Thesis (Ph. D.)--Miami University, Dept. of Microbiology, 2007. / Title from second page of PDF document. Includes bibliographical references (p. 91-102).

Maintenance of genomic integrity with high fidelity is of prime importance to any organism. An insult which may result in compromised genome integrity is prevented or its consequences are monitored by advanced cellular networks, collectively called the DNA damage response (DDR). Various DNA repair pathways, which are part of DDR, constantly correct the genome in the event of any undesirable change in the genetic material and prevent the transmission of any impairment to daughter cells. Non homologous DNA end joining (NHEJ) is the predominant DNA repair pathway associated with DDR in higher eukaryotes, correcting double-strand breaks (DSBs). Microhomology mediated end joining (MMEJ), an alternate mechanism to NHEJ also exists in cells, which is associated with erroneous joining of broken DNA, leading to mutagenesis. DDR is of paramount importance in cellular viability and therefore, any defects in DDR or the imbalance of repair pathways contribute to mutations, cellular transformations and various neurodegenerative and congenital abnormalities. Here, we investigate the DDR via NHEJ and MMEJ pathways during embryonic development in mice as well as in presence of an environmental pollutant, Endosulfan, in order to understand how physiological and exogenous factors condition the balance of repair pathways. Among various classes of pesticides known to cause side effects, organochlorine pesticides (OCPs) lead the list, possessing high transport potential, and a variety of toxic and untoward health effects. Endosulfan is a widely used organochlorine pesticide and is speculated to be detrimental to human health. However, very little is known about mechanism of its genotoxicity. Using in vivo and ex vivo model systems, we showed that exposure to Endosulfan induced reactive oxygen species (ROS) in a concentration dependent manner. Using an array of assays and equivalents of sub-lethal concentrations comparable to the detected level of Endosulfan in humans living in active areas of exposure, we demonstrated that ROS production by Endosulfan resulted in DNA double-strand breaks in mice, rats and human cells. In mice, the DNA damage was predominantly detected in type II pneumocytes of lung tissue; spermatogonial mother cells and primary spermatids of testes. Importantly, Endosulfan-induced DNA damage evoked DDR, which further resulted in elevated levels of classical NHEJ. However, sequence analyses of NHEJ junctions revealed that Endosulfan treatment resulted in extensive processing of broken DNA, culminating in increased and long junctional deletions, thereby favouring erroneous repair. We also find that exposure to Endosulfan led to significantly increased levels of MMEJ, which is a LIGASE III dependent, alternative, non classical repair pathway, encompassing long deletions and processing of DNA. Further, we show that the differential expression of proteins following exposure to Endosulfan correlated with activation of alternative DNA repair. At the physiological level, using mouse model system, we showed that exposure to Endosulfan affected physiology and cellular architecture of organs and tissues. Among all organs, damage to testes was extensive and it resulted in death of different testicular cell populations. We also found that the damage in testes resulted in qualitative and quantitative defects during spermatogenesis in a time dependent manner, increasing epididymal ROS levels and affecting sperm chromatin integrity. This further culminated in reduced number of epididymal sperms and actively motile sperms, which finally resulted in reduced fertility in male but not in female mice. Repair of DSBs is important for maintaining genomic integrity during the successful development of a fertilized egg into a whole organism. To date, the mechanism of DSB repair in post implantation embryos has been largely unknown except for the differential requirement of DNA repair genes in the course of development. These studies relied on null mutation analysis of animal phenotypes and therefore a quantitative understanding of repair pathways was absent. In the present study, using a cell free repair system derived from different embryonic stages of mice, we found that canonical NHEJ is predominant at 14.5 day of embryonic development. Interestingly, all types of DSBs tested were repaired by LIGASE IV/XRCC4 and Ku-dependent classical NHEJ. Characterization of end-joined junctions and expression studies further showed evidence for C-NHEJ. Strikingly, we observed non canonical end joining accompanied by DSB resection, dependent on microhomology and LIGASE III in 18.5-day embryos. Further we observed an elevated expression of CtIP, MRE11, and NBS1 at this stage, suggesting that it could act as a switch between classical and microhomology-mediated end joining at later stages of embryonic development. Keeping these observations in mind, we wondered if Endosulfan affected the differential regulation of DDR during development, similar to mice tissues. Upon analysing the effect of endosulfan on NHEJ/MMEJ at above mentioned stages of mouse embryonic development, we found that C-NHEJ efficiency remained low or unaltered while the efficiency of MMEJ was upregulated significantly, perturbing the repair balance during embryo development and hence facilitating mutagenic repair. Thus, our results establish the existence of both classical and non classical NHEJ pathways during the post implantation stages of mammalian embryonic development. Our studies also provide deeper insights into physiological and molecular events leading to male infertility upon Endosulfan exposure and its impact on impairing the differential regulation of DNA repair during embryonic development. Our findings suggest the plasticity of DNA repair pathways in physiological and pathological conditions and provide insights into mechanism of genome instability due to DNA repair imbalance, when exposed to environmental mutagens.

