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Open Access Publications from the University of California

Scholarly Works (45 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2021)

The superfamily II (SF2) DNA helicase XPB is an essential protein involved in twobiologically important processes: transcription and DNA repair. In eukaryotes, XPB is the largest subunit of the TFIIH complex and is essentially required in both transcription initiation and the nucleotide excision repair (NER) pathway. Previous structural and biochemical data of TFIIH all have showed that eukaryotic XPB binds and translocates on the double-stranded (ds) DNA for DNA unwinding, strikingly different from other conventional DNA helicases that requires a single-stranded (ss) DNA extension for strand separation. XPB was proposed to work as a “molecular wrench” or dsDNA translocase and use its ATPase activity for achieving its DNA opening function in transcription. However, it still remains elusive how this unconventional enzyme achieves DNA opening in the context of NER. XPB also plays a key role in coordinating the DNA incision by nucleases like XPF or XPG, and the underlying mechanisms are unclear. In archaea, there is no TFIIH-like complex. XPB is in complex with a nuclease called Bax1 for DNAunwinding and incision, but how this helicase-nuclease complex binds, opens and cleaves DNA is unknown. The objective of my research is to obtain structures and biochemical data of XPB with nuclease/DNA substrates for better understanding the DNA opening mechanisms of XPB and the crosstalk between XPB and nuclease for damage incision. A combination of biochemical, structural, and molecular biology techniques has been employed throughout to achieve these goals. Mutational and biochemical analyses based on crystal structures of archaeal XPB-Bax1 complexes from Sulfurisphaera tokodaii (St) and Archaeogloubus fulgidus (Af) demonstrates that this helicase-nuclease complex is a dynamic machinery and the activities of XPB are regulated by protein-protein interactions. Crystal structures of the StXPB-Bax1ΔC with and without DNA substrate reveal how the XPB-Bax1 complex interacts with the repair bubble DNA, and adopts different conformations in DNA-free and DNA-bound states. Biochemical and mutational data confirmed that the conserved RED and ThM motifs of XPB play key roles in DNA binding and XPB activities. My investigation uncovered the unconventional helicase activity of archaeal XPB using its ThM motif to unzip DNA while translocating in 3'-5' direction on the duplex. Biochemical data together with structure comparison of the StXPB-Bax1ΔC-DNA ternary complex with the cryo-EM structure of human TFIIH-XPA suggest human XPB cooperates with XPA for the initial DNA opening around the lesion. In sum, my findings provide new insights into the molecular mechanisms of XPB-mediated DNA binding and opening during the repair bubble formation, and how XPB and nucleases may coordinate DNA incision in archaeal and eukaryotic NER.

