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Series GSE15477 Query DataSets for GSE15477
Status Public on Apr 15, 2009
Title Data integration from two microarray platforms identifies genetic inactivation of RIC8A in a breast cancer cell line
Organism Homo sapiens
Experiment type Expression profiling by array
Genome variation profiling by array
Summary Using array comparative genomic hybridization (aCGH), a large number of deleted genomic regions have been identified in human cancers. However, subsequent efforts to identify target genes selected for inactivation in these regions have often been challenging. We integrated here genome-wide copy number data with gene expression data and non-sense mediated mRNA decay rates in breast cancer cell lines to prioritize gene candidates that are likely to be tumour suppressor genes inactivated by bi-allelic genetic events. The candidates were sequenced to identify potential mutations. This integrated genomic approach led to the identification of RIC8A at 11p15 as a putative candidate target gene for the genomic deletion in the ZR-75-1 breast cancer cell line. We identified a truncating mutation in this cell line, leading to loss of expression and rapid decay of the transcript. We screened 127 breast cancers for RIC8A mutations, but did not find any pathogenic mutations. No promoter hypermethylation in these tumours was detected either. However, analysis of gene expression data from breast tumours identified a small group of aggressive tumours that displayed low levels of RIC8A transcripts. Real-time PCR analysis of 38 breast tumours showed a strong association between low RIC8A expression and the presence of TP53 mutations (P=0.006). We demonstrate a data integration strategy leading to the identification of RIC8A as a gene undergoing a classical double-hit genetic inactivation in a breast cancer cell line, as well as in vivo evidence of loss of RIC8A expression in a subgroup of aggressive TP53 mutant breast cancers.
Overall design Gene expression data: Samples GSM388181-GSM388198.
The experiment utilized six breast cancer cell lines: MDA-MB-468, MDA-MB-231, ZR-75-1, MCF7, BT-474 and T-47D, and three non-malignant cell lines: HMECs (non-malignant human mammary epithelial cells), IMR90 (normal lung fibroblasts) and WS1 (normal skin fibroblasts). All cell lines were obtained from American Type Culture Collection and grown in accordance with the distributor's instructions. Both malignant and non-malignant cell lines were treated with the translation inhibitor emetine dihydrochloride hydrate. For each cell line, parallel cell cultures were grown in 175 cm2 flasks until 70-80 % confluence. Half of the subconfluent cultures were treated with 100 μg ml-1 of emetine dihydrochloride hydrate while the other half were left as untreated controls.

Genome-wide copy number data: Samples GSM388211-GSM388216.
The experiment utilized six breast cancer cell lines; MDA-MB-468, MDA-MB-231, ZR-75-1, MCF7, BT-474 and T-47D. All cell lines were obtained from American Type Culture Collection and grown in accordance with the distributor's instructions. All samples were hybridized once on 44k Agilent Human Genome CGH microarrays according to manufacturers instructions. Genomic DNA pooled from healthy female donors was used as a reference in all hybridizations. DNA from cell line samples were labeled with Cy5 and DNA from reference were labeled with Cy3.
Contributor(s) Muggerud AA, Edgren H, Wolf M, Kleivi K, Dejeux E, Tost J, Sørlie T, Kallioniemi O
Citation(s) 19432969
Submission date Mar 31, 2009
Last update date Mar 25, 2019
Contact name Henrik Edgren
Organization name Institute for Molecular Medicine, University of Helsinki
Street address Tukholmankatu 8
City Helsinki
ZIP/Postal code 00290
Country Finland
Platforms (2)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL8355 Agilent-012700 Human Genome CGH Microarray 44A G4410A_beta (Feature Number version)
Samples (24)
GSM388181 BT474_untreated
GSM388182 BT474_emetine_10h
GSM388183 HMEC_untreated
BioProject PRJNA115919

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE15477_RAW.tar 202.8 Mb (http)(custom) TAR (of CEL, TXT)
Processed data included within Sample table

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