To protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among... Show moreTo protect the genome, cells have evolved a diverse set of pathways designed to sense, signal, and repair multiple types of DNA damage. To assess the degree of coordination and crosstalk among these pathways, we systematically mapped changes in the cell's genetic network across a panel of different DNA-damaging agents, resulting in ~1,800,000 differential measurements. Each agent was associated with a distinct interaction pattern, which, unlike single-mutant phenotypes or gene expression data, has high statistical power to pinpoint the specific repair mechanisms at work. The agent-specific networks revealed roles for the histone acetyltranferase Rtt109 in the mutagenic bypass of DNA lesions and the neddylation machinery in cell-cycle regulation and genome stability, while the network induced by multiple agents implicates Irc21, an uncharacterized protein, in checkpoint control and DNA repair. Our multiconditional genetic interaction map provides a unique resource that identifies agent-specific and general DNA damage response pathways. Show less
Genetic alterations such as mutations, genomic rearrangements and aneuploidy, are commonly observed in tumors. To counteract this cells have multiple genome maintenance and surveillance systems to... Show moreGenetic alterations such as mutations, genomic rearrangements and aneuploidy, are commonly observed in tumors. To counteract this cells have multiple genome maintenance and surveillance systems to minimize the rate at which genomic alterations arise. The aim of the thesis is to gain understanding of processes and pathways that contribute to the maintenance of genome stability and to establish how defects in these processes and pathways abrogate the DNA damage response and consequently may promote genomic instability and development of cancer. The work described in this thesis addresses various aspects of the cellular response of mammalian cells to DNA damaging agents including changes in post translational modifications that occur after genotoxic stress. The role of poly-adenosyl ribose modification in nucleotide excision repair is investigated and found to be important for the recruitment of a chromatin remodeling protein and repair. Phosphoproteomic analysis identified changes in the global phosphorylation state of proteins following genotoxic stress. Key kinases responding to DNA damage are ATR and related kinases. A detailed study into the requirements for ATR activation after UV exposure indicates that at least two distinct modes of activation exist. Finally we describe the profound sensitivity of Cornelia de Lange Syndrome cells to DNA damage. Show less
DNA damage, mutations and genomic instability are established driving forces of cancer and other age-related diseases. Mutations in tumor suppressor genes and oncogenes are very frequently found in... Show moreDNA damage, mutations and genomic instability are established driving forces of cancer and other age-related diseases. Mutations in tumor suppressor genes and oncogenes are very frequently found in tumors and genomic instability is the most common enabling characteristic of cancer. Aging is also believed to be enabled, amongst others, by genomic instability. DNA repair pathways, like the nucleotide excision repair (NER) pathway and cell cycle control (e.g. p53-dependent) processes are therefore vital to organisms, since these processes counteract or prevent genomic instability, and are thought to underlie, when affected, aging and age-related diseases like cancer. To unravel the functions, mechanisms and pathways involved in the onset of aging and age-related diseases we have investigated several mouse models deficient in either DNA repair (NER) capacity (Chapter 3, 4), cell cycle control (p53) (Chapter 6) or both (Chapter 5), and compared this to a wild type situation (Chapter 2). The use of mouse models enabled us to investigate cancer and aging in a controlled environment, minimizing possible confounding factors. Additionally, the mouse models can be useful as an alternative tool to identify genotoxic and non-genotoxic carcinogens that can be harmful to the society and the environment (Chapter 5). Show less
During my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin... Show moreDuring my PhD project, I studied the role of several chromatin remodelers in the DNA double strand break (DSB) response. We discovered that both CHD4 and SMARCA5 are required for ubiquitin signaling through the E3 ubiquitin ligases RNF8 and RNF168, which is a central signaling event in the response to DSBs. Furthermore, we found that SMARCA5 actually interacts with RNF168. Both CHD4 and SMARCA5 act at the break site itself and modulate DSB repair. Additionally we found that the DSB repair protein Rad51 is essential for mouse development since Rad51C knock out mice were embryonic lethal. Show less
