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Open Access Publications from the University of California

Scholarly Works (13 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2018)

As life expectancy prolongs, the incidence of neurodegenerative diseases continues to rise. The pathogenesis of neurodegenerative diseases is poorly understood and there is no effective long-term therapy. This thesis focus on two neurodegenerative disease: Parkinson’s disease (PD), the second most common neurodegenerative disease and inclusion body myopathy, Paget disease with frontotemporal dementia (IBMPFD) caused by Valosin-containing protein (VCP) mutants. Recent studies accentuate the key role of mitochondrial dysfunction in disease-onset. Mitochondrial fusion/fission is critical for mitochondrial integrity with Mitofusins (Mfn) control the initial step of fusion. We found that Mitofusins are key targets in both Parkinson’s disease and in disease by VCP mutants.

Mutations in PTEN-induced putative kinase 1 (PINK1) and parkin cause autosomal recessive PD. Genetic studies indicate PINK1 and parkin function in a common pathway and negatively regulate Mfn. In chapter two, we identify VCP as a suppressor for PINK1 and parkin mutants and its suppression is achieved through Mfn degradation. VCP missense mutations cause IBMPFD and other neurodegenerative disorders. The pathological mechanism of IBMPFD is not clear and there is no cure. we generated an in vivo IBMPFD model in Drosophila, which recapitulates disease pathologies in human patients; we demonstrated common VCP disease mutants act as hyperactive alleles and found that VCP inhibitors reverse the disease pathology in in vivo disease models as well as in patients’ fibroblasts. Our results strongly suggest VCP inhibitors have therapeutic value.

Mitofusins are key substrates of ubiquitin E3 ligase Parkin. Yet the exact mechanism of the ubiquitination is not well-understood. In chapter three, we identified critical lysine sites for Mitofusin ubiquitination by Parkin in Drosophila as well as in mammalian cells. Flies harboring mutated lysine sites display severe tissue defects. Parkin-mediated mitophagy plays a major role in mitochondrial quality control. Lysine mutants delay Parkin-mediated degradation of Mitofusins and mitophagy. Our results uncover the important regulatory role of Mitofusins in mitochondrial quality control and tissue health.

Together, our work demonstrates that utilizing Drosophila and human cells, we could establish reliable in vivo and in vitro models of neurodegenerative disease, unravel novel disease mechanism and identify therapy for these devastating diseases.

