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<p>Mitochondria are responsible for producing the vast majority of cellular ATP, and are therefore critical to organismal health [1]. They contain thir own genomes (mtDNA) which encode 13 proteins that are all subunits of the mitochondrial respiratory chain (MRC) and are essential for oxidative phosphorylation [2]. mtDNA is present in multiple copies per cell, usually between 103 and 104 , though this number is reduced during certain developmental stages [3, 4]. The health of the mitochondrial genome is also important to the health of the organism, as mutations in mtDNA lead to human diseases that collectively affect approximately 1 in 4000 people [5, 6]. mtDNA is more susceptible than nuclear DNA (nucDNA) to damage by many environmental pollutants, for reasons including the absence of Nucleotide Excision Repair (NER) in the mitochondria [7]. NER is a highly functionally conserved DNA repair pathway that removes bulky, helix distorting lesions such as those caused by ultraviolet C (UVC) radiation and also many environmental toxicants, including benzo[a]pyrene (BaP) [8]. While these lesions cannot be repaired, they are slowly removed through a process that involves mitochondrial dynamics and autophagy [9, 10]. However, when present during development in C. elegans, this damage reduces mtDNA copy number and ATP levels [11]. We hypothesize that this damage, when present during development, will result in mitochondrial dysfunction and increase the potential for adverse outcomes later in life.</p><p>To test this hypothesis, 1st larval stage (L1) C. elegans are exposed to 3 doses of 7.5J/m2 ultraviolet C radiation 24 hours apart, leading to the accumulation of mtDNA damage [9, 11]. After exposure, many mitochondrial endpoints are assessed at multiple time points later in life. mtDNA and nucDNA damage levels and genome copy numbers are measured via QPCR and real-time PCR , respectively, every 2 day for 10 days. Steady state ATP levels are measured via luciferase expressing reporter strains and traditional ATP extraction methods. Oxygen consumption is measured using a Seahorse XFe24 extra cellular flux analyzer. Gene expression changes are measured via real time PCR and targeted metabolomics via LC-MS are used to investigate changes in organic acid, amino acid and acyl-carnitine levels. Lastly, nematode developmental delay is assessed as growth, and measured via imaging and COPAS biosort.</p><p>I have found that despite being removed, UVC induced mtDNA damage during development leads to persistent deficits in energy production later in life. mtDNA copy number is permanently reduced, as are ATP levels, though oxygen consumption is increased, indicating inefficient or uncoupled respiration. Metabolomic data and mutant sensitivity indicate a role for NADPH and oxidative stress in these results, and exposed nematodes are more sensitive to the mitochondrial poison rotenone later in life. These results fit with the developmental origin of health and disease hypothesis, and show the potential for environmental exposures to have lasting effects on mitochondrial function.</p><p>Lastly, we are currently working to investigate the potential for irreparable mtDNA lesions to drive mutagenesis in mtDNA. Mutations in mtDNA lead to a wide range of diseases, yet we currently do not understand the environmental component of what causes them. In vitro evidence suggests that UVC induced thymine dimers can be mutagenic [12]. We are using duplex sequencing of C. elegans mtDNA to determine mutation rates in nematodes exposed to our serial UVC protocol. Furthermore, by including mutant strains deficient in mitochondrial fission and mitophagy, we hope to determine if deficiencies in these processes will further increase mtDNA mutation rates, as they are implicated in human diseases.</p> / Dissertation

published_or_final_version / Community Medicine / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Anatomy / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Biochemistry / Master / Master of Philosophy

Barrett's esophagus (BE) is a premalignant disease associated with esophageal adenocarcinoma (EAC). This condition is highly associated with gastroesophageal reflux disease (GERD) which is characterized as chronic exposure of the esophagus to acid and bile acids. An understanding of the cytotoxic and tumorigenic capacity of bile acids and acid during a reflux episode will lead to the identification of markers for therapeutic intervention. The major goal of the following studies was to determine the mechanisms responsible for bile acid-induced alteration in intracellular pH (pHi) the effect on DNA damage, apoptosis and the adaptive resistance to reflux episodes in cells derived from normal esophagus (HET1A) or BE (CP-A) and EAC (JH-EsoAd1). In addition, I explored the therapeutic potential of UDCA oral therapy in BE cells.Here we show a novel mechanism of bile acid-induced, nitric oxide-mediated inhibition of the sodium-hydrogen exchanger (NHE) is a pathway bile acids utilize to induce acid-mediated DNA damage. This same mechanism can elicit apoptosis-resistance which we demonstrate by the complete inhibition of NHE with pharmacological inhibitor of NHE, EIPA. In addition, chronic exposure of bile acids and acid, in-vitro, confers resistance to cytotoxicity and makes cells derived from the squamous epithelium of the esophagus resemble BE and EAC. Finally, modifying the bile acid composition with glycol-Ursodeoxycholic acid (GUDCA) prevents many of the malignant effects of bile acids and acid and suggests a possible therapeutic strategy for those that suffer from GERD. The conclusion from this study suggest that bile acid reflux should be controlled in patients who suffer from GERD

