I have been interested in the molecular mechanisms of Haematopoietic malignant diseases such as leukaemia and lymphoma, especially those involving oncogenic tyrosine kinases. About 30 of the 90 tyrosine kinases in the human genome have been implicated in cancer (Blume-Jensen P, 2001). The oncogenic tyrosine kinases (OTKs), such as Bcr-Abl (product of chromosomal translocations of two genes bcr and abl) in Chronic Myelogenous Leukaemia, and Erythroblastic leukaemia viral oncogene homolog 2(Erb-B2) in mammary and other cancers, mediate their transforming effects via a diverse array of signalling pathways involved in DNA damage, cell survival and cell cycle regulation (Deutsch E, 2001; Skorski T, 2002; Kumar R, 1996). My work has been centred around the analysis of a mouse cancer model that is driven by an oncogenic tyrosine kinase – p56 Lck-F505 expressed on CD45 knock- out background (Baker M, 2000). The investigation of this mouse model has revealed that oncogenic inhibition of deamidation of the Bcl-xL survival protein plays a critical role in protecting thymocytes from DNA-damage induced apoptosis. Cells that would normally be eliminated due to accumulating DNA damage are instead preserved with an increasing load of double-stranded breaks, leading to genomic instability, chromosomal abnormalities and transformation. This work was published in Cancer Cell (An oncogenic tyrosine kinase inhibits DNA repair and DNA-damage-induced BclxL deamidation in T cell transformation. Zhao R, 2004). Following that I have tried to elucidate the different roles of the two deamidated species of Bcl-xL in apoptosis, and also the molecular mechanisms of DNA damage- induced Bcl-xL deamidation in order to understand the inhibition of Bcl-xL deamidation by oncogenic tyrosine kinases. Recently I have shown that Bcl-xL deamidation, whereby two critical Asn residues are converted to iso-Asp, cripples the ability of the protein to sequester pro-apoptotic BH3-only proteins such as Bim and p53- upregulated modulator of apoptosis (PUMA), thereby explaining its loss of pro-survival functionality. In vivo, DNA damage causes intracellular alkalinisation that is both necessary and sufficient to deamidate Bcl-xL, promoting apoptosis: no enzyme is necessary for this process. In pre-tumourigenic thymocytes alkalinisation is blocked, so preserving Bcl-xL in its pro-survival mode. Furthermore murine tumours are protected from genotoxic attack by native Bcl-xL, but enforced alkalinisation and consequent Bcl-xL deamidation promotes apoptosis. This part of work was published in Plos Biology (DNA damage-induced Bcl-xL deamidation is mediated by NHE-1 antiport regulated intracellular pH. Zhao R, 2007). Through collaboration with Prof AR Green’s research group at the Department of Haematology of the University of Cambridge, I have also analysed the Bcl-xL deamidation pathway in human myeloproliferative disorders, e.g. Polycythemia vera(PV) and Chronic Myelogenous Leukaemia (CML). We found that the oncogenic tyrosine kinases involved in these disorders, i.e. Jak2V617F and Bcr-Abl also inhibit the Bcl-xL deamidation pathway in DNA damage responses. These findings shed light on potential therapeutic application of the Bcl-xL deamidation pathway in human malignancies. This piece of work was recently published in the New England Journal of Medicine (Inhibition of the Bcl-xL deamidation pathway in myeloproliferative disorders. Zhao R, 2008). Overall the cited work has led to several important new insights into the molecular mechanisms involved in oncogenesis: first, that Bcl-xL deamidation is important in the cascade of events leading from DNA damage to apoptosis; second, that oncogenic tyrosine kinases inhibit these events in both the murine and human context; third, that up-regulation of the NHE-1 antiport and consequent intracellular alkalinisation are critical events in this DNA damage-induced cascade leading to apoptosis. In the process I have demonstrated the first in vivo mechanism for the deamidation of an internal protein Asn. Essentially, a completely new and unexpected signalling pathway has been uncovered that seems to pertain to all murine and human haematopoietic cell lineages that have been investigated so far.

