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Open Access Publications from the University of California

Scholarly Works (37 results)

  • Article
  • Peer Reviewed
UC San Diego Previously Published Works (2014)
The pathology of granulomatosis with polyangiitis (GPA), formerly Wegener granulomatosis, typically features a granulomatous and sometimes necrotizing vasculitis targeting the respiratory tract and kidneys. However, orbital involvement occurs in up to 60% of patients and is frequently the first or only clinical presentation in patients with systemic or limited forms of GPA. Orbital GPA can cause significant morbidity and potentially lead to complete loss of vision and permanent facial deformity. Fortunately, GPA is highly responsive to medical treatment with corticosteroids combined with cyclophosphamide or, more recently, rituximab. Therefore, it is imperative for this disease to be accurately diagnosed on orbital biopsy and distinguished from other histologically similar orbital lesions. Herein, we review the clinical and pathologic findings of orbital GPA, focusing on the differentiation of this disease from other inflammatory orbital lesions.
    Cover page: Orbital Granulomatosis With Polyangiitis (Wegener Granulomatosis): Clinical and Pathologic Findings
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2021)

    Tauopathies, such as Alzheimer’s Disease (AD) and Progressive Supranuclear Palsy (PSP), are characterized by the central nervous system accumulation of misfolded tau protein. Endoplasmic reticulum (ER) stress and Unfolded Protein Response (UPR) may be cellular mechanisms that cause tauopathies. As one of three major branches of UPR, PERK was identified as a genetic risk factor for AD and PSP in several GWAS studies. Upon activation, PERK attenuates protein translation to restore ER homeostasis but prolonged PERK activation can induce apoptosis. Here, we studied the role of PERK in tau aggregation in human AD and PSP brain tissues and in a cell culture model. We prepared protein lysates from the hippocampus region of advanced AD patient brains (Braak 6) and normal brains (Braak 1). We found more tau aggregated protein in Braak 6 brains in comparison to Braak 1 brains by immunoblotting. We also found a statistically significant increase of phosphorylated PERK in Braak 1 brains in comparison to Braak 6 brains in AD patients. This finding suggests that PERK activity is inversely proportional to insoluble misfolded tau aggregation. We did not find any correlation between PERK-haplotype and PERK functional in AD brains. We also prepared protein lysates from 3 different anatomic regions from PSP patient brains (midbrain, frontal cortex, and occipital cortex). The PSP results were highly variable due to technical problems, and we did not identify any reproducible correlations between tau levels and phosphorylated PERK levels.We further studied how PERK and tau interact utilizing HEK293 cells stably expressing TauRD-YFP (Biosensor cells) developed by Marc Diamond’s group as a cellular model of tau protein aggregation. We activated or inhibited PERK activity in TauRD biosensor cells by treating them with pharmacochemical small molecule modulators (GSK2656157, GSK2606414, salubrinal, ISRIB). We monitored tau aggregation by the formation of YFP fluorescent puncta in the cells. We found an inverse association between PERK pathway activation and tau aggregation. In summary, our brain and cell culture findings implicate PERK as a regulator of tau protein accumulation. PERK pathway activation may have high therapeutic potential for tauopathy treatment.

      Cover page: Function of Protein Kinase RNA-like Endoplasmic Reticulum Kinase in regulating tau protein aggregation in Alzheimer’s Disease and Progressive Supranuclear Palsy
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2014)
      Many mutations in rhodopsin gene linked to retinitis pigmentosa (RP) cause rhodopsin misfolding. Rod photoreceptor cells expressing misfolded rhodopsin eventually die. Identifying mechanisms to prevent rhodopsin misfolding or to remove irreparably misfolded rhodopsin could provide new therapeutic strategies. IRE1, ATF6, and PERK signaling pathways, collectively called the unfolded protein response (UPR), regulate the functions of endoplasmic reticulum, responsible for accurate folding of membrane proteins such as rhodopsin. We used chemical and genetic approaches to selectively activate IRE1, ATF6, or PERK signaling pathways one at a time and analyzed their effects on mutant rhodopsin linked to RP. We found that both artificial IRE1 and ATF6 signaling promoted the degradation of mutant rhodopsin with lesser effects on wild-type rhodopsin. Furthermore, IRE1 and ATF6 signaling preferentially reduced levels of aggregated rhodopsins. By contrast, PERK signaling reduced levels of wild-type and mutant rhodopsin. These studies indicate that activation of either IRE1, ATF6, or PERK prevents mutant rhodopsin from accumulating in the cells. In addition, activation of IRE1 or ATF6 can selectively remove aggregated or mutant rhodopsin from the cells and may be useful in treating RP associated with rhodopsin protein misfolding.
        Cover page: The Effects of IRE1, ATF6, and PERK Signaling on adRP-Linked Rhodopsins
        • Thesis
        • Peer Reviewed
        UC San Diego Electronic Theses and Dissertations (2016)

        The endoplasmic reticulum is an organelle that responsible for the folding and processing of newly synthesized proteins. When unfolded or misfolded proteins accumulate in the ER and disrupt proper function this leads to a phenomenon known as ER stress. When this occurs, the UPR is activated in order to reduce ER load and restore the ER to its normal function. ATF6, IRE1, and PERK are the three pathways of the UPR. Here, I studied ER stress and the UPR in relation to retinitis pigmentosa, achromatopsia, and retinal degeneration in a tauopathy mouse model. I found that P23H rhodopsin, which is one of the most common mutated proteins involved with the development of retinitis pigmentosa, is highly ubiquitinated by several E3 ubiquitin ligases in order to be targeted for degradation. In addition, knocking out ATF6 seems to increase activation of IRE1 and preserve rhodopsin levels in the case of Rho+/P23H mice. In the achromatopsia study, Class 2 ATF6 mutants experience constitutive transcriptional activation and Class 3 ATF6 mutants are transcriptionally inactive, which can help explain causation of disease development. In the preliminary studies of the PS19 mouse model, I found that there is retinal degeneration and loss of visual function occurring in these mice compared to their wildtype littermates.

          Cover page: Endoplasmic Reticulum Stress in Mouse Models of Neurodegeneration
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2014)
          Rhodopsin mutations cause many types of heritable retinitis pigmentosa (RP). Biochemical and in vitro studies have demonstrated that many RP-linked mutant rhodopsins produce misfolded rhodopsin proteins, which are prone to aggregation and retention within the endoplasmic reticulum, where they cause endoplasmic reticulum stress and activate the Unfolded Protein Response signaling pathways. Many vertebrate models of retinal degeneration have been created through expression of RP-linked rhodopsins in photoreceptors including, but not limited to, VPP/GHL mice, P23H Rhodopsin frogs, P23H rhodopsin rats, S334ter rhodopsin rats, C185R rhodopsin mice, T17M rhodopsin mice, and P23H rhodopsin mice. These models have provided many opportunities to test therapeutic strategