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A portrait of cisplatin-induced transcriptional changes in mouse embryonic stem cells reveals a dominant p53-like response
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology, Oncology.
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2007 (English)In: Mutation research, ISSN 0027-5107, E-ISSN 1873-135X, Vol. 617, no 1-2, 58-70 p.Article in journal (Refereed) Published
Abstract [en]

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 24 h) and concentrations (1, 2, 5 and 10 μM). 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.

Place, publisher, year, edition, pages
2007. Vol. 617, no 1-2, 58-70 p.
Keyword [en]
Apoptosis, Differentiation, DNA damage, Microarrays
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-94915DOI: 10.1016/j.mrfmmm.2006.12.004ISI: 000245901000007PubMedID: 17327130OAI: oai:DiVA.org:uu-94915DiVA: diva2:168935
Available from: 2006-09-29 Created: 2006-09-29 Last updated: 2011-02-03Bibliographically approved
In thesis
1. Systematic Modular Approaches to Reveal DNA Damage Responses in Mammalian Cells
Open this publication in new window or tab >>Systematic Modular Approaches to Reveal DNA Damage Responses in Mammalian Cells
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cancer therapy operates by inflicting damage in malignant cells. The most lethal target is the genomic DNA. As a single double strand DNA break has the potential to kill the cell, mechanisms have evolved to detect and block propagation of the damage. Genes and their products function in a highly connected network-structure with ample cross-talk between different pathways. This interplay can be studied by genome-wide experiments, such as expression profiling. The aim of this thesis is to study the cellular effects of DNA damaging agents.

A theoretical framework is explored to improve understanding of expression profiling results. To analyse large datasets, computational methods were developed to model the data. Further, the response to DNA damage was investigated in different cellular systems. As late radiation toxicity is a severe limitation of radiotherapy of cancer patients, patients were enrolled in a study to search for a molecular signature to identify high-risk patients. Ex vivo irradiation of lymphocytes revealed a signature of functionally related gene sets that were capable to separate patients with regard to toxicity status.

The gene set analysis was also applied to a dataset where mouse embryonic stem cells had been exposed to various doses of cisplatin. At several time-points after administration of the drug, expression profiles were determined. In addition to the expected increase of genes related to apoptosis and cell cycle progression, damaged cells also seemed to have embarked upon a p53-dependent differentiation programme. Finally, in a study of cardiac rodent cells, the genotoxic treatment with irradiation was compared to the mechanical stress induced in heart tissue.

In conclusion, this thesis presents evidence for the advantage of using functionally related sets of genes in analysis and interpretation of genome-wide experiments. This strategy may improve clinical understanding of the effects of DNA damaging agents used for cancer therapeutics.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2006. 70 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine, ISSN 1651-6206 ; 176
Molecular biology, gene expression profiling, DNA damage, network, cancer, ionizing radiation, cisplatin, Molekylärbiologi
urn:nbn:se:uu:diva-7163 (URN)91-554-6667-2 (ISBN)
Public defence
2006-10-21, Auditorium Minus, Gustavianum, Akademigatan 3, Uppsala, 09:15
Available from: 2006-09-29 Created: 2006-09-29Bibliographically approved

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