Ataxia telangiectasia mutated (ATM) is a serine-threonine protein kinase and major regulator of the DNA damage response (DDR). One critical ATM target is protein phosphatase 2A (PP2A) known to regulate diverse cellular processes such as mitosis and cell growth as well as dephosphorylation of many proteins during the recovery from the DDR while returning the cell to normalcy. Interestingly, ATM and PP2A are known to form an auto-regulatory yin-yang kinase-phosphatase relationship. Herein, we show that the phosphorylation of the PP2A-Aα structural subunit at S401 by ATM results in nuclear export, which regulates the DDR at multiple levels and affects genomic stability and cell growth. We generated PP2A-Aα conditional knockout mouse embryonic fibroblasts expressing PP2A-Aα-WT, S401A (cannot be phosphorylated), or S401D phosphomimetic) transgenes by floxing out the endogenous PP2A-Aα alleles with Cre. The S401D mutant cells displayed increased ERK and AKT signaling, resulting in an enhanced growth rate. Phosphorylation of PP2A-Aα at S401 caused the dissociation of ATM with the holoenzyme, an effect that could be recapitulated with S401D. Additionally, the S401A and S401D mutants exhibited significantly more chromosomal aberrations and underwent increased mitotic catastrophe after radiation. Both the S401A and the S401D cells showed impaired DSB repair (Non-homologous end joining and Homologous recombination repair) and exhibited delayed DNA damage recovery, which was reflected in reduced radiation survival. Time-lapse video and cellular localization experiments showed that the PP2A-Aα subunit was exported to the cytoplasm after radiation possibly by CRM1, a nuclear export protein, in line with the very rapid pleiotropic effects seen. In conclusion, our study demonstrates using a genetically defined system that ATM phosphorylation of a single, critical amino acid S401 is essential for regulating DDR. To study how the interplay between ATM and PP2A affects DDR in the brain, we are in the process of generating a brain specific PP2A-Aα conditional knockout mouse. Loss of many DDR related proteins like ATM and PP2A can lead to severe neuropathological effects. This model will be helpful in dissecting the PP2A-Aα/ATM regulatory circuit in the brain in response to DDR.

Irradiamos amostras de DNA com luz UVA em diferentes condições para estudar os possíveis mecanismos envolvidos na indução de lesões de DNA por essa radiação. As lesões de DNA formadas após as irradiações foram quantificadas com enzimas de reparo de DNA que reconhecem e clivam os sítios contendo bases oxidadas e dímeros de pirimidina (CPDs). Complementando essas análises, foram realizados ensaios com anticorpos e HPLC-ED. NaCl e uma maior concentração de DNA são capazes de diminuir a indução de CPDs. Danos gerados por estresse oxidativo são inibidos na presença de azida de sódio e quelantes de metais, indicando o envolvimento de oxigênio singlete e reações de Fenton, na geração dessas lesões. Água deuterada e DNA mais concentrado aumentaram a indução de bases oxidadas. Quanto maior a quantidade de DNA irradiado, mais oxigênio singlete é formado, o que indica um possível mecanismo de fotossensibilização endógeno. / DNA samples were irradiated with UVA light in different conditions for studying the possible mechanisms involved in the induction of DNA lesions by this radiation. DNA lesions formed after irradiation were quantified with DNA repair enzymes, which recognize and cleave the sites containing oxidized bases and pyrimidine dimers (CPDs). Complementing these analyses, tests were performed with antibodies and HPLC-ED. NaCl and more concentrated DNA are capable of reducing the induction of CPDs. Damage caused by oxidative stress is inhibited in the presence of sodium azide and metal chelators, indicating the involvement of singlet oxygen and Fenton reactions, in the generation of these lesions. Deuterated water and more concentrated DNA increased the induction of oxidized bases. The bigger the amount of irradiated DNA, the more singlet oxygen is formed, which indicates a possible endogenous photosensitization mechanism.