    Cover page: The role of Mitofusin (Mfn) in the pathogenesis of Parkinson’s disease and myopathy/frontotemporal dementia
    • Article
    • Peer Reviewed
    LBL Publications (2017)
    The doping mechanism of poly (1-pyrenemethyl methacrylate) (PPy) is investigated through electrochemical analytical and spectroscopic method. The performance of PPy as a Si materials binder is studied and compared with that of a commercial available lithium polyacrylate (PAALi) binder. The pyrene moiety consumes lithium ions according to the cyclic voltammogram (CV) measurement, as a doping to the PPy binder. Based on the lithium consumption, PPy based Si/graphite electrode doping is quantified at 1.1 electron/pyrene moiety. The PPy binder based electrodes surface are uniform and crack free during lithiation/delithiation, which is revealed through Scanning electron microscope (SEM) imaging.
      Cover page: Investigating the Doping Mechanism of Pyrene Based Methacrylate Functional Conductive Binder in Silicon Anodes for Lithium-Ion Batteries
      • Article
      • Peer Reviewed
      UC Santa Barbara Previously Published Works (2022)
      BACKGROUND: Human embryonic stem cell-derived retinal pigment epithelial cells (hESC-derived RPE) are a promising source for cell-replacement therapy to treat retinal degenerative diseases, but research on RPE cryopreservation is limited. This study aimed to determine the best phase for RPE cryopreservation to preserve the post-thaw function and uncover the mechanism underlying RPE freezing tolerance. METHODS: hESC-derived RPE cells were cryopreserved at various time points after seeding. After thawing, the survival and attachment rates, RPE marker gene expression, apical-basal polarity, PEDF secretion, transepithelial resistance, and phagocytotic ability of post-thaw RPE cells were evaluated. RNA sequencing was performed on RPE cells at three-time points, differentially expressed genes were identified, and gene ontology, Kyoto encyclopedia of genes and genomes, and protein-protein interaction analyses were used to investigate the key pathways or molecules associated with RPE cell freezing tolerance. RESULTS: RPE frozen at passage 2 day 5 (P2D5) had the highest cell viability and attachment after thawing. They also retained properly localized expression of RPE marker genes and biological functions such as PEDF secretion, high transepithelial resistance, and phagocytic ability. The RNA-sequencing analysis revealed that RPE cells at P2D5 expressed high levels of cell cycle/DNA replication and ECM binding associated genes, as well as THBS1, which may serve as a possible hub gene involved in freezing tolerance. We also confirmed that the RPE cells at P2D5 were in the exponential stage with active DNA replication. CONCLUSIONS: We propose that freezing hESC-derived RPE cells during their exponential phase results in the best post-thawing outcome in terms of cell viability and preservation of RPE cell properties and functions. The high expression levels of the cell cycle and ECM binding associated genes, particularly THBS1, may contribute to better cell recovery at this stage.
        Cover page: Determining the optimal stage for cryopreservation of human embryonic stem cell-derived retinal pigment epithelial cells.
        • Article
        • Peer Reviewed
        UC Berkeley Previously Published Works (2019)
        Listeria monocytogenes can cause a life-threatening illness when the foodborne pathogen spreads beyond the intestinal tract to distant organs. Many aspects of the intestinal phase of L. monocytogenes pathogenesis remain unknown. Here, we present a foodborne infection model using C57BL/6 mice that have been pretreated with streptomycin. In this model, as few as 100 L. monocytogenes CFU were required to cause self-limiting enterocolitis, and systemic dissemination followed previously reported routes. Using this model, we report that listeriolysin O (LLO) and actin assembly-inducing protein (ActA), two critical virulence determinants, were necessary for intestinal pathology and systemic spread but were dispensable for intestinal growth. Sequence tag-based analysis of microbial populations (STAMP) was used to investigate the within-host population dynamics of wild-type and LLO-deficient strains. The wild-type bacterial population experienced severe bottlenecks over the course of infection, and by 5 days, the intestinal population was highly enriched for bacteria originating from the gallbladder. In contrast, LLO-deficient strains did not efficiently disseminate and gain access to the gallbladder, and the intestinal population remained diverse. These findings suggest that systemic spread and establishment of a bacterial reservoir in the gallbladder imparts an intraspecies advantage in intestinal occupancy. Since intestinal L. monocytogenes is ultimately released into the environment, within-host population bottlenecks may provide purifying selection of virulence genes.IMPORTANCEListeria monocytogenes maintains capabilities for free-living growth in the environment and for intracellular replication in a wide range of hosts, including livestock and humans. Here, we characterized an enterocolitis model of foodborne L. monocytogenes infection. This work highlights a multiorgan trafficking circuit and reveals a fitness advantage for bacteria that successfully complete this cycle. Because virulence factors play critical roles in systemic dissemination and multiple bottlenecks occur as the bacterial population colonizes different tissue sites, this multiorgan trafficking circuit likely provides purifying selection of virulence genes. This study also serves as a foundation for future work using the L. monocytogenes-induced enterocolitis model to investigate the biology of L. monocytogenes in the intestinal environment.
          Cover page: A Multiorgan Trafficking Circuit Provides Purifying Selection of Listeria monocytogenes Virulence Genes
          • Article
          • Peer Reviewed
          LBL Publications (2018)
