens¹

¹Translational Genomics Research Institute, Phoenix, AZ 85004, USA

²Department of Neurosurgery, Kanazawa University, Ishikawa 920-0934, Japan

³Department of Human Pathology, Kanazawa University Graduate School of Medicine, Kanazawa, Ishikawa 920-0934, Japan

⁴Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA

author email corresponding author email* Contributed equally

BMC Genomics 2008, 9:54doi:10.1186/1471-2164-9-54


Published:	29 January 2008

Abstract

Background

Glioblastoma multiforme (GBM) is the most common primary intracranial tumor and despite recent advances in treatment regimens, prognosis for affected patients remains poor. Active cell migration and invasion of GBM cells ultimately lead to ubiquitous tumor recurrence and patient death.

To further understand the genetic mechanisms underlying the ability of glioma cells to migrate, we compared the matched transcriptional profiles of migratory and stationary populations of human glioma cells. Using a monolayer radial migration assay, motile and stationary cell populations from seven human long term glioma cell lines and three primary GBM cultures were isolated and prepared for expression analysis.

Results

Gene expression signatures of stationary and migratory populations across all cell lines were identified using a pattern recognition approach that integrates a priori knowledge with expression data. Principal component analysis (PCA) revealed two discriminating patterns between migrating and stationary glioma cells: i) global down-regulation and ii) global up-regulation profiles that were used in a proband-based rule function implemented in GABRIEL to find subsets of genes having similar expression patterns. Genes with up-regulation pattern in migrating glioma cells were found to be overexpressed in 75% of human GBM biopsy specimens compared to normal brain. A 22 gene signature capable of classifying glioma cultures based on their migration rate was developed. Fidelity of this discovery algorithm was assessed by validation of the invasion candidate gene, connective tissue growth factor (CTGF). siRNA mediated knockdown yielded reduced in vitro migration and ex vivo invasion; immunohistochemistry on glioma invasion tissue microarray confirmed up-regulation of CTGF in invasive glioma cells.

Conclusion

Gene expression profiling of migratory glioma cells induced to disperse in vitro affords discovery of genomic signatures; selected candidates were validated clinically at the transcriptional and translational levels as well as through functional assays thereby underscoring the fidelity of the discovery algorithm.