Telomere dysfunction is one mechanism of cellular and tissue ageing. Dysfunctional telomeres in fibroblasts are recognised as DNA double-strand breaks (DSBs) and trigger the DNA damage pathway of senescence. However, telomere uncapping in normal human epidermal keratinocytes, via expression of the dominant negative mutant of the telomere repeat-binding factor 2 (TRF2!B!M), resulted in a senescent-like arrest without a significant DNA damage response (DDR). This suggests that either keratinocytes are unusually sensitive to telomere uncapping and the low DDR is sufficient to induce senescence or that dysfunctional telomeres may also be signalled through an alternative pathway. Subsequent analysis revealed genes HIST2H2BE, ICEBERG, S100A7 and HOPX as potential markers for telomere dysfunction-induced senescence (TDIS) since they were induced by telomere uncapping and seemed to be regulated by telomerase. The aim of this project was to assess the specificity of these candidate markers for TDIS and to select the most promising for use as a biomarker. To this end, keratinocytes were exposed to doses of ionising radiation, capable of generating transient or permanent damage to the DNA, or transduced with retroviral constructs expressing p14ARF, p16INK4a, p53 or TRF2!B!M and the gene expression levels of the candidates assessed after a recovery period or at the early stages of senescence. Whilst S100A7, HOPX or ICEBERG were not induced by a transient or persistent DDR or by p16INK4a, ICEBERG and HOPX were induced by p53 and p14ARF when these were ectopically expressed at higher levels. Thus, S100A7 seems to be the most specific early marker for telomere dysfunction in keratinocytes since it was selectively induced by telomere uncapping via expression of TRF2!B!M and not by DSBs or by over expression of p14ARF, p53 or p16INK4a. S100A7 may have the potential to identify cells with telomere dysfunction in human epithelia and body fluids.

Defects within the DNA damage response (DDR) pathways are common in human malignancies. This is especially true in high-grade serous ovarian cancer (HGSOC) where defects within the Homologous Recombination (HR) pathway may be present in up to 50% of tumours. Oncolytic adenovirus is a potential novel therapy for human malignancies. These viruses infect malignant cells and multiply selectively within them causing cell death and release of mature virions. Here, I have investigated the role of the DDR in determining the efficacy of the E1A-CR2 deleted adenovirus type 5 (Ad5) vector, dl922-947, in ovarian cancer. I show that infection with dl922-947 stimulates a robust DDR within the host cell, which the virus manipulates in order to ensure optimal viral replication. In a panel of HGSOC cell lines, the extent of overreplication of genomic DNA and the degree of genomic damage following infection with dl922-947 was shown to correlate closely with viral efficacy. Functional HR, however, promoted viral DNA replication and augmented overall anti-cancer efficacy. Mechanistically, both BRCA2 and RAD51 localised to viral replication centres within the infected cell nucleus. RAD51 co-localisation was also demonstrated in cells with defective HR and occurred independently of BRCA2. In addition, a direct interaction was identified between RAD51 and adenovirus E2 DNA binding protein. Using functional assays of HR competence, I show that Ad5 infection does not alter cellular ability to repair DNA double-strand break damage via HR. These data suggest that oncolytic adenoviral therapy may be most clinically relevant in tumours with intact HR function. Using a high-throughput siRNA DNA repair screen, potential novel targets have been identified that can increase the efficacy of dl922-947 (for example: NONO) and also result in increased resistance (RPA). These results highlight the complex interplay between adenovirus and host cell. Further understanding of these pathways is vital to increase efficacy, develop biomarkers and improve patient selection into clinical trials for these therapies.

