Transcriptomics

Dataset Information

0

Validation study: Response-predictive gene expression profiling of glioma progenitor cells in vitro


ABSTRACT: Background. In a previous publication we introduced a novel approach to identify genes that hold predictive information about treatment outcome. A linear regression model was fitted by using the least angle regression algorithm (LARS) with the expression profiles of a construction set of 18 glioma progenitor cells enhanced for brain tumor initiating cells (BTIC) before and after in vitro treatment with the tyrosine kinase inhibitor Sunitinib. Profiles from treated progenitor cells allowed predicting therapy-induced impairment of proliferation in vitro. Prediction performance was validated in leave one out cross validation. Methods. In this study, we used an additional validation set of 18 serum-free short-term treated in vitro cell cultures to test the predictive properties of the signature in an independent cohort. We assessed proliferation rates together with transcriptome-wide expression profiles after Sunitinib treatment of each individual cell culture, following the methods of the previous publication. Results. We confirmed treatment-induced expression changes in our validation set, but our signature failed to predict proliferation inhibition. Conclusion. Although the gene signature published from our construction set exhibited good prediction accuracy in cross validation, we were not able to validate the signature in an independent validation data set. Reasons could be regression to the mean, the moderate numbers of samples, or too low differences in the response to proliferation inhibition. At this stage and based on the presented results, we conclude that the signature does not warrant further developmental steps towards clinical application. 40 samples; 18 brain tumor initiating cells (BTICs); 2 treatment conditions: 1 µM Sunitinib or 0.00025% DMSO with supplementation of VEGF and PDGF-AB for 6 hours

ORGANISM(S): Homo sapiens  

SUBMITTER: Peter Hau   Sylvia Moeckel  Anja-Katrin Bosserhoff  Rainer Spang 

PROVIDER: E-GEOD-76990 | ArrayExpress | 2016-02-21

SECONDARY ACCESSION(S): GSE76990PRJNA309187

REPOSITORIES: GEO, ArrayExpress

Similar Datasets

2014-10-07 | E-GEOD-51305 | ArrayExpress
| GSE70970 | GEO
| GSE54323 | GEO
2010-06-05 | E-GEOD-2591 | ArrayExpress
2015-04-14 | E-GEOD-54323 | ArrayExpress
2015-05-11 | E-GEOD-68629 | ArrayExpress
2012-04-03 | E-GEOD-30258 | ArrayExpress
| GSE93291 | GEO
2011-02-15 | GSE27290 | GEO
2011-01-20 | GSE26712 | GEO