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Series GSE6042 Query DataSets for GSE6042
Status Public on Feb 01, 2007
Title DNA copy numbers of malignant glioma in culture
Organism Homo sapiens
Experiment type Genome variation profiling by genome tiling array
Summary Therapeutic screening of potential anticancer agents relies on representative cancer models. In vitro cell culture models have been long questioned to be representative for human malignant glioma. Therefore, in the present study genomic profiles of both short-term (2 weeks; n=8) and long-term (6 and 12 weeks; n=3) primary cell cultures and spheroid cultures were compared with their parental malignant gliomas. Cancer genomic profiles were obtained by 6400 BAC array comparative genomic hybridization. In 7 out of 8 short-term primary cell cultures, the genomic profiles clustered further from their parental tumors than the spheroid cultures. In 4 out of 8 samples, the changes were substantial and included chromosomal regions associated with prognosis and therapeutic response. The average correlation coefficients between parental tumor profiles and spheroid profiles was 0.89 (range: 0.79 to 0.97), whereas those between parental tumors and cell cultures was 0.62 (range: 0.10 to 0.96). In 2 out of 3 primary cell cultures progressive genetic changes appeared at 6 and 12 weeks after initial preservation, whereas the spheroid cultures were genetically stable throughout. It is concluded that the cancer genomic profile of primary cell cultures from malignant glioma is inconsistent with the parental tumor’s profile already after 2 weeks with subsequent progressive genetic changes. Because malignant glioma spheroids are genetically stable, biological characteristics of the parental tumor are better reflected. This indicates that the spheroid model is better for therapeutic screening.
Keywords: comparative genomic hybridization
Overall design Two in vitro culture models (primary cell culture and organotypic spheroid culture) and their parental tumor were compared in whole-genome DNA copy number profile. Malignant glioma surgical specimens from 8 patients were divided in parental tumor (T), primary cell culture (C) and organotypic spheroid culture (S). After 2 weeks, genomic DNA was extracted from culture harvests. For 3 of 8 surgical specimens (patient 55, 58, 60) cultures were extended to 6 and 12 weeks to determine DNA copy number changes in time. Primary cell culture harvests at 2, 6 and 12 weeks were named C1, C2, C3 and organotypic spheroid cultures harvests at 2, 6 and 12 weeks were named S1, S2, S3.
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Submission date Oct 16, 2006
Last update date Mar 16, 2012
Contact name Philip C De Witt Hamer
Phone +31 20 5663542
Fax +31 20 5669590
Organization name Academic Medical Center Amsterdam
Department Neurosurgery
Street address PO Box 22660
City Amsterdam
ZIP/Postal code 1100 DD
Country Netherlands
Platforms (1)
GPL2843 VUMC MACF human 6K BAC v45
Samples (36)
GSM140130 parental malignant glioma, patient 32
GSM140131 primary cell culture after 2 weeks from malignant glioma, patient 32
GSM140132 organotypic spheroid culture after 2 weeks from malignant glioma, patient 32
BioProject PRJNA97775

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Supplementary file Size Download File type/resource
GSE6042_RAW.tar 47.2 Mb (http)(custom) TAR (of XLS)

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