Double-strand breaks (DSBs) are highly cytotoxic DNA lesions that are usually repaired by two major mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). HR is initiated by 5'-3' resection, generating 3' single stranded DNA tails coated by Replication protein A (RPA), which can be used in later steps for homology search and repair. The 5'-3' resection step is a critical determinant of repair pathway choice that commits cells to HR instead of NHEJ, and it's also required for DNA damage checkpoint activation. Studies in the budding yeast Saccharomyces cerevisiae have shown that the conserved Mre11-Rad50-Xrs2 (MRX) complex, together with Sae2, initiates end resection while more extensive processing of 5' strands requires the 5'-3' exonuclease Exo1, or the combined activities of the Sgs1 helicase and Dna2 endonuclease. In this thesis we will discuss the function of RPA and Sae2 based on our experimental observations. RPA is an essential eukaryotic single-stranded DNA binding protein with a central role in DNA metabolism. It has been shown in vitro that RPA directly participates in end resection by stimulating the Sgs1 helicase and Dna2 endonuclease. To investigate the role of RPA for end resection in vivo, we used a heat-inducible degron allele (td-RFA1) that allows rapid conditional depletion of RPA in Saccharomyces cerevisiae. Complete loss of RPA resulted in a defect in both the Exo1 and Sgs1-Dna2 extensive resection mechanisms, while resection initiation by MRX-Sae2 was unaffected. Interestingly, Dna2 was unable to localize to DSBs in the absence of RPA, whereas Exo1 localization was unaffected indicating that the role of RPA in the resection pathways is distinct. The short single-stranded DNA tails formed in the absence of RPA were unstable, represented by 3' strand loss and formation of foldback hairpin structures. Thus, RPA is required to generate ssDNA, and also to protect ssDNA from degradation and inappropriate annealing that could lead to genome rearrangements. While Mre11 possesses 3'-5' dsDNA exonuclease and ssDNA endonuclease activities, Sae2 was reported to activate its endonuclease activity, which initiates end resection. We identified mre11-P110L and four more mutants from a screen that bypass Sae2 for camptothecin (CPT) and MMS resistance. None of them restored endonuclease activity, neither did they improve resection. Persistent Mre11 foci and hyper-checkpoint signaling caused by sae2Δ upon DNA damage was suppressed by mre11-P110L. These findings demonstrate that the DNA damage sensitivity of sae2Δ is not caused by defective resection, but by failure to remove MRX from ends and switch off checkpoint.

DNA is continuously subjected to various types of damage during normal cellular metabolism. Among these, a DNA double-strand break (DSB) is one of the most cytotoxic lesions, and can lead to genomic instability or cell death if misrepaired or left unrepaired. The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex orchestrates the cellular response to DNA damage through its structural, enzymatic, and signaling roles. It senses DSBs and is essential for both of the two major repair mechanisms: non-homologous end joining (NHEJ) and homologous recombination (HR). In addition, the complex tethers DNA ends, activates Tel1/ATM kinase, resolves hairpin capped DNA ends and maintains telomere homeostasis. Although significant progress has been made in characterizing the complex, many questions regarding the precise mechanism of how this highly conserved, multifunctional complex manages its various activities in chromosome metabolism remain to be solved. The overarching focus of this thesis is to further expand our understanding of the molecular mechanism and regulation of the MRX complex. Specifically, the contributions of Xrs2, Tel1, and Mre11 3’-5’ dsDNA exonuclease in the multiple roles of the MRX complex are examined. Xrs2/Nbs1, the eukaryotic-specific component of the complex, is required for the nuclear transport of Mre11 and Rad50 and harbors several protein-interacting domains. In order to define the role of Xrs2 as a component of the MRX complex once inside the nucleus, we fused a nuclear