          A highly graphitized carbon on a silicon monoxide (SiO) surface coating at low temperature, based on polymer precursor π⁻π stacking, was developed. A novel conductive and electrochemically stable carbon coating was rationally designed to modify the SiO anode materials by controlling the sintering of a conductive polymer, a pyrene-based homopolymer poly (1-pyrenemethyl methacrylate; PPy), which achieved high graphitization of the carbon layers at a low temperature and avoided silicon carbide formation and possible SiO material transformation. When evaluated as the anode of a lithium-ion battery (LIB), the carbon-coated SiO composite delivered a high discharge capacity of 2058.6 mAh/g at 0.05 C of the first formation cycle with an initial Coulombic efficiency (ICE) of 62.2%. After 50 cycles at 0.1 C, this electrode capacity was 1090.2 mAh/g (~82% capacity retention, relative to the capacity of the second cycle at 0.1 °C rate), and a specific capacity of 514.7 mAh/g was attained at 0.3 C after 500 cycles. Furthermore, the coin-type full cell composed of the carbon coated SiO composite anode and the Li[Ni0.5Co0.2Mn0.3O₂] cathode attained excellent cycling performance. The results show the potential applications for using a π⁻π stacking polymer precursor to generate a highly graphitize coating for next-generation high-energy-density LIBs.
            Cover page: Highly Graphitized Carbon Coating on SiO with a π–π Stacking Precursor Polymer for High Performance Lithium-Ion Batteries
            • Article
            • Peer Reviewed
            UCLA Previously Published Works (2019)
            Strand-selection is the final step of microRNA biogenesis in which functional mature miRNAs are generated from one or both arms of precursor. The preference of strand-selection is diverse during development and tissue formation, however, its pathological effect is still unknown. Here we find that two miRNA arms from the same precursor, miR-574-5p and miR-574-3p, are inversely expressed and play exactly opposite roles in gastric cancer progression. Higher-5p with lower-3p expression pattern is significantly correlated with higher TNM stages and poor prognosis of gastric cancer patients. The increase of miR-574-5p/-3p ratio, named miR-574 arm-imbalance is partially due to the dynamic expression of their highly complementary targets in gastric carcinogenesis, moreover, the arm-imbalance of miR-574 is in turn involved and further promotes gastric cancer progression. Our results indicate that miR-574 arm-imbalance contribute to gastric cancer progression and re-modification of the miR-574-targets homeostasis may represent a promising strategy for gastric cancer therapy.
              Cover page: microRNA arm-imbalance in part from complementary targets mediated decay promotes gastric cancer progression.
              • Article
              • Peer Reviewed
              LBL Publications (2019)
              The trap-assisted charge injection in polyfluorene-poly(3,4-ethylenedioxythiophene): poly(styrenesulfonate) (PEDOT:PSS) model systems with an Al or Al/LiF cathode is investigated. We find that inserting 1.3 nm LiF increases electron and hole injections simultaneously and the increase of holes is greater than electrons. The evolution of internal interfaces within polymer light-emitting diodes is observed by transmission electron microscopy, which reveals that the introduction of LiF improves the interface stability at both the cathode (cathode/polymer) and the anode (indium tin oxide (ITO)/PEDOT:PSS). Above-mentioned experimental results have been compared to the numerical simulations with a revised Davids model and potential physical mechanisms for the trap-assisted charge injection are discussed.
                Cover page: Trap-Assisted Charge Injection into Large Bandgap Polymer Semiconductors
                • Article
                • Peer Reviewed
                UCLA Previously Published Works (2021)
                Coronavirus disease 2019 (COVID-19) is emerging as the greatest public health crisis in the early 21stcentury. Its causative agent, Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), is an enveloped single stranded positive-sense ribonucleic acid virus that enters cells via the angiotensin converting enzyme 2 receptor or several other receptors. While COVID-19 primarily affects the respiratory system, other organs including the brain can be involved. In Western clinical studies, relatively mild neurological dysfunction such as anosmia and dysgeusia is frequent (~70-84%) while severe neurologic disorders such as stroke (~1-6%) and meningoencephalitis are less common. It is unclear how much SARS-CoV-2 infection contributes to the incidence of stroke given co-morbidities in the affected patient population. Rarely, clinically-defined cases of acute disseminated encephalomyelitis, Guillain-Barré syndrome and acute necrotizing encephalopathy have been reported in COVID-19 patients. Common neuropathological findings in the 184 patients reviewed include microglial activation (42.9%) with microglial nodules in a subset (33.3%), lymphoid inflammation (37.5%), acute hypoxic-ischemic changes (29.9%), astrogliosis (27.7%), acute/subacute brain infarcts (21.2%), spontaneous hemorrhage (15.8%), and microthrombi (15.2%). In our institutional cases, we also note occasional anterior pituitary infarcts. COVID-19 coagulopathy, sepsis, and acute respiratory distress likely contribute to a number of these findings. When present, central nervous system lymphoid inflammation is often minimal to mild, is detected best by immunohistochemistry and, in one study, indistinguishable from control sepsis cases. Some cases evince microglial nodules or neuronophagy, strongly supporting viral meningoencephalitis, with a proclivity for involvement of the medulla oblongata. The virus is detectable by reverse transcriptase polymerase chain reaction, immunohistochemistry, or electron microscopy in human cerebrum, cerebellum, cranial nerves, olfactory bulb, as well as in the olfactory epithelium; neurons and endothelium can also be infected. Review of the extant cases has limitations including selection bias and limited clinical information in some cases. Much remains to be learned about the effects of direct viral infection of brain cells and whether SARS-CoV-2 persists long-term contributing to chronic symptomatology.
                  Cover page: Neuropathology of COVID-19 (neuro-COVID): clinicopathological update.
                  • Article
                  • Peer Reviewed
                  UC San Francisco Previously Published Works (2022)

