Repository logo

Browsing by Author "Bailey, Susan M., advisor"

Now showing 1 - 8 of 8
  • Thumbnail Image
    ItemOpen Access
    AI for personalized medicine
    (Colorado State University. Libraries, 2023) Lewis, Aidan Michael, author; Bailey, Susan M., advisor; LaRocca, Tom J., committee member; Nishimura, Erin O., committee member
    In 2021, Americans spent an estimated $4.3 trillion dollars on healthcare, an extraordinary amount for treatment that is often less effective than care in other developed nations (1-3). Precision, or personalized, medicine represents a new frontier in healthcare that promises treatment plans and optimized health strategies tailored to an individual (4) thereby making medicine more effective and less costly. Contemporary Artificial Intelligence (AI) and Machine Learning (ML) approaches have tremendous potential to advance the field of precision medicine by leveraging the technology's power of deciphering patterns in the data to make predictions about an individual's health outcomes (3, 5-8). However, many developing AI/ML approaches to precision medicine have not proven particularly successful in making accurate predictions and conclusions mostly due to the limited availability of high-quality medical data for input. The Wake Forrest University Non-Human Primate Radiation Late Effects Cohort (NHP RLEC) provides an unprecedented opportunity to test AI's ability to be trained on a comprehensive human health analog data set in an experimentally irradiated Rhesus monkey cohort with extraordinary life-time records of biomarker levels and health outcomes. Here, we test prevalent, scalable ML models to improve accuracy of predictions specifically related to radiation biomarkers, dose, and health outcomes. We find that CatBoost, ElasticNet, and XGBoost models can accurately predict lymphocyte counts for both monkey populations and individual monkeys. Furthermore, these models can accurately predict radiation dose and biomarker levels using only five other features within the models. Although the models were only marginally successful at predicting lymphocyte counts using radiation-related data alone, and at predicting the health outcomes of the monkeys, these findings and this unique dataset represent key steps toward refining the combinations of factors necessary for the successful use of AI/ML models in precision medicine for humans.
  • Thumbnail Image
    ItemOpen Access
    DNA repair and sister chromatid exchange
    (Colorado State University. Libraries, 2008) Hagelstrom, R. Tanner, author; Bailey, Susan M., advisor; Liber, Howard, advisor
    Mitotic recombination that occurs between sister chromatids, known as sister chromatid exchange (SCE), is a common event in mammalian cells; yet very little is understood about SCE. Likewise, the biological relevance of SCE to humans is also unclear. It is generally thought that SCE represents no permanent alteration to genetic information, however, many cancer prone syndromes present elevated levels of SCE and it is not known whether they are a causal factor in cancer progression or simply a symptom of underlying genomic instability. It has also been purposed that SCE occurring in telomeres (T-SCE) may contribute to the aging phenotype seen in progeroid syndromes. Several accelerated aging syndromes, such as progeria, show highly elevated levels of SCE within telomeric regions. The role of DNA repair in SCE regulation and formation is also under investigation. While it has been shown that at least one of the DNA repair pathways, homologous recombination (HR), is likely to be involved in the formation of SCE, it is less clear whether other DNA repair pathways are also involved in either the formation or suppression of SCE. Therefore, the goal of this research has been to better understand how DNA repair pathways can influence SCE frequency, and how SCE relates to cancer progression and aging. This research also examines how the physical location of SCE, whether it be in genomic (G-SCE) or telomeric (T-SCE) DNA, influence which DNA repair pathways are involved. I examined the role of HR by investigating the Werner (WRN), Bloom (BLM), and FANCD2 proteins. I also investigated the role of non-homologous end joining (NHEJ) by examining the DNA-dependent protein kinase (DNA-PKcs), both the Ku70/80 heterodimer and the catalytic subunit (DNA-PKcs), and Artemis. ERCC1 is a representative member of the final DNA repair pathway examined, nucleotide excision repair (NER). Lastly, I determined if/how DNA repair status can influence the ionizing radiation induced bystander effect (BSE). I was able to determine that at least some of the DNA repair proteins are critical in the generation of a bystander signal providing the first evidence that DNA repair can have an influence via an inter-cellular pathway.