    Cover page: Molecular Mechanisms of DNA Opening by XPB Helicase and its Interaction With Nuclease in Nucleotide Excision Repair
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2020)
    Nuclear factor erythroid 2-related factor 2 (NRF2) is a master transcriptional regulator of genes whose products defend our cells for toxic and oxidative insults. Although NRF2 activation may reduce cancer risk by suppressing oxidative stress and tumor-promoting inflammation, many cancers exhibit elevated NRF2 activity either due to mutations that disrupt the negative control of NRF2 activity or other factors. Importantly, NRF2 activation is associated with poor prognosis and NRF2 has turned out to be a key activator of cancer-supportive anabolic metabolism. In this review, we summarize the diverse roles played by NRF2 in cancer focusing on metabolic reprogramming and tumor-promoting inflammation.
      Cover page: NRF2 as a regulator of cell metabolism and inflammation in cancer
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2021)
      Hepatocellular carcinoma (HCC), the most common type of primary liver cancer provides the prototypical example of an obesity-related cancer. The obesity epidemic gave rise to an enormous increase in the incidence of non-alcoholic fatty liver disease (NAFLD), a condition that affects one third of American adults. In about 20% of these individuals, simple liver steatosis (hepatosteatosis) progresses to non-alcoholic steatohepatitis (NASH) characterized by chronic liver injury, inflammation, and fibrosis. In addition to liver failure, NASH greatly increases the risk of HCC. Here we discuss the metabolic processes that control the progression from NAFLD to NASH and from NASH to HCC, with a special emphasis on the role of free-non-esterified cholesterol in the process.
        Cover page: From Liver Fat to Cancer: Perils of the Western DietCreative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2016)
        p62/SQSTM1 is a multifunctional signaling hub and autophagy adaptor with many binding partners, which allow it to activate mTORC1-dependent nutrient sensing, NF-κB-mediated inflammatory responses, and the NRF2-activated antioxidant defense. p62 recognizes polyubiquitin chains via its C-terminal domain and binds to LC3 via its LIR motif, thereby promoting the autophagic degradation of ubiquitinated cargos. p62 accumulates in many human liver diseases, including nonalcoholic steatohepatitis (NASH) and hepatocellular carcinoma (HCC), where it is a component of Mallory-Denk bodies and intracellular hyaline bodies. Chronic p62 elevation contributes to HCC development by preventing oncogene-induced senescence and death of cancer-initiating cells and enhancing their proliferation. In this review, we discuss p62-mediated signaling pathways and their roles in liver pathophysiology, especially NASH and HCC.
          Cover page: p62/SQSTM1—Dr. Jekyll and Mr. Hyde that prevents oxidative stress but promotes liver cancer
          • Article
          • Peer Reviewed
          UC Riverside Previously Published Works (2020)
          Nucleotide excision repair (NER) is a major DNA repair pathway for a variety of DNA lesions. XPB plays a key role in DNA opening at damage sites and coordinating damage incision by nucleases. XPB is conserved from archaea to human. In archaea, XPB is associated with a nuclease Bax1. Here we report crystal structures of XPB in complex with Bax1 from Archaeoglobus fulgidus (Af) and Sulfolobus tokodaii (St). These structures reveal for the first time four domains in Bax1, which interacts with XPB mainly through its N-terminal domain. A Cas2-like domain likely helps to position Bax1 at the forked DNA allowing the nuclease domain to incise one arm of the fork. Bax1 exists in monomer or homodimer but forms a heterodimer exclusively with XPB. StBax1 keeps StXPB in a closed conformation and stimulates ATP hydrolysis by XPB while AfBax1 maintains AfXPB in the open conformation and reduces its ATPase activity. Bax1 contains two distinguished nuclease active sites to presumably incise DNA damage. Our results demonstrate that protein-protein interactions regulate the activities of XPB ATPase and Bax1 nuclease. These structures provide a platform to understand the XPB-nuclease interactions important for the coordination of DNA unwinding and damage incision in eukaryotic NER.
            Cover page: Structural basis of the XPB–Bax1 complex as a dynamic helicase–nuclease machinery for DNA repair
            • Article
            • Peer Reviewed
            UC Riverside Previously Published Works (2020)
            Nucleotide excision repair (NER) removes various DNA lesions caused by UV light and chemical carcinogens. The DNA helicase XPB plays a key role in DNA opening and coordinating damage incision by nucleases during NER, but the underlying mechanisms remain unclear. Here, we report crystal structures of XPB from Sulfurisphaera tokodaii (St) bound to the nuclease Bax1 and their complex with a bubble DNA having one arm unwound in the crystal. StXPB and Bax1 together spirally encircle 10 base pairs of duplex DNA at the double-/single-stranded (ds-ss) junction. Furthermore, StXPB has its ThM motif intruding between the two DNA strands and gripping the 3'-overhang while Bax1 interacts with the 5'-overhang. This ternary complex likely reflects the state of repair bubble extension by the XPB and nuclease machine. ATP binding and hydrolysis by StXPB could lead to a spiral translocation along dsDNA and DNA strand separation by the ThM motif, revealing an unconventional DNA unwinding mechanism. Interestingly, the DNA is kept away from the nuclease domain of Bax1, potentially preventing DNA incision by Bax1 during repair bubble extension.
              Cover page: Structural basis of the XPB helicase–Bax1 nuclease complex interacting with the repair bubble DNA
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2023)

              Background

              Multisystem Inflammatory Syndrome in Children (MIS-C), which occurs 2-6 weeks after initial exposure to SARS-CoV-2, was first identified in early 2020 when patients presented with fever and significant inflammation, often requiring management in the intensive care unit. To date, there has been no clinical trial to determine the most effective treatment. This study compares anti-inflammatory treatments that were selected based on current treatments for Kawasaki disease, a coronary artery vasculitis that shares many clinical features with MIS-C.

              Methods

              This randomized, comparative effectiveness trial of children with MIS-C uses the small N Sequential Multiple Assignment Randomized Trial (snSMART) design for rare diseases to compare multiple therapies within an individual. Study participants were treated first with intravenous immunoglobulin (IVIG), and if needed, subjects were then randomized to one of three additional treatments (steroids, anakinra, or infliximab). Participants were re-randomized to remaining treatments if they did not demonstrate clinical improvement.

              Conclusion

              This trial continues to enroll eligible participants to determine the most effective therapies in addition to IVIG and best order in which to use them to treat MIS-C.

