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Series GSE29244 Query DataSets for GSE29244
Status Public on Aug 01, 2011
Title Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines [SNP array data]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Several copy number altered regions (CNA) have been identified in the genome of cervical cancer, especially amplifications of 3q and 5p. However, the contribution of those alterations to cervical carcinogenesis is still a matter of debate, since genome-wide, there is a lack of correlation between CNAs and gene expression. In this study, we investigated whether the CNAs in cell lines (CaLo, CasKi, HeLa, SiHa), at a gene-by-gene level, are related to changes in gene expression. On average 19.2% of the whole genome of cell lines had CNA. However, only 2.4% consisted of minimal recurrent regions (MRR), common to all cell lines. Whereas 3q had just some sparse common gains (13%), 5p was entirely duplicated recurrently. Genome-wide, only 11% of genes located in CNAs changed gene expression. In contrast, the rate increased over 3 fold times in MRRs. Chr 5p was confirmed entirely amplified by FISH. In spite of this, at most 32.9% of the explored genes in 5p (n=202) were de-regulated. In 3q, the rate was just 11.8%. Even in 3q26, which had five MRRs and 38.7% of SNPs was gained recurrently, the rate rose slightly to 13.6% (10 out of 73). Interestingly, up to 16% of de-regulated genes in 5p and 80% in 3q26 were down-regulated, suggesting additional factors are involved in gene repression. The de-regulated genes in 3q and 5p were found in clusters, suggesting local chromatin factors may also influence gene expression. In regions amplified discontinuously, the rate of down-regulated genes rose steadily as the number of amplified SNPs increased (p<0.01, Spearman's correlation). This suggests partial gene amplification as a mechanism of silencing gene expression. Additional genes were identified up- or down-regulated in 5p and 3q, which could be involved in cervical carcinogenesis, especially implicated in apoptosis. Those include CLPTM1L, AHRR, PDCD6 and DAP in 5p and TNFSF10 and ECT2 in 3q. Overall, the gene expression and copy number profiles suggest other factors, like epigenetic or chromatin domains, may influence gene expression within the entirely amplified genome segments. Further studies are needed to elucidate how these mechanisms regulate gene expression.
 
Overall design Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cell lines or peripheral blood samples. Copy number analysis of Affymetrix 100K SNP arrays was performed for 4 cervical cancer cell lines. DNA from 38 healty women were used as references for copy number inference.
 
Contributor(s) Berumen J, Vazquez-Mena O
Citation(s) 22412903
Submission date May 12, 2011
Last update date Dec 22, 2017
Contact name Jaime Berumen
E-mail(s) jaimeberumen@hotmail.com
Phone +52(55)27892000
Organization name Universidad Nacional Autonoma de Mexico
Department Departamento de Medicina Experimental
Lab Unidad de Medicina Genómica
Street address Dr. Balmis #148 Col. Doctores
City Mexico City
ZIP/Postal code 06726
Country Mexico
 
Platforms (2)
GPL2004 [Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array
GPL2005 [Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array
Samples (84)
GSM723051 Cervical cancer cell line CaLo_Hind
GSM723052 Cervical cancer cell line CaLo_Xba
GSM723053 Cervical cancer cell line CaSki_Hind
This SubSeries is part of SuperSeries:
GSE29245 Amplified genes are not necessarily over expressed, they can be unchanged or down regulated in cervical cancer cell lines
Relations
BioProject PRJNA142945

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE29244_RAW.tar 1.1 Gb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file
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