  • Thumbnail Image
    ItemOpen Access
    DNA strand break associated bystander effect (DSB-ABE) is linked to gene mutations in naïve cells and indicates the involvement of a MAPK pathway
    (Colorado State University. Libraries, 2012) Jalal, Nasir, author; Liber, Howard L., advisor; Bailey, Susan M., advisor; Nickoloff, Jac, committee member; Bamburg, James, committee member
    The goal of this project was to investigate whether radiation independent DNA damage, specifically a single induced DNA double strand break (DSB) can produce bystander signal, which is capable of inducing genomic instability in non-targeted cells. Previously uncharacterized E18 (modified TK6 cells) with a unique I-Sce1 insert in intron 2 of the thymidine kinase (TK1) gene were allowed to generate a bystander signal following electroporation of the rare cutting restriction enzyme I-Sce1 carried by a plasmid to induce DNA damage at the I-Sce1 site. Mutation assays were carried out to measure mutation fraction (MF) in directly targeted cells and using medium transfer, in non-targeted cells as a measure of bystander signal production. Transfection of the plasmid carrying I-Sce1 gene resulted in production of sufficient bystander signal into the medium to increase the bystander MF, when conditioned medium was applied from directly targeted to naïve E18 cells. The DSB-ABE exhibited temporal kinetics over a 10 hour duration. The relative direct and bystander MF increase due to the electroporation of three rare cutting restriction enzymes namely Not1 an 8 base cutter, Sfi1 a 13 base cutter (technically 8 because of the 5 non-specific bases in sequence) and I-Sce1 an 18 base cutter, showed that DSB-ABE does not show a dose-response. The bystander signal inhibition using superoxide dismutase (an enzyme that degrades reactive oxygen species) and PD 98059 (MEK1/2 inhibitor) indicated that the bystander signal activated the MAPK pathway in naïve cells. Higher levels of bystander mutation fraction were attempted through chemical inhibition of the three known enzymes of DNA repair (ATM, ATR and DNA PK) in directly targeted cells. Results reveal that inhibition of repair of I-Sce1 induced damage was not linked to bystander response. Further, sufficient bystander signal was produced by a presumably single I-Sce1 induced DNA break. The bystander signal produced, exhibited a dose-response in naïve cells and there was suggestion for the involvement of MAPK pathway.
  • Thumbnail Image
    ItemOpen Access
    Examination of molecular genetic factors involved in sensitivity to breast cancer following radiation exposure
    (Colorado State University. Libraries, 2008) Williams, Abby J., author; Ullrich, Robert L., advisor; Bailey, Susan M., advisor
    Understanding DNA repair is not only an important aspect of cell biology, but also has important implications for the field of carcinogenesis since cancer most likely occurs from genetic damage that occurs over one's lifetime. DNA repair needs to be accurate and efficient in order for a cell to maintain genomic stability, and defects in repair systems can result in radiosensitivity. Because radiation exposure, DNA repair deficiency and telomere malfunction are associated with cancer risk, we investigated Lymphoblastoid Cell Lines (LCLs) from breast cancer patients and controls for chromosomal radiosensitivity, relative telomere length, and gene expression changes. The importance of studying peripheral blood lymphocytes from cancer patients lies in the fact that minimally invasive techniques are lacking for the detection of individuals with high risk for cancer, and that telomere length has been proposed to be useful in this regard. Identification of radiosensitivity markers would be a valuable contribution for clinicians in hopes of avoiding excessive radiation or chemotherapy treatment given to patients. Failure to adequately repair DNA damage can result in cell suicide or halting of cell cycle progression in an attempt to allow repair mechanisms to operate. If damage persists, a cell can be pushed toward transformation and the pathway of carcinogenesis. A second aspect of the current work was to study the Homologous Recombination double-strand break repair protein, Rad51D. The emerging interrelations between DNA repair and telomere maintenance also prompted us to evaluate Rad51D's role in telomere function. The final aspect of this research involved examination of how DNA repair related proteins are linked to the indirect effect of ionizing radiation exposure known as the bystander effect (BSE). We are the first to demonstrate that DNA-PKcs and ATM are required to generate, but not receive, a bystander signal. We also show that mouse embryonic fibroblasts do not generate bystander signals to neighboring cells, while their adult cell counterparts do. Taken together, this work makes important contributions to our appreciation of the many and varied roles DNA repair related proteins play in maintenance of chromosomal integrity, proper telomere function, inhibition of carcinogenesis and now, regulation of the BSE.