                  Objective

                  Current lupus nephritis (LN) treatments are effective in only 30% of patients, emphasizing the need for novel therapeutic strategies. We undertook this study to develop mechanistic hypotheses and explore novel biomarkers by analyzing the longitudinal urinary proteomic profiles in LN patients undergoing treatment.

                  Methods

                  We quantified 1,000 urinary proteins in 30 patients with LN at the time of the diagnostic renal biopsy and after 3, 6, and 12 months. The proteins and molecular pathways detected in the urine proteome were then analyzed with respect to baseline clinical features and longitudinal trajectories. The intrarenal expression of candidate biomarkers was evaluated using single-cell transcriptomics of renal biopsy sections from LN patients.

                  Results

                  Our analysis revealed multiple biologic pathways, including chemotaxis, neutrophil activation, platelet degranulation, and extracellular matrix organization, which could be noninvasively quantified and monitored in the urine. We identified 237 urinary biomarkers associated with LN, as compared to controls without systemic lupus erythematosus. Interleukin-16 (IL-16), CD163, and transforming growth factor β mirrored intrarenal nephritis activity. Response to treatment was paralleled by a reduction in urinary IL-16, a CD4 ligand with proinflammatory and chemotactic properties. Single-cell RNA sequencing independently demonstrated that IL16 is the second most expressed cytokine by most infiltrating immune cells in LN kidneys. IL-16-producing cells were found at key sites of kidney injury.

                  Conclusion

                  Urine proteomics may profoundly change the diagnosis and management of LN by noninvasively monitoring active intrarenal biologic pathways. These findings implicate IL-16 in LN pathogenesis, designating it as a potentially treatable target and biomarker.
                    Cover page: Urine Proteomics and Renal Single‐Cell Transcriptomics Implicate Interleukin‐16 in Lupus Nephritis
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2023)
                    Ferroptosis is an iron-dependent programmed cell death associated with severe kidney diseases, linked to decreased glutathione peroxidase 4 (GPX4). However, the spatial distribution of renal GPX4-mediated ferroptosis and the molecular events causing GPX4 reduction during ischemia-reperfusion (I/R) remain largely unknown. Using spatial transcriptomics, we identify that GPX4 is situated at the interface of the inner cortex and outer medulla, a hyperactive ferroptosis site post-I/R injury. We further discover OTU deubiquitinase 5 (OTUD5) as a GPX4-binding protein that confers ferroptosis resistance by stabilizing GPX4. During I/R, ferroptosis is induced by mTORC1-mediated autophagy, causing OTUD5 degradation and subsequent GPX4 decay. Functionally, OTUD5 deletion intensifies renal tubular cell ferroptosis and exacerbates acute kidney injury, while AAV-mediated OTUD5 delivery mitigates ferroptosis and promotes renal function recovery from I/R injury. Overall, this study highlights a new autophagy-dependent ferroptosis module: hypoxia/ischemia-induced OTUD5 autophagy triggers GPX4 degradation, offering a potential therapeutic avenue for I/R-related kidney diseases.
                      Cover page: Autophagy of OTUD5 destabilizes GPX4 to confer ferroptosis-dependent kidney injury.
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