Arsenic is a universal environmental toxicant associated mostly with skin related diseases in people exposed to low doses over a long term. Low dose arsenic trioxide (ATO) with long exposure will lead to chronic exposure. Experiments were performed to provide new knowledge on the incompletely understood mechanisms of action of chronic low dose inorganic arsenic in keratinocytes. Cytotoxicity patterns of ATO on long-term cultures of HaCaT cells on collagen IV was studied over a time course of 14 days. DNA damage was also assessed. The percentages of viable cells after exposure were measured on Day 2, Day 5, Day 8, and Day 14. Statistical and visual analytics approaches were used for data analysis. In the result, a biphasic toxicity response was observed at a 5 μg/ml dose with cell viability peaking on Day 8 in both chronic and acute exposures. Furthermore, a low dose of 1 μg/ml ATO enhanced HaCaT keratinocyte proliferation but also caused DNA damage. Global gene expression study using microarray technique demonstrated differential expressions of genes in HaCaT cell exposed to 0.5 μg/ml dose of ATO up to 22 passages. Four of the up-regulated and 1 down-regulated genes were selected and confirmed with qRT-PCR technique. These include; Aldo-Keto Reductase family 1, member C3 (AKR1C3), Insulin Growth Factor-Like family member 1 (IGFL1), Interleukin 1 Receptor, type 2 (IL1R2) and Tumour Necrosis Factor [ligand] Super-Family, member 18 (TNFSF18), and down-regulated Regulator of G-protein Signalling 2 (RGS2). The decline in growth inhibiting gene (RGS2) and increase in AKR1C3 may be the contributory path to chronic inflammation leading to metaplasia. This pathway is proposed to be a mechanism leading to carcinogenesis in skin keratinocytes. The observed over expression of IGFL1 may be a means of triggering carcinogenesis in HaCaT keratinocytes. In conclusion, it was established that at very low doses, arsenic is genotoxic and induces aberrations in gene expression though it may appear to enhance cell proliferation. The expression of two genes encoding membrane proteins IL1R2 and TNFSF18 may serve as possible biomarkers of skin keratinocytes intoxication due to arsenic exposure. This research provides insights into previously unknown gene markers that may explain the mechanisms of arsenic-induced dermal disorders including skin cancer / Environmental Sciences / D. Phil. (Environmental science)

A specific feature of ionising radiation is the formation of clustered DNA damage, where two or more lesions form within one to two helical turns of the DNA induced by a single radiation track. The complexity of ionising radiation-induced DNA damage increases with increasing ionisation density and it has been shown that complex DNA damage has reduced efficiency of repairability. In mammalian cells, base excision repair (BER) is the predominant pathway for the repair of non-DSB clustered DNA lesions and is split into two sub-pathways known as short patch (SP) BER and long patch (LP) BER. SP-BER is the predominant pathway, especially in the repair of isolated DNA lesions. However, LP-BER is thought to play a greater role in the repair of radiation-induced clustered lesions. In this study, cell lines were generated stably expressing the fluorescently tagged BER proteins, XRCC1-YFP (marker for SP-BER) or FEN1-GFP (marker for LP-BER). The recruitment and loss of XRCC1-YFP and FEN1-GFP to sites of DNA damage induced by both ultrasoft X-ray (USX), a form of low linear energy transfer (LET) radiation, and near infrared (NIR) laser microbeam irradiation (‘mimic’ high LET radiation) was visualised in real-time and the decay kinetics of the fluorescently-tagged proteins determined. The half-life of fluorescence decay of FEN1-GFP following USX irradiation was longer than that of XRCC1-YFP, indicating that LP-BER is a slower process than SP-BER. Additionally, the fluorescence decay of XRCC1-YFP after NIR laser microbeam irradiation was fitted by bi-exponential decays with a fast component and a slow component, reflecting the involvement of XRCC1 in the repair of different types of DNA damage. In contrast to USX irradiation, where the XRCC1-YFP fluorescence decay reached background levels by 20 min, XRCC1-YFP still persisted at some of the NIR laser induced DNA damage sites even after 4 hours. This is consistent with the fact that the laser induces more complex damage that presents a major challenge to the repair proteins, persisting for much longer than the simple damage caused by low LET USX irradiation. Persistent, unrepaired DNA damage can potentially lead to mutations and replication-induced DSBs if it persists into S-phase. PARP1 inhibition reduced the recruitment of XRCC1 to DNA damage sites. However, a considerable amount of XRCC1 was still detected at the DNA damage sites, leading to the conclusion that there is a subset of DNA damage that requires XRCC1 but not PARP1 for repair. Understanding how clustered damage is repaired by the BER pathway can aid the design of future therapies which can be used in combination with radiotherapy to enhance the radiosensitisation effect. Knockdown of FEN1 was investigated and found to radiosensitise A549 (adenocarcinoma) cells, possibly as a result of an excess of unrepaired radiation-induced lesions requiring LP-BER for repair, although FEN1 knockdown alone induced cell death in non-cancerous BEAS-2B cells.

