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Open Access Publications from the University of California

Scholarly Works (106 results)

  • Article
  • Peer Reviewed
UC San Francisco Previously Published Works (2013)
DNA damage created by endogenous or exogenous genotoxic agents can exist in multiple forms, and if allowed to persist, can promote genome instability and directly lead to various human diseases, particularly cancer, neurological abnormalities, immunodeficiency and premature aging. To avoid such deleterious outcomes, cells have evolved an array of DNA repair pathways, which carry out what is typically a multiple-step process to resolve specific DNA lesions and maintain genome integrity. To fully appreciate the biological contributions of the different DNA repair systems, one must keep in mind the cellular context within which they operate. For example, the human body is composed of non-dividing and dividing cell types, including, in the brain, neurons and glial cells. We describe herein the molecular mechanisms of the different DNA repair pathways, and review their roles in non-dividing and dividing cells, with an eye toward how these pathways may regulate the development of neurological disease.
    Cover page: DNA repair mechanisms in dividing and non-dividing cells
    • Article
    • Peer Reviewed
    UC San Francisco Previously Published Works (2014)
    Hyperpolarization using dissolution dynamic nuclear polarization has emerged as a versatile method to dramatically improve the MR signal of low-sensitivity nuclei. This technique facilitates the study of real-time metabolism in vitro and in vivo using (13)C-enriched substrates and has been applied to numerous models of human disease. In particular, several mechanisms underlying prostate cancer have been interrogated using hyperpolarized (13)C MR spectroscopy. This review highlights key metabolic shifts seen in prostate cancer, their study by hyperpolarized (13)C MR spectroscopy, and the development of new platforms for metabolic study.
      Cover page: Hyperpolarized 13C MR for Molecular Imaging of Prostate Cancer
      • Article
      • Peer Reviewed
      UC San Francisco Previously Published Works (2014)

      Significance

      Human apurinic/apyrimidinic endonuclease 1 (APE1, also known as REF-1) was isolated based on its ability to cleave at AP sites in DNA or activate the DNA binding activity of certain transcription factors. We review herein topics related to this multi-functional DNA repair and stress-response protein.

      Recent advances

      APE1 displays homology to Escherichia coli exonuclease III and is a member of the divalent metal-dependent α/β fold-containing phosphoesterase superfamily of enzymes. APE1 has acquired distinct active site and loop elements that dictate substrate selectivity, and a unique N-terminus which at minimum imparts nuclear targeting and interaction specificity. Additional activities ascribed to APE1 include 3'-5' exonuclease, 3'-repair diesterase, nucleotide incision repair, damaged or site-specific RNA cleavage, and multiple transcription regulatory roles.

      Critical issues

      APE1 is essential for mouse embryogenesis and contributes to cell viability in a genetic background-dependent manner. Haploinsufficient APE1(+/-) mice exhibit reduced survival, increased cancer formation, and cellular/tissue hyper-sensitivity to oxidative stress, supporting the notion that impaired APE1 function associates with disease susceptibility. Although abnormal APE1 expression/localization has been seen in cancer and neuropathologies, and impaired-function variants have been described, a causal link between an APE1 defect and human disease remains elusive.

      Future directions

      Ongoing efforts aim at delineating the biological role(s) of the different APE1 activities, as well as the regulatory mechanisms for its intra-cellular distribution and participation in diverse molecular pathways. The determination of whether APE1 defects contribute to human disease, particularly pathologies that involve oxidative stress, and whether APE1 small-molecule regulators have clinical utility, is central to future investigations.
        Cover page: Human Apurinic/Apyrimidinic Endonuclease 1
        • Thesis
        • Peer Reviewed
        UC San Francisco Electronic Theses and Dissertations (2024)

        Staphylococcus aureus (S. aureus) is a gram-positive bacterium that can cause severe infections such as pneumonia, osteomyelitis, and endocarditis when it breaches the skin. This study aimed to enhance the chemoenzymatic radiosynthesis of 2-deoxy-2-[18F]-fluoro-sakebiose ([18F]FSK), a radiotracer potentially useful for imaging S. aureus infections. By optimizing the synthesis of 2-deoxy-2-[19F]-fluoro-sakebiose ([19F]FSK), we identified key factors—such as increased enzyme concentration and decreased precursor levels—that significantly improved the yield. Applying these optimized conditions to the synthesis of [18F]FSK resulted in a 30% increase in the radiochemical yield (RCY%) from the control experiment. In vitro evaluation showed that [18F]FSK was successfully incorporated into two strains of S. aureus, suggesting its potential utility for imaging bacterial infections in vivo. This work lays the groundwork for using [18F]FSK in PET/CT imaging to diagnose and monitor S. aureus infections.