  • Thumbnail Image
    ItemOpen Access
    Investigations into the mechanisms of telomere structure and function
    (Colorado State University. Libraries, 2012) Le, Phuong Nam, author; Bailey, Susan M., advisor; Ullrich, Robert L., committee member; Weil, Michael M., committee member; Laybourn, Paul J., committee member
    Telomere dysfunction is most commonly defined as critical shortening; i.e., loss of telomere sequence due to a variety of causes, usually the end-replication problem. However telomeres and their arsenal of associated proteins also provide essential end-capping structure that protects the ends of linear eukaryotic chromosomes. The overall goal of the studies presented here was to provide new insight into underlying mechanisms of telomeric structure and function. We examined the role of telomere function in Acute Myeloid Leukemia. We observed genomic instability in association with radiation-induced AML, and this association was observed following AML induction with both gamma (γ)- ray and 1 Gev 56Fe ion exposure. Furthermore, we observed a clonal fusion event involving telomeres in a human AML cell line. Taken together, our AML studies underline the importance of genome stability and its link to carcinogenesis. We previously reported a role for the DNA damage repair protein DNA-PKcs in mammalian telomere end-capping function, where inappropriate telomere fusions, as well as telomere fusions to other broken DNA ends, were observed in DNA-PKcs deficient backgrounds. DNA-PKcs has many proposed phosphorylation substrates, one of the most intriguing and relevant being the recently identified heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), an RNA binding protein that associates with telomeres. It is also now well accepted that telomeres are transcribed into telomeric repeat-containing RNAs, or TERRA, which are thought to contribute to telomeric chromatin structure. Taken together, we hypothesized that DNA-PKcs mediated phosphorylation of hnRNA1 plays an important role in tethering TERRA to telomere ends, thereby possibly contributing to telomere chromatin structure and function. Our data suggests that TERRA localization at telomeres is independent of hnRNP A1 and DNA-PKcs kinase activity. Rather, we observed decreased TERRA levels following DNA-PKcs kinase inhibition, suggesting DNA-PKcs indirectly regulates TERRA levels. Depletion of hnRNP A1 did not influence TERRA levels, but resulted in elevated frequencies of what have previously been termed "fragile" telomeres and telomere sister chromatid exchange (T-SCE), both indicative of a role for hnRNP A1 in facilitating telomere replication.
  • Thumbnail Image
    ItemOpen Access
    Tankyrase 1 influences telomere recombination, stability of the NHEJ protein DNA-PKcs and genomic integrity
    (Colorado State University. Libraries, 2011) Dregalla, Ryan Christopher, author; Bailey, Susan M., advisor; Liber, Howard L., committee member; Weil, Michael M., committee member; Nyborg, Jennifer K., committee member; Laybourn, Paul J., committee member
    The Poly(ADP-ribosyl)ating Polymerase (PARP) family of enzymes has gained considerable attention recently due to the success of inhibiting their activities in breast cancers with BRCA 1/2 deficient backgrounds. PARPs serve as key regulators of protein recruitment, stability and activity in specific intracellular pathways including DNA-repair, telomere stability, transcription factor regulation and mitotic integrity. The PARP family member, PARP-5a, otherwise known as tankyrase 1 is unique in that it lacks a DNA-binding domain and interacts with proteins specifically. First found to regulate telomere length by promoting access to telomerase, tankyrase 1 has since become associated with a multitude of critical cellular processes. In our studies investigating the role of DNA-dependent Protein Kinase catalytic subunit (DNA-PKcs) and tankyrase 1 at telomeres, we find that tankyrase 1 is required for the suppression of sister chromatid recombination events at the telomere and that the leucine zipper domain of DNA-PKcs is necessary for accurate end-capping function. Interestingly, during our investigation we also identified a link between the stability of the DNA-PKcs protein and tankyrase 1. We find that under conditions in which tankyrase 1 is depleted or catalytically inhibited, DNA-PKcs becomes a substrate for proteasome mediated degradation. The depletion of tankyrase 1 by siRNA-mediated knockdown or PARP inhibition resulted in the failure of DNA-PKcs function in both telomere end-capping and the DNA damage response following exposure to ionizing radiation; i.e., increased sensitivity to ionizing radiation-induced cell killing, mutagenesis, chromosome aberrations and telomere fusions. Further, we find that the loss of DNA-PKcs is not coupled with depletion of Ku70, Ku80 or the PI3-kinase ATM, illustrating that tankyrase 1 acts to regulate DNA-PKcs specifically. Taken together, we identify important and novel roles of tankyrase 1 with implications not only for DNA repair and telomere biology, but also for cancer and aging.