Inherited mutations in the BRCA2 gene predispose individuals to the development of breast and ovarian cancers. The BRCA2 protein plays a fundamental role in the repair of DNA double strand breaks by homologous recombination (HR). BRCA2 mediates the recruitment of the RAD51 recombinase to DNA damage sites, which in turn promotes homologous pairing and strand exchange during HR. It has been reported that increased BRCA2 mRNA levels correlate with poor cancer prognosis, and recently it has been shown that increased levels of BRCA2 suppress HR. As HR is regulated through the cell cycle and can only be employed during S and G2 phases of the cell cycle, in this study, the cell cycle-dependent regulation of BRCA2, as a key player of HR, was investigated. In this study I report that BRCA2 stability is regulated by the ubiquitin-proteasome system (UPS), which has become increasingly evident as an important regulator of DNA repair. In line with this, I found that BRCA2 can be ubiquitylated in vivo and that it interacts with proteins of the UPS. Interestingly, I observed that BRCA2 levels and its ubiquitylation status change during the cell cycle. Using a siRNA-based approach, I identified a candidate E3 ubiquitin ligase, the SCF^FBXW7 complex, which is also a known major cell cycle regulator. siRNA-mediated knockdown of FBXW7 led to stabilization of BRCA2 and overexpression of FBXW7 resulted in BRCA2 ubiquitylation in vivo. Furthermore, I have refined the regions that the SCF^FBXW7 interacts with on BRCA2, which likely occurs in a phosphorylation-dependent manner. Taken together, these observations suggest that BRCA2 stability is regulated by the UPS in a cell cycle-dependent manner, which may be an important regulatory mechanism for BRCA2 function.

DNA damage in spermatozoa is a crucial contributor to spontaneous abortion, severe genetic disease in the offspring and infertility. The chromatin of spermatozoa is highly compacted, transcriptionally and translationally silent, hence lacking DNA damage response (DDR). DDR foci follow within seconds after a DNA double strand break (DSB) and correlate to an abortive topoisomerase-IIb activity during spermiogenesis. When comparing the DSB frequencies at the two most fragile genomic loci (fragile sites FRA3B, FRA16D) in human and murine spermatozoa with lymphocytes, significantly increased DSB levels were detected in spermatozoa in both species. This corroborates that spermatozoa are more prone to DSBs than somatic cells. When comparing the DSB frequencies at FRA3B/FRA16D in spermatozoa of smokers with non-smokers, two-fold increases were found, probably caused by cigarette smoke components triggering abortive topoisomerase-IIβ activity. The phosphorylated DDR proteins H2AX and ATM were identified in human spermatozoa and murine spermatids using multicolour immunostaining with laser-scanning confocal microscopy (LSCM) and Western blots. Based on significantly increased DDR foci in spermatozoa of smoking men, but lacking DDR foci in response to in vitro challenge with H2O2, an abortive topoisomerase-IIb activity is the likely cause of DDR foci in spermatozoa. As DDR foci are susceptible to cigarette smoke, they can potentially be used as a novel biomarker. When comparing paternal spermatozoa, and lymphocytes as well as maternal and cord lymphocytes from 39 families for DSBs (via high-throughput LSCM pH2AX detection) and DNA fragmentation (Comet assay), significant increases were found in newborns of mothers exposed to environmental tobacco smoke and smoking fathers. When challenging lymphocytes and spermatozoa to different genotoxicants, significantly increased DNA damage in newborns compared to adults was found. This confirms an exceptional vulnerability in newborns, believed to cause increased susceptibly to disease in later life, including cancer.