          Cover page: Improved chemoenzymatic radiosynthesis of fluorine-18 labeled sakebiose for microPET-CT imaging of Staphylococcus aureus
          • Article
          • Peer Reviewed
          UC San Francisco Previously Published Works (2013)
          The repair of damaged DNA is essential to maintain longevity of an organism. The brain is a matrix of different neural cell types including proliferative astrocytes and post-mitotic neurons. Post-mitotic DNA repair is a version of proliferative DNA repair, with a reduced number of available pathways and most of these attenuated. Base excision repair (BER) is one pathway that remains robust in neurons; it is this pathway that resolves the damage due to oxidative stress. This oxidative damage is an unavoidable byproduct of respiration, and considering the high metabolic activity of neurons this type of damage is particularly pertinent in the brain. The accumulation of oxidative DNA damage over time is a central aspect of the theory of aging and repair of such chronic damage is of the highest importance. We review research conducted in BER mouse models to clarify the role of this pathway in the neural system. The requirement for BER in proliferating cells also correlates with high levels of many of the BER enzymes in neurogenesis after DNA damage. However, the pathway is also necessary for normal neural maintenance as larger infarct volumes after ischemic stroke are seen in some glycosylase deficient animals. Further, the requirement for DNA polymerase β in post-mitotic BER is potentially more important than in proliferating cells due to reduced levels of replicative polymerases. The BER response may have particular relevance for the onset and progression of many neurodegenerative diseases associated with an increase in oxidative stress including Alzheimer's.
            Cover page: Base excision repair in the mammalian brain: Implication for age related neurodegeneration
            • Thesis
            • Peer Reviewed
            UC San Francisco Electronic Theses and Dissertations (2021)

            One of the major challenges in imaging bacterial infection using Positron Emission Tomography (PET) is the insufficiency of fluorine-18 labeled probes. Several carbon-11 D-amino acid probes have been developed to mimic bacteria-specific metabolic pathways and have been translated into the clinical realm.1 However, the short half-life of carbon-11 limits its applicability and reach in examining populations of interest. Several attempts to make fluorine-18 probes through direct radiolabeling techniques have failed, and thus a pressing need to fulfill this gap exists. Click chemistry, an indirect alternative tool to tag biomolecules, has been shown to shown to tag and study molecules, including bacteria specific biomarkers such as peptidoglycan.2 Utilizing the cell’s biosynthetic machinery to incorporate essential components to peptidoglycan synthesis such as modified sugars or amino acids, these modified compounds can then selectively ligate to a second probe bearing a visible component.3 By utilizing these well-established bio-orthogonal techniques,4 we developed an optimized, high-throughput azide-alkyne click chemistry assay to indirectly label gram-positive Staphylococcus aureus and gram-negative Escherichia coli with three fluorine-18 PET tracers: [18F]FB-DBCO, [18F]PEG4-DBCO, and [18F]Sulfo-DBCO. Tracer ligation to D-azido-alanine, a modified D-alanine metabolite, via copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) was quantified to determine the efficiency of the fluorine-18 PET tracer and to propose the development of the next generation of PET tracers for infection imaging.