              Trial registration

              NCT04898231.
                Cover page: Multisystem Inflammatory Syndrome therapies in children (MISTIC): A randomized trial
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2020)
                Background Coronary artery aneurysms and myocarditis are well-recognized complications of Kawasaki disease (KD) but no systematic evaluation of the consequences of myocarditis has been performed in the subset presenting with low ejection fraction (EF). We postulated that more severe myocardial inflammation as evidenced by low EF during the acute phase could lead to late myocardial fibrosis. Methods and Results We measured the carboxyterminal propeptide of procollagen type I (PIPC), soluble suppressor of tumorigenicity 2, galectin-3 (Gal-3), growth-differentiation factor-15, and calprotectin by ELISA in late convalescent blood samples from 16 KD patients who had an EF ≤55% on their initial echocardiogram. Results were compared with samples from sex- and age-matched KD patients with initial EF >60%. In the univariate analysis, the median Gal-3 and PIPC levels in the low EF group were significantly higher than those in the normal EF group (Gal-3: low EF 6.216 versus normal EF 4.976 mg/dL P=0.038, PIPC: low EF 427.4 versus normal EF 265.2 mg/dL, P=0.01). In a multivariable analysis, there were significant differences for Gal-3 and PIPC levels between the low and normal EF groups, adjusting for age, sex, and worst z score. Conclusions Convalescent KD patients with a history of low EF during the acute illness had significantly elevated levels of Gal-3 and PIPC when compared with matched-control KD patients with normal EF. These findings raise concern for myocardial fibrosis as a potential late sequela of the more severe myocarditis experienced by a subset of KD patients during the acute phase.
                  Cover page: Biomarkers of Inflammation and Fibrosis in Kawasaki Disease Patients Years After Initial Presentation With Low Ejection Fraction
                  • Article
                  • Peer Reviewed
                  UC San Diego Previously Published Works (2011)

                  Goals of work

                  The goal of this study was to examine the relationship between menopausal symptoms, sleep quality, and mood as measured by actigraphy and self-report prior to treatment and at the end of four cycles of chemotherapy in women with breast cancer.

                  Patients and methods

                  Data on sleep quality (measured using actigraphy and self-report) and mood were collected prior to treatment and 12 weeks later at the end of four cycles of chemotherapy in 69 women with newly diagnosed breast cancer. In addition, each filled out the Greene Climacteric Scale. Based on reported occurrence of menses, participants were categorized post hoc into three menopausal status groups: pre-menopausal before and after chemotherapy (Pre-Pre), pre-menopausal or peri-menopausal before and peri-menopausal after chemotherapy (Pre/Peri-Peri), and post-menopausal before and after chemotherapy (Post-Post).

                  Main results

                  Results suggested that women within the Pre-Pre group evidenced more fragmented sleep with less total sleep time (TST) after chemotherapy compared to baseline. Compared to the other groups, the Pre-Pre group also experienced less TST and more awakenings before and after chemotherapy. Although the Pre/Peri-Peri group evidenced a greater increase in vasomotor symptoms after chemotherapy, there was no relationship with sleep. All groups evidenced more depressive symptoms after chemotherapy, but depression was not related to measures of sleep.

                  Conclusions

                  Contrary to the study hypothesis, these results suggest that women who are pre-menopausal or having regular menses before and after four cycles of chemotherapy have worse sleep following chemotherapy. Those women who maintain or become peri-menopausal (irregular menses) experience an increase in climacteric symptoms but do not experience an associated worsening of sleep. These results are preliminary and more research is necessary to further explain these findings.
                    Cover page: Relationship of menopausal status and climacteric symptoms to sleep in women undergoing chemotherapy
                    • Article
                    • Peer Reviewed
                    UCLA Previously Published Works (2022)
                    Herein, we leverage the Ni-catalyzed enantioselective reductive dicarbofunctionalization of internal alkenes with alkyl iodides to enable the synthesis of chiral pyrrolidinones bearing vicinal stereogenic centers. The application of newly developed 1-Nap Quinim is critical for formation of two contiguous stereocenters in high yield, enantioselectivity, and diastereoselectivity. This catalytic system also improves both the yield and enantioselectivity in the synthesis of α,α-dialkylated γ-lactams. Computational studies reveal that the enantiodetermining step proceeds with a carbamoyl-NiI intermediate that is reduced by the Mn reductant prior to intramolecular migratory insertion. The presence of the t-butyl group of the Quinim ligand leads to an unfavorable distortion of the substrate in the TS that leads to the minor enantiomer. Calculations also support an improvement in enantioselectivity with 1-Nap Quinim compared to p-tol Quinim.
                      Cover page: Nickel-Catalyzed Enantioselective Reductive Alkyl-Carbamoylation of Internal Alkenes.
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