Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells

BMC Cancer
Mohamed Ali-SeyedCarlos S Moreno

Abstract

We previously analyzed human embryonic kidney (HEK) cell lines for the effects that simian virus 40 (SV40) small tumor antigen (ST) has on gene expression using Affymetrix U133 GeneChips. To cross-validate and extend our initial findings, we sought to compare the expression profiles of these cell lines using an alternative microarray platform. We have analyzed matched cell lines with and without expression of SV40 ST using an Applied Biosystems (AB) microarray platform that uses single 60-mer oligonucleotides and single-color quantitative chemiluminescence for detection. While we were able to previously identify only 456 genes affected by ST with the Affymetrix platform, we identified 1927 individual genes with the AB platform. Additional technical replicates increased the number of identified genes to 3478 genes and confirmed the changes in 278 (61%) of our original set of 456 genes. Among the 3200 genes newly identified as affected by SV40 ST, we confirmed 20 by QRTPCR including several components of the Wnt, Notch, and Hedgehog signaling pathways, consistent with SV40 ST activation of these developmental pathways. While inhibitors of Notch activation had no effect on cell survival, cyclopamine had a potent killing effect on ...Continue Reading

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Citations

Jul 11, 2006·Nature Biotechnology·Winston Patrick KuoTor-Kristian Jenssen
Dec 22, 2016·The Journal of Cell Biology·Jennifer M DysonChristina A Mitchell
Apr 6, 2017·International Journal of Cancer. Journal International Du Cancer·Jill KnipsNicole Fischer
Mar 21, 2007·Environmental and Molecular Mutagenesis·Carole L Yauk, M Lynn Berndt
May 18, 2007·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Béatrice JacquelinMichaela C Müller-Trutwin

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Datasets Mentioned

BETA
E-MEXP-519
E-MEXP-156

Methods Mentioned

BETA
PCR
enzyme-linked immunosorbent assay

Software Mentioned

Affymetrix
Ingenuity Pathway Analysis
SAM
Significance Analysis of Microarrays ( SAM )
CONFAC
GenMAPP
Microarray Suite
Ingenuity Pathways Knowledgebase
MATCH
GOstat

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