Apurinic/apyrimidinic endonuclease 1 (APE1) is a key DNA repair factor involved in the DNA base excision repair (BER) pathway that is required for the maintenance of genome stability. In this pathway, APE1 cleaves DNA at an abasic site to generate a DNA single strand break, allowing for repair completion by a DNA polymerase and a DNA ligase. High levels of APE1 have been observed in multiple cancer types however it is not understood if this contributes to cancer onset and development. What is known is that these cancers tend to display increased resistance to DNA damaging treatments and APE1 is therefore considered a key target for inhibition in the treatment of APE1-overexpressing cancers. Considering the relevance of modulating APE1 levels in disease and cancer treatment, very little is known about how cellular APE1 levels are regulated. Our lab has previously shown that the levels of the BER factors Pol β, XRCC1 and DNA Lig IIIα are regulated by ubiquitylation-mediated proteasomal degradation. The aim of this doctoral thesis was therefore to determine if ubiquitylation also regulates APE1 stability in cells. I present evidence that APE1 is ubiquitylated in cells and have identified the UBR3 E3 ligase that is responsible for this activity. Using mouse embryonic fibroblasts generated from Ubr3 knockout mice, I demonstrate that UBR3 regulates APE1 cellular levels. I furthermore show that a loss of cellular UBR3 leads to the formation of DNA double strand breaks and genome instability.

Radiation-induced damage to the genomic DNA of cells may lead to errors in transcription and replication and, if not repaired correctly, these may result in mutations, genomic instability and cell death. Laser microbeams have generally been used by many research groups to investigate the real-time dynamics of protein recruitment in response to DNA insults in mammalian cells; however, such irradiations induce a plethora of DNA damage (including UV base damage, base damage, SSBs and DSBs and complex damage). A novel experimental setup has been designed capable of following the dynamics of protein recruitment in response to DNA insults in mammalian cells shortly following submicrosecond- pulsed electron irradiation of living mammalian cells, not possible using conventional irradiation techniques. This arrangement was developed based on a 6 MeV electron pulse linear accelerator, to deliver sparsely ionising radiation, coupled to an automated, time-lapse inverted epifluorescence microscope imaging system. An integrated robotic system contained within a physiological environment of 37°C and 5% CO₂ was used to transfer remotely and repetitively custom-designed cell dishes containing the mammalian cells between irradiation and imaging locations. Following the development of the linear accelerator and associated imaging devices, preliminary ‘proof-of-principle’ investigations were carried out using living HT1080 mammalian cells containing YFP-tagged 53BP1, an established biomarker of DSB, to follow the recruitment and loss of 53BP1 to sites of radiation-induced DNA damage in real-time. This novel experimental setup has allowed for the first time observations of the appearance and disappearance of radiation-induced foci in the same cell population at very early times. These single-foci studies have provided evidence for the formation of not only promptly formed DSBs but also late appearing DNA damage signalled by 53BP1. These data highlight different classes of DSBs formed in response radiation damage. Additionally, the role of cell cycle on the repair kinetics was undertaken using HT1080- 53BP1-YFP cells which also express Geminin-mCherry under appropriate selection. Geminin is increasingly expressed from early S-phase onwards, but is degraded following mitosis. Geminin-associated fluorescence can be used as a marker of progression through the cell cycle. 53BP1 repair kinetics were characterised in response to radiation damage in combination with ATM and PARP inhibitors. These studies provided supporting evidence for the existence of different classes of DSBs, potentially assigned to radiation-induced replication breaks and DSBs formed by enzymatic conversion of clustered damage. These preliminary ‘proof-of-principle’ findings using DNA damage repair as an example, emphasize the use of this novel technology to explore the dynamics of numerous other biochemical processes in living cells in real-time with the knowledge of being able to quantify the range of damage induced by IR coupled with accurate dosimetry. The knowledge obtained may be used to identify potential biological targets coupled with drug discovery for translation into adjuncts for radiotherapy.

Hypoxia (low physiological O₂ levels) is a characteristic of solid tumours. It not only alters the chemical microenvironment of a tumour but initiates a number of mechanisms which enable cells to cope and thrive under these conditions, resulting in therapy-resistant and aggressive tumours. The replication stress induced by severe hypoxia activates a DNA damage response which involves the kinases ATR and Chk1. Moreover, periods of hypoxia are often followed by reoxygenation, which induces DNA damage. Chk1 inhibitors have been used to potentiate chemotherapy with cytotoxic agents and have recently been proposed as single agents in tumours with high levels of replication stress. However, inhibition of Chk1 also affects normal DNA replication, cell cycle progression and DNA repair. The herein presented study chose known inhibitors of Chk1 and, with methods of synthetic organic chemistry, modified them into agents to selectively target hypoxic cells. Three different Chk1 inhibitors were selected and bioreductive analogues synthesised which were evaluated in chemical, biochemical and cellular assays. We found a convenient route to access a precursor of the bioreductive 2-nitroimidazole group and established a three-step protocol for the testing of bioreductive drugs. This protocol allows us to determine whether a bioreductive drug undergoes reduction and prodrug activation. In addition, bioreductive Chk1 inhibitors were shown to induce DNA damage and cellular toxicity in a hypoxia-selective fashion. While reduction of the prodrugs occurred in all three cases, fragmentation was always the rate-limiting step. We propose that the use of bioreductive Chk1 inhibitors is a promising strategy to target the most therapy-resistant tumour fraction while sparing normal tissue.