Cells in the human body have to deal with DNA damage daily, either caused by external or internal sources. The DDR is particularly strong in stem cells. Since these cells have a long life span and... Show moreCells in the human body have to deal with DNA damage daily, either caused by external or internal sources. The DDR is particularly strong in stem cells. Since these cells have a long life span and are essential for tissue homeostasis, tolerance to damaged DNA would lead to accumulation of mutations and malignant transformation. In addition, accumulation of damaged DNA would lead to loss of the stem cell pool and contribute to aging. In this thesis I investigated the role of the DNA damage response in the context of stem cells as well as cancer cells, from the response to different DNA damaging agents, to the importance of the interaction with the extracellular matrix in combination with the presence of oncogenes. In order to acquire a complete picture of the DNA damage response in mES cells, and therefore elucidate novel pathways involved in this particular response, we combined OMICS techniques such as Functional Genomics, Transcriptomics and Phosphoprotoemics, that once overlapped, allowed us to find novel pathways that where not previously described to be involved in the DNA damage response. Show less
In this thesis we attempt to provide a better understanding of the principles that underlie the spatial dynamic organization of the cell nucleus. Chapter 1 reviews the current status of knowledge... Show moreIn this thesis we attempt to provide a better understanding of the principles that underlie the spatial dynamic organization of the cell nucleus. Chapter 1 reviews the current status of knowledge about the structural and functional organization of the cell nucleus. In chapter 2, the development of a computer program is described that has been designed to track the 2D and 3D motion of objects in the nucleus of living cells. In chapter 3, evi-dence is provided for the existence of a nuclear matrix structure that is composed of lamin proteins, emerin and actin. By analyzing the dynamics of telomeres in nuclei of cells showing reduced levels of lamin expression, it is investigated whether telomeres anchor to an inner nuclear lamina structure. In chapter 4 the de novo formation of PML nuclear bodies is described. Using live cell imaging and immunocytochemistry it is dem-onstrated that telomeres play a role in the de novo formation of PML bodies. In chapter 5 it is investigated whether nuclear bodies are associated with chromatin in the cell nucleus. After treating cells with DNA alkylating agent MMS, the dynamics of PML bodies, Cajal bodies and speckles has been analyzed relative to chromatin in the 3D space of the cell nucleus Show less
The work presented in this thesis has focused on the role of Mitogen Activated Protein Kinases (MAPKs) and their major downstream targets, the AP-1 transcription factors, in particular the AP-1... Show moreThe work presented in this thesis has focused on the role of Mitogen Activated Protein Kinases (MAPKs) and their major downstream targets, the AP-1 transcription factors, in particular the AP-1 components ATF3, Fra1, c-Jun, ATF-2 and c-Fos. Chapter II provides information on the signaling pathways involved in the activation of ATF-2 and ATF3 in the response of primary human fibroblasts to ionizing radiation. In chapter III c-Jun and ATF3, the MAPK JNK and the MAPK-phosphatase MKP-1 are identified as important sensors of UV-induced-DNA damage in transcribed genes. Chapter IV shows that ATF3 acts as an antiapoptotic JNK target in T98G glioblastoma cells, whereas Fra1 seems to act as a proapoptotic effector of both JNK and ERK. In addition, it is shown that ATF3 and Fra1 have opposite effects on cisplatin-induced S phase arrest. Chapter V shows that Fra1 also can exhibit a pro-apoptotic function in UV-irradiated fibroblasts. Furthermore, this chapter reports an as yet unknown function of JNK: repression of the transactivating activity of c-Jun/Fos(- like) dimers, mediated via hyper-phosphorylation of the c-Jun transactivation domain. The data further emphasizes that c-Jun/Fos(-like) and c-Jun/ATF dimers and their respective target genes can exhibit opposite functions in DNA damage responses. Show less
Sunlight has many beneficial effects. However, from a biological point of view, solar UV radiation has also detrimental effects, especially at high doses of exposure. Because of its genotoxic... Show moreSunlight has many beneficial effects. However, from a biological point of view, solar UV radiation has also detrimental effects, especially at high doses of exposure. Because of its genotoxic properties, UV radiation plays an important role in the induction of skin cancer. In the last decennia, the incidence of skin cancer is rapidly increasing. This can partly be explained by an ageing population. However, the rise in skin cancer incidence appears to be primarily due to a change in human lifestyle in which sunbathing has become very popular. Our skin is continuously challenged by UV radiation, which may lead to irreversible damage. In order to withstand sustained physical, chemical and biological damage from the environment, among which UV radiation, the skin is continuously renewed. The regenerative capacity of skin is conferred by stem cells, which persist throughout the organism__s lifetime. Because of their long residency and unlimited capacity to replicate, stem cells might accumulate DNA damage and generate the multiple genetic lesions necessary for tumour development, despite efficient cellular defence mechanisms against DNA damage. Thus, stem cells may play an important role in carcinogenesis. The aim of this study is to investigate the role of stem cells in skin carcinogenesis. Show less