Uranium has been mined for many years and used for fuel for nuclear reactors and materials for atomic weapons, ammunition, and armor. While the radioactivity associated with uranium mining has been linked to the development of lung and kidney cancers, and leukemia, little is known about the direct chemical genotoxicity of uranium. The overall hypothesis of the current research is that uranium can produce DNA damage by chemical genotoxicity mechanisms. Three specific aims were tested. In Aim 1, specific DNA lesions caused by direct interaction of uranium and DNA were investigated. Chinese Hamster Ovary cells (CHO) with mutations in various DNA repair pathways were exposed to 0 – 300 μM of soluble depleted uranium (DU) as uranyl acetate (UA) for 0 – 48 hr. Results indicate that UA readily enters CHO cells, with the highest concentration localizing in the nucleus. Clonogenics assay shows that UA is cytotoxic in each cell line with the greatest cytotoxicity in the base excision repair deficient EM9 cells and the nuclear excision repair deficient UV5 cells compared to the non-homologous end joining deficient V3.3 cells and the parental AA8 cells after 48 hr. This indicates that UA is forming DNA adducts that may be producing single strand breaks through hydrolysis rather than double strand breaks in CHO cells. Fast Micromethod® results indicate an increased amount of single strand breaks in the EM9 cells after 48 hr UA exposure compared to the V3.3 and AA8 cells. In Aim 2, the role of oxidative stress in producing DNA lesions was determined. Cellular oxidative stress has been implicated in the genotoxicity of many heavy metals as a mechanism of induced DNA damage. To investigate this possible mechanism, human bronchial epithelial cells (16HBE14o⁻) were exposed to 30 ppb (0.13 μM U) UA for 2 – 24 hr. UA did not significantly induce oxidative stress compared to untreated cells at 3 – 4 hr time points. These results suggest that cellular oxidative stress is not a major pathway of DU genotoxicity at low concentrations. In Aim 3, DNA damage response to uranium-induced DNA damage was investigated. It has been widely reported that metals can be genotoxic by inhibiting DNA repair. Cultured cells were co-exposed to 0.13 μM UA in the presence of 0 – 25 μM of etoposide for 0 – 48 hr. Results indicate that UA inhibited double strand break repair. Coexposures of etoposide and UA synergistically induced cytotoxicity compared to individual treatments and untreated cells. Co-exposed UA and etoposide treated 16HBE14o⁻ cells exhibited a decrease in phosphorylation of DNA repair proteins compared to etoposide treatments. Untreated and UA-treated 16HBE14o⁻ cells did not induce phosphorylation of DNA repair proteins. These results suggest that DU inhibits double strand break DNA repair at low concentrations in the presence of a known DNA double-strand damaging agent, etoposide. The inhibition of DNA repair by DU at environmentally relevant concentrations suggests a novel means by which uranium may exert its genotoxic effects. Results found at low dose exposures are not consistent with alterations seen with radioactivity, suggesting that the effects of uranium at low doses are due to its chemical genotoxic effects. Understanding how uranium reacts with DNA is important to better understand how this suspected carcinogen induces cancer and to help to elucidate mechanisms that produce cancers in people exposed to uranium.

Telomeres are physical ends of chromosomes consisting of (TTAGGG)n DNA sequence and a specialized set of proteins that protect chromosomal ends from degradation and from eliciting DNA damage response. These specialized set of proteins, known as shelterin, directly bind to telomeric DNA. In addition, some DNA double-strand break (DSB) repair proteins such as, DNA-PKcs and KU70/80, play active roles in telomere maintenance. Mouse knock-out experiments have revealed that deletion of either DNA-PKcs or Ku70/80 resulted in elevated levels of telomeric fusion, indicative of dysfunctional telomeres. Artemis protein is involved in DNA DSB repair through non-homologous end joining (NHEJ) and it is phosphorylated by DNAPKcs. Human cells defective in Artemis have been identified and shown to be radiosensitive and patients with an Artemis defective gene suffer from radiosensitive severe-combined immune deficiency syndrome (RS-SCID). Mouse cells defective in Artemis have elevated levels of telomeric fusion. We have demonstrated in this thesis that Artemis defective human cell lines show a mild telomeric dysfunction phenotype detectable at the cytological level. The nature of telomere dysfunction phenotype appears to be similar to that observed in DNAPKcs defective cells as exemplified by the presence of IR induced chromatid telomeric fusions. We have also shown that (a) DNA damage occurring within the telomeric DNA is difficult to repair or irreparable in older cells and that (b) Artemis defective older cells show higher proportion of DNA damage at telomeres than their normal counterparts. Finally, we have demonstrated that inhibition of DNA-PKcs causes (a) an increase in telomeric fusions in Artemis defective cell lines relative to both normal cell lines after inhibition and Artemis cell lines before inhibition and (b)elevated levels of DNA damage at telomeres following exposure of cells to radiation relative to both irradiated normal cells exposed to a DNA-PKcs inhibitor and irradiated Artemis defective cells but not exposed to the DNA-PKcs inhibitor. These results suggest that the effects of Artemis and DNA-PKcs on telomeres are cumulative. We have also performed (a) experiments to examine telomere function in Artemis defective cell lines after knocking down DNA-PKcs levels by RNAi and b) preliminary experiments to knock-down Artemis in DNA-PKcs defective cells. Taken together, our results suggest that the Artemis defect causes mild telomere dysfunction phenotype in human cells.