localization signal (NLS) to the C terminus of Mre11 and assayed for complementation of xrs2Δ defects. We found that nuclear localization of Mre11 (Mre11-NLS) is able to bypass several functions of Xrs2, including DNA end resection, meiosis, hairpin resolution, and cellular resistance to clastogens. Using purified components, we showed that the MR complex has the equivalent activity to MRX in cleavage of protein-blocked DNA ends. Although Xrs2 physically interacts with Sae2, end resection in its absence remained Sae2 dependent in vivo and in vitro. MRE11-NLS was unable to rescue the xrs2Δ defects in Tel1 kinase signaling and NHEJ, consistent with the role of Xrs2 as a chaperone and adaptor protein coordinating interactions between the MR and other repair proteins. To further characterize the role of Xrs2 in Tel1 activation, we fused the Tel1 interaction domain of Xrs2 to Mre11-NLS (Mre11-NLS-TID). Mre11-NLS-TID was sufficient to restore telomere elongation and Tel1 signaling to Xrs2-deficient cells, indicating that Tel1 recruitment and activation are separate functions of the MRX complex. Unexpectedly, we found a role for Tel1 in stabilizing Mre11-DNA association independently of its kinase activity. This stabilization function becomes important for DNA damage resistance in the absence of Xrs2. Moreover, while nuclear-localized MR complex is sufficient for HR without Xrs2, MR is insufficient for DNA tethering, stalled replication fork stability, and suppression of chromosomal rearrangements. Enforcing Tel1 recruitment to the MR complex fully rescued these defects, highlighting the important roles for Xrs2 and Tel1 in stabilizing the MR complex to prevent replication fork collapse and genomic instability. Lastly, in order to decipher the functional significance of the Mre11 3’-5’ dsDNA exonuclease activity in DSB repair, mre11 mutant alleles reported to be proficient endonuclease and deficient exonuclease were analyzed in vivo and in vitro. Although we did not observe a clear separation of the nuclease activities in vitro, our genetic analysis of the mutant allele is consistent with the current two-stepped, bidirectional model of end resection.

DNA sequence information is constantly threatened by damage. In the clinic, intentional DNA damage is often used to treat cancer. Cisplatin, a first-line chemotherapy used to treat millions of patients, functions specifically by generating physical links within DNA strands, blocking DNA replication, and killing dividing cells. To maintain genome integrity, organisms have evolved the capacity to repair, respond, or otherwise resist change to the DNA sequence through a network of genetically encoded DNA damage tolerance pathways. In chapter 1, I present advances in experimental design and current progress for a systems genetics approach, using Saccharomyces cerevisiae, to reveal relationships between cisplatin tolerance pathways. Additionally, recent efforts to sequence thousands of cancer genomes have revealed recurrent genetic changes that cause overexpression of specific cisplatin tolerance genes. In chapter 2, I present a submitted manuscript that models overexpression of an essential cisplatin tolerance gene. This study uses a systems genetics approach to reveal the genetic pathways that are essential for tolerating this perturbation, which ultimately led to mechanistic insights for this gene. Convenient genome engineering in Saccharomyces has made this organism an ideal model to develop systems genetics concepts and approaches. In chapter 3, I present a published manuscript that demonstrates a new approach to disrupting genes by making site-specific nonsense mutations. Importantly, this approach does not require cytotoxic double-strand DNA breaks and is applicable to many model organisms for disrupting almost any gene, which may advance systems genetics into new model organisms. Systems genetics provides a framework for determining how DNA damage tolerance pathways act together to maintain cellular fitness and genome integrity. Such insights may one day help clinicians predict which cancers will respond to treatment, potentially sparing patients from unnecessary chemotherapy.

