title: A portrait of cisplatin-induced transcriptional changes in mouse embryonic stem cells reveals a dominant p53-like response.
abstract: Accumulation of damage in undifferentiated cells may threaten homeostasis and regenerative capacity. Remarkably, p53 has been suggested to be transcriptionally inactive in these cells. To gain insight in the kinetics and interplay of the predominant transcriptional responses of DNA damage signalling pathways in undifferentiated cells, mouse embryonic stem cells were exposed to cisplatin at four different time points (2, 4, 8 and 24h) and concentrations (1, 2, 5 and 10 microM). RNA was isolated and subjected to genome-wide expression profiling. Up to one fourth of the tested genes could be identified as being differentially expressed (false discovery rate=10%) after the cisplatin treatment. Clustering of the expression changes showed a strong time dependency. To investigate the relationship between affected genes, a gene set analysis method was used. Functionally related gene sets were defined using gene ontologies or transcription factor binding sites and were tested for overrepresentation within the differentially expressed genes. A variety of gene sets were clearly enriched among which 'apoptosis' and 'cell cycle' were the most pronounced. Furthermore, there was a strong enrichment of genes with a p53-binding motif. The involvement of the 'cell cycle' and 'apoptosis' gene sets in the cisplatin response was detected at concentrations and time points where the respective biological assays were still negative. The results reveal novel insights into the mechanisms which maintain the genomic integrity in undifferentiated cells. Additionally the results illustrate that gene set analysis of genome-wide expression changes provides a sensitive instrument to detect cellular stress responses to DNA damage.
authors.affiliation: Department of Toxicogenetics, LUMC, Leiden, The Netherlands.
authors.forename: Jacqueline J C M
authors.initials: JJ
authors.lastname: Kruse
authors.forename: J Peter
authors.initials: JP
authors.lastname: Svensson
authors.forename: Merei
authors.initials: M
authors.lastname: Huigsloot
authors.forename: Micheline
authors.initials: M
authors.lastname: Giphart-Gassler
authors.forename: Willem G E J
authors.initials: WG
authors.lastname: Schoonen
authors.forename: Jan E M
authors.initials: JE
authors.lastname: Polman
authors.forename: G
authors.initials: G
authors.lastname: Jean Horbach
authors.forename: Bob
authors.initials: B
authors.lastname: van de Water
authors.forename: Harry
authors.initials: H
authors.lastname: Vrieling
mesh_terms: D000818:Animals; D000970:Antineoplastic Agents / Q000494:pharmacology*; D017209:Apoptosis / Q000187:drug effects; D020169:Caspases / Q000378:metabolism; D002454:Cell Differentiation; D002478:Cells, Cultured; D002945:Cisplatin / Q000494:pharmacology*; D053595:Embryonic Stem Cells / Q000187:drug effects / Q000378:metabolism*; D005347:Fibroblasts / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000187:drug effects*; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic / Q000187:drug effects*; D016159:Tumor Suppressor Protein p53 / Q000494:pharmacology*
chemical_list: D000970:Antineoplastic Agents; D016159:Tumor Suppressor Protein p53; D020169:Caspases; D002945:Cisplatin