Studies were undertaken to determine toxicological effects in a model species, Cyprinus carpio L. following hypoxic exposure either alone or in combination with representative heavy metal (i.e. copper; Cu) via a dietary route, at different levels of biological organisation (viz. biochemical, histological and individual level effects). Initially, the validation study of biological responses using a range of concentrations of dietary Cu as a relevant environmental contaminant was carried out (Chapter 3). The results showed a range of biological responses in exposed fish including significant genotoxic response as determined by induction of DNA strand breaks (i.e. the Comet assay) with bacterial enzymes Fpg and Endo-III (for detection of oxidative DNA damage) and reduction in growth rate suggesting the robustness of selected biomarkers. Subsequently, this approach was used initially to determine the biological responses following chronic hypoxic and hyperoxic exposure (Chapter 4). The results suggested that both hypoxic and hyperoxic conditions lead to a range of comparable biological responses. Following relative evaluation of chronic hypoxic and hyperoxic exposures, experiments were carried out to elucidate potential interactive effect of hypoxia in combination with dietary Cu (Chapter 5). The combined exposure of hypoxia and Cu induced a significantly higher level of DNA damage suggesting that DNA damage in fish can serve as a sensitive biomarker for changes in water quality as well as presence of genotoxic chemicals. The final sets of experiment were carried out to determine the biological responses in C. carpio following exposure to chronic hypoxic stress and subsequent recovery in normoxic condition for 7 days. Real-time PCR (qPCR) technology was used to examine the hypoxia inducible Factor-1 α (HIF-1α) gene expression pattern (Chapter 6). The results suggested that the expression levels of HIF-1α in response to hypoxia were significantly higher compared to normoxic controls, a high level of oxidative DNA damage under hypoxia and re-exposure to normoxic condition (i.e. recovery period). This will shed lights for development of adaptive response in higher vertebrates, which could also have significant clinical implications in human health.

The Saccharomyces cerevisiae Rmi1 protein is a component of the highly conserved Sgs1-Top3-Rmi1 complex, which is required for the maintenance of genome stability. The rmi1Δ deletion mutant has proven difficult to study because it exhibits very poor growth, and rapidly accumulates second site suppressor mutations. Furthermore, deletion of the putative HJ resolvase genes, MUS81-MUS81 or SLX1-SLX4 in rmi1Δ mutants causes synthetic lethality. In order to study phenotypes caused by loss of functional Rmi1, and to explore the genetic interactions between RMI1 and the MUS81, MUS81, SLX1 and SLX4 genes, a temperature sensitive mutant of RMI1 was isolated, named rmi1-1. Similar to rmi1Δ deletion mutants, rmi1-1 cells are highly sensitive to the DNA damaging agent, MMS and the replication inhibitor, HU. In addition, rmi1-1 mutants accumulate replication-associated branched DNA structures, and arrest in G₂/M after a transient exposure to MMS. These cells are proficient in DNA damage checkpoint activation. Deletion of SLX1, SLX4, MUS81 or MUS81 in the rmi1-1 strain causes synthetic lethality, which is associated with cell cycle defects. Following a transient exposure to MMS, rmi1-1 mutants accumulate homologous recombination intermediates. These intermediates are slowly resolved at the restrictive temperature, revealing a redundant resolution activity in the absence of functional Rmi1. This resolution depends upon Mus81-Mms4, but not on Slx1-Slx4 or Yen1. I propose that while the Sgs1-Top3-Rmi1 complex constitutes the main pathway for removal of homologous recombination intermediates following a perturbed S-phase, Mus81-Mms4 can act as a back up for resolution of these intermediates, which most likely represent double Holliday junctions. In this study, I also present screens for high copy suppressors of rmi1-1 phenotypes, and for novel Rmi1 interaction partners.