  • Thumbnail Image
    ItemOpen Access
    Telomere length, telomerase activity, and structural variants as biomarkers of extreme environments
    (Colorado State University. Libraries, 2017) McKenna, Miles J., author; Bailey, Susan M., advisor; Dow, Steven, committee member; Kato, Takamitsu, committee member; Simon, Steven, committee member; Thamm, Douglas, committee member
    Mammals, and in particular humans, are masterful at overcoming and adapting to extreme environments. Whether astronauts in low earth orbit aboard the International Space Station (ISS) or U.S. military veterans exposed to nuclear fallout from atomic weapons testing, humans can persist through a wide range of physical, psychological, and environmental stressors. The overall goal of the studies presented here was to evaluate the biological influences of extreme environments not commonly experienced by the general population. Whether spaceflight or exposure to nuclear fallout, results improve our understanding of short- and long-term effects of low gravity environments, exposure to ionizing radiation (IR) of mixed qualities, as well as low dose and low dose effects of IR. We explored these scenarios by evaluating biomarkers of stress, specifically telomere length dynamics, and biomarkers of DNA damage, specifically transmissible structural rearrangements. Telomeres are not only regarded as valuable biomarkers of aging and age-related degenerative pathologies like cardiovascular disease and cancer, and so are reflective of overall health status, they also serve as "hallmarks" of radiosensitivity. Stable chromosomal structural rearrangements (translocations and inversions) persist with time and so provide informative signatures of IR exposure as well. During the 1950's United States military personnel and weathermen, collectively known as the atomic veterans, were unintentionally exposed to nuclear fallout during atomic bomb testing following WWII. Here, directional Genomic Hybridization (dGH) for high-resolution detection of IR-induced chromosomal inversions and translocations was assessed as a more sensitive, quantitative retrospective biodosimetry approach. The influence of IR exposure on telomere length dynamics was also evaluated to determine the long-term influence of such exposures. Our results illustrate that even for nuclear events that occurred six decades in the past, evidence of exposure is still present. We find that although translocations and inversions are reliable biodosimeters independently, a combined approach provides a more sensitive measurement of past radiation exposure. We also report, for the first time, the influence of age and smoking on background inversion frequencies. Furthermore, telomere length was inversely related to IR dose, suggesting that a single acute exposure to nuclear fallout may lead to persistent long-term effects on overall health. Telomere length dynamics and structural rearrangements were also monitored longitudinally in monozygotic twin and unrelated astronauts. NASA astronauts are a unique group of individuals who experience an extreme environment that the human body is not adapted for. Little is known about the biological health effects of a low gravity environment with increased IR exposure including galactic cosmic rays (GCRs), solar particle events, and secondary neutrons. Not only do astronauts have shorter telomeres than age-/gender-matched controls at baseline (pre-flight), but a transient increase in telomere length during space flight was also observed. Results suggest this unexpected finding may be due to an upregulation of telomerase, the enzyme responsible for maintaining telomere length. Moreover, telomerase activity also increased post-flight in both twins, Scott and Mark Kelly. Although not spaceflight specific, this is the first report of telomerase upregulation in humans due to a psychologically traumatic event. A dose dependent increase in inversions, and to a lesser extent, translocations, as a consequence of IR exposure on the ISS was also seen in Scott Kelly. Collectively, the studies presented here demonstrate a profound influence of extreme environments, particularly those involving low dose IR, on human biological responses. Telomere length dynamics and chromosome aberration frequencies (e.g. translocations and inversions) provide insight into the long-term health effects and implications of spaceflight and exposure to nuclear events.
  • Thumbnail Image
    ItemOpen Access
    Telomere recombination and regulation
    (Colorado State University. Libraries, 2012) Eadaim, Abdunaser Omar, author; Bailey, Susan M., advisor; Laybourn, Paul, committee member; Paule, Marvin R., committee member
    Telomeres, tandem arrays of repetitive G-rich sequence at the physical ends of linear chromosomes, serve to protect chromosomal termini from enzymatic activity and prevent recognition of natural DNA ends as double strand breaks (DSBs). The telomeric Shelterin complex and other associated proteins play critical roles in maintaining stability of the telomere. Telomere length can be maintained by telomerase enzymatic activity or by an alternative lengthening of telomere (ALT) recombination based mechanism, which has been characterized by increased frequencies of telomere sister chromatid exchange (T-SCE). Telomeres have been shown to be especially sensitive to oxidative stress and ultraviolet (UV)-induced DNA damage, for example cyclobutane pyrimidine dimers (CPDs) between two adjacent pyrimidines. In this project, exposure to ultraviolet C (UVC) was evaluated for its ability to induce sister chromatid exchange (SCE) in cell lines with different telomerase status. Our results showed that sister chromatid exchanges, both genome-wide (G-SCE) and within telomeres (T-SCE), were increased in a dose-dependent manner following UVC exposure in telomerase negative normal human fibroblast (BJ1) and ALT human dermal fibroblasts. However, in telomerase positive human fibroblasts, while G-SCE frequencies increased in response to UVC, T-SCE frequencies did not. These results have important implications not only for aging, but for carcinogenesis as well, since UV exposure from the sun (and tanning beds) is linked to increased risk of both aging of the skin and skin cancer. The susceptibility of telomeric DNA to oxidative stress and the dampened DNA damage response in this region provide likely explanations for the increased frequencies of T-SCE observed following UV exposure. Although certainly not the only contributor, T-SCE themselves provide intriguing insight into possible mechanisms of increased telomere shortening, senescence, and carcinogenesis, and may therefore represent informative biomarkers of aging and cancer.