title: Cross-platform expression profiling demonstrates that SV40 small tumor antigen activates Notch, Hedgehog, and Wnt signaling in human cells.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  RESULTS
  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 cells expressing SV40 ST.
  
  
  CONCLUSIONS
  These data show that SV40 ST expression alters cell survival pathways to sensitize cells to the killing effect of Hedgehog pathway inhibitors.
authors.affiliation: Department of Pathology & Laboratory Medicine, Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, USA. mseyedm@emory.edu
authors.forename: Mohamed
authors.initials: M
authors.lastname: Ali-Seyed
authors.forename: Noelani
authors.initials: N
authors.lastname: Laycock
authors.forename: Suresh
authors.initials: S
authors.lastname: Karanam
authors.forename: Wenming
authors.initials: W
authors.lastname: Xiao
authors.forename: Eric T
authors.initials: ET
authors.lastname: Blair
authors.forename: Carlos S
authors.initials: CS
authors.lastname: Moreno
mesh_terms: D000952:Antigens, Polyomavirus Transforming / Q000378:metabolism*; D002460:Cell Line; D002470:Cell Survival; D004791:Enzyme Inhibitors / Q000494:pharmacology; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D053823:Hedgehog Proteins; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016133:Polymerase Chain Reaction / Q000379:methods; D051880:Receptors, Notch / Q000037:antagonists & inhibitors / Q000378:metabolism*; D015203:Reproducibility of Results; D015398:Signal Transduction; D015534:Trans-Activators / Q000037:antagonists & inhibitors / Q000378:metabolism*; D014704:Veratrum Alkaloids / Q000494:pharmacology; D051153:Wnt Proteins / Q000378:metabolism*
chemical_list: D000952:Antigens, Polyomavirus Transforming; D004791:Enzyme Inhibitors; D053823:Hedgehog Proteins; D051880:Receptors, Notch; D015534:Trans-Activators; D014704:Veratrum Alkaloids; D051153:Wnt Proteins; C000541:cyclopamine