              Cover page: Targeting Peptidoglycan using Radiolabeled Click Chemistry for PET Infection Imaging
              • Article
              • Peer Reviewed
              UC San Francisco Previously Published Works (2014)
              The study of transient chemical phenomena by conventional NMR has proved elusive, particularly for non-(1)H nuclei. For (13)C, hyperpolarization using the dynamic nuclear polarization (DNP) technique has emerged as a powerful means to improve SNR. The recent development of rapid dissolution DNP methods has facilitated previously impossible in vitro and in vivo study of small molecules. This review presents the basics of the DNP technique, identification of appropriate DNP substrates, and approaches to increase hyperpolarized signal lifetimes. Also addressed are the biochemical events to which DNP-NMR has been applied, with descriptions of several probes that have met with in vivo success.
                Cover page: Chemistry and biochemistry of 13 C hyperpolarized magnetic resonance using dynamic nuclear polarization
                • Article
                • Peer Reviewed
                UC San Francisco Previously Published Works (2017)
                Cancer and other diseases are increasingly understood in terms of their metabolic disturbances. This thinking has revolutionized the field of ex vivo metabolomics and motivated new approaches to detect metabolites in living systems, including proton magnetic resonance spectroscopy (1H-MRS), hyperpolarized 13C MRS, and PET. For PET, imaging abnormal metabolism in vivo is hardly new. Positron-labeled small-molecule metabolites have been used for decades in humans, including 18F-FDG, which is used frequently to detect upregulated glycolysis in tumors. Many current 18F metabolic tracers including 18F-FDG have evolved from their 11C counterparts, chemically identical to endogenous substrates and thus approximating intrinsic biochemical pathways. This mimicry has stimulated the development of new radiochemical methods to incorporate 11C and inspired the synthesis of a large number of 11C endogenous radiotracers. This is in spite of the 20-minute half-life of 11C, which generally limits its use in patients to centers with an on-site cyclotron. Innovation in 11C chemistry has persisted in the face of this limitation, because (1) the radiochemists involved are inspired, (2) the methods of 11C incorporation are diverse, and (3) 11C compounds often show more predictable in vivo behavior, thus representing an important first step in the validation of new tracer concepts. In this mini-review we will discuss some of the general motivations behind PET tracers, rationales for the use of 11C, and some of the special challenges encountered in the synthesis of 11C endogenous compounds. Most importantly, we will try to highlight the exceptional creativity used in early 11C tracer syntheses, which used enzyme-catalyzed and other "green" methods before these concepts were commonplace.
                  Cover page: Exploring Metabolism In Vivo Using Endogenous 11C Metabolic Tracers
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2014)
                  Repetitive DNA sequences, such as those present in microsatellites and minisatellites, telomeres, and trinucleotide repeats (linked to fragile X syndrome, Huntington disease, etc.), account for nearly 30% of the human genome. These domains exhibit enhanced susceptibility to oxidative attack to yield base modifications, strand breaks, and abasic sites; have a propensity to adopt non-canonical DNA forms modulated by the positions of the lesions; and, when not properly processed, can contribute to genome instability that underlies aging and disease development. Knowledge on the repair efficiencies of DNA damage within such repetitive sequences is therefore crucial for understanding the impact of such domains on genomic integrity. In the present study, using strategically designed oligonucleotide substrates, we determined the ability of human apurinic/apyrimidinic endonuclease 1 (APE1) to cleave at apurinic/apyrimidinic (AP) sites in a collection of tandem DNA repeat landscapes involving telomeric and CAG/CTG repeat sequences. Our studies reveal the differential influence of domain sequence, conformation, and AP site location/relative positioning on the efficiency of APE1 binding and strand incision. Intriguingly, our data demonstrate that APE1 endonuclease efficiency correlates with the thermodynamic stability of the DNA substrate. We discuss how these results have both predictive and mechanistic consequences for understanding the success and failure of repair protein activity associated with such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains.
                    Cover page: APE1 Incision Activity at Abasic Sites in Tandem Repeat Sequences
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2016)
                    Metabolic imaging is a field of molecular imaging that focuses and targets changes in metabolic pathways for the evaluation of different clinical conditions. Targeting and quantifying metabolic changes noninvasively is a powerful approach to facilitate diagnosis and evaluate therapeutic response. This review addresses only techniques targeting metabolic pathways. Other molecular imaging strategies, such as affinity or receptor imaging or microenvironment-dependent methods are beyond the scope of this review. Here we describe the current state of the art in clinically translatable metabolic imaging modalities. Specifically, we focus on PET and MR spectroscopy, including conventional (1)H- and (13)C-MR spectroscopy at thermal equilibrium and hyperpolarized MRI. In this article, we first provide an overview of metabolic pathways that are altered in many pathologic conditions and the corresponding probes and techniques used to study those alterations. We then describe the application of metabolic imaging to several common diseases, including cancer, neurodegeneration, cardiac ischemia, and infection or inflammation.
                      Cover page: The Potential of Metabolic Imaging
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