Severing the DNA double helix is a requisite step in the exchange of genetic material between homologous chromosomes in meiosis and between immunoglobulin domains during the generation of immune-receptor diversity. While these DNA transactions are essential for human fertility and the development of the immune system, misrepaired or unrepaired DNA double-strand breaks (DSBs) can lead to chromosome rearrangements or cell death. Indeed, ionizing radiation which generates DSBs in tumors is a cornerstone of cancer therapy. However, tumor cells can tolerate otherwise lethal levels of DNA damage by exploiting DNA repair pathways. Thus, discovering new strategies to selectively inhibit the repair of DSBs remains a major goal in the development of more effective cancer therapies. DSB repair may occur by multiple pathways, and the decision to use one pathway over another is influenced by cell cycle stage, the chromatin state, and the complexity of the inciting lesion. Mammalian cells primarily resolve DSBs by ligating the free ends together during a process termed “non-homologous end joining” (NHEJ). However, chemically modified or damaged DSB ends cannot be directly ligated by the NHEJ machinery. If NHEJ fails, DSBs may be nucleolytically cleaved to generate 3’ single-stranded DNA overhangs via a process called end resection. The resected DNA strands are poor substrates for NHEJ and instead search for homology in the genome to resynthesize the sequence surrounding the break site. This process is termed “homology-directed repair” (HDR). HDR is tightly coupled to cell cycle phase to ensure that resection occurs during late S and G2 when the ideal template, the sister chromatid, may be utilized. Following DNA damage, repair factors accumulate at DSB sites and form microscopically-detectable DNA repair foci. The dynamics of these foci may be observed by time-lapse microscopy making it possible to observe the behavior of breaks undergoing HDR and NHEJ. Interestingly, in yeast and mammalian cells, DNA motion is increased following DSB generation. DNA movements can lead to the clustering of DSBs into a common repair focus. DSB movements are intricately related to repair by HDR and require factors critical for resection initiation and downstream recombination. In contrast, DSBs undergoing NHEJ are relatively immobile. These observations suggest that the commitment of DSB repair to HDR regulates DSB movement and clustering; however, how DSB clustering might promote repair and whether active mechanisms drive this process remain relatively obscure. Recent studies have proposed roles for cytoskeletal proteins in genome organization and chromosomal dynamics. The Arp2/3 complex generates propulsive forces by nucleating a highly branched network of actin filaments. Genotoxic agents trigger actin polymerization in the nucleus. However, how DSB repair pathways might harness nuclear Arp2/3 machinery is unknown. Chapter 1 provides an overview of these pathways including the key steps of DSB repair, the regulation of actin nucleation, and the proteins involved in chromatin mobility. Chapter 1 provides context for the rest of the thesis in which I explore the contribution of nuclear actin polymerization to DSB repair. In Chapter 2, I detail our studies assessing the contribution of the Arp2/3 complex to DSB movement and clustering. Using Xenopus laevis cell-free extracts and mammalian cells, we show that actin nucleation machinery (WASP, Arp2/3, and actin) is recruited to damaged chromatin undergoing HDR. In this chapter, I also investigate how Arp2/3-driven DSB movements specifically promote the dynamics of HDR breaks, while Arp2/3 activity does not influence NHEJ breaks. Finally, I show that reduced DSB movement produces defects in DNA end processing and HDR efficiency, while the efficiency of end-joining is unaffected. I summarize all of these findings in Chapter 3 and discuss their implications for DNA repair, translocation formation, and clinical applications.

The ability of organisms to sense and respond to challenges to their genome integrity is key to survival. In particular, the ability to detect and respond to double-stranded DNA breaks (DSBs) is of fundamental importance as not only are DSBs potentially lethal as they can trigger apoptosis, but there is also the potential for the loss of genetic information. The response to DSBs is well conserved across Eukaryotes and comprises two stages: detection of the break and subsequent remedial action. The remedial action involves cell cycle arrest, DNA repair, and, if repair cannot be effected, possible apoptosis. Whilst many of the key components, especially in the initial detection of the break, are conserved there are also differences between plants and animals in some of the main components and their roles. In this thesis I have proposed an overall framework for the cellular response to DSBs in plants and have proposed two candidate genes, TCP20 and SOG1, as novel plant specific activators in this response. Their suitability has been addressed by considering their activation and their downstream targets. I have shown that TCP20 is necessary for growth arrest observed in shoot apical meristems after exposure to genotoxic stress. I have also shown that activation of one of the key targets of TCP20, CYCB1;1 requires TCP20 and that a key TCP20 binding motif in the promoter of CYCB1;1 is necessary for the up-regulation of CYCB1;1 in response to genotoxic stress. This motif is over-represented in the promoters of many of the genes involved in DNA damage repair, suggesting that TCP20 plays a role in the co-ordination of the cellular response to DSBs.