Aim: Cisplatin is the first platinum drug that shows promising anti-tumor effect clinically. Oxaliplatin, a third-generation platinum drug that incorporates a diaminocyclohexane (DACH) structural entity, can overcome cisplatin resistance. R,R-5, a novel platinum compound that integrates the DACH entity with a demethylcantharidin (DMC) component that is derived from a traditional Chinese medicine (TCM) , can also overcome cisplatin resistance. The principal objectives of this study was to investigate in detail, the effect of these compounds at the antephase and G2 checkpoints of the cell cycle, and to establish the relationship (if any) between different structural entities with checkpoint activation. The ultimate aim of the study was to ascertain the potential for the development of novel checkpoint abrogators as anti-tumor agents. / Background: A common procedure in current cancer chemotherapy is to induce genomic stress in cancer cells, leading to irreparable DNA damage and eventually cell death. However, there are several DNA repair mechanisms in cancer cells to maintain genomic stability, which require cell cycle checkpoints to stop cell proliferation for DNA damage repair, thereby avoiding errors in cellular events like DNA replication, transcription and mitosis. Among these cell cycle checkpoints, antephase and G2 checkpoints are two gate checkpoints for mitosis. Abrogation of G2 checkpoint has been reported to give rise to synergistic cytotoxic effect with DNA damaging agents, representing a means of circumventing drug resistance in chemotherapy. / Conclusions: Acute stress to cisplatin can activate the MMR/c-Abl/MEKK1/p38MAPK pathway, leading to the activation of antephase checkpoint, and stop cells from entering mitosis immediately. DACH-containing platinum compound oxaliplatin fails to activate this antephase checkpoint. However, both cisplatin and oxaliplatin can activate the G2 checkpoint, which can be abrogated by DMC. In contrast, RR-5 can bypass both the antephase and G2 checkpoints. In summary, novel TCM-platinum compound R,R-5 can bypass mitotic DNA damage checkpoints in cancer cells and thus has the potential for further development as an anti-cancer drug. / Methods: Microarray analysis was used to detect gene transcription profiles after drug treatments. The activation of mitotic checkpoints was inspected by counting mitotic cells and utilizing flow cytometry. Using Western blotting, the activation of certain key players in the antephase and G2 checkpoint was revealed. MTT assays were performed to show the outcome of checkpoint activation. / Results: In HCT116 cells, 35 genes that facilitate G2/M transition were found to be up-regulated after R,R-5 treatment compared with oxaliplatin in the microarray analysis, implying the bypass of mitotic checkpoints by R,R-5 rather than oxaliplatin. Acute stress (2 hour) of cisplatin activated the antephase checkpoint, resulting in a rapid decrease in mitotic index and phosphorylation of histone H1, which avoided mitotic catastrophe and promoted cell survival in HeLa cells. Further experiments demonstrated that this antephase checkpoint could be abrogated by c-Abl and p38MAPK inhibitors, or siRNAs against c-Abl or MEKK1, suggesting that this checkpoint may be controlled by an MMR/c-Abl/MEKK1/p38MAPK pathway. In contrast, oxaliplatin and R,R-5 did not activate this antephase checkpoint. Moreover, after 24 hour oxaliplatin treatment in HeLa cells, the mitotic index and CDK1 activity were decreased, which could be restored by concomitant treatment with ATM/ATR inhibitor and DMC. This indicated the activation of G2 checkpoint by oxaliplatin and implied that DMC can abrogate oxaliplatin-activated G2 checkpoint by restoring CDK1 activity. Cisplatin could also activate G2 checkpoint, whereas R,R-5 apparently bypassed this G2 checkpoint. / Guan, Huaji. / Adviser: Vincent Hon Leung Lee. / Source: Dissertation Abstracts International, Volume: 72-04, Section: B, page: . / Thesis (Ph.D.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 212-249). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Electronic reproduction. Ann Arbor, MI : ProQuest Information and Learning Company, [200-] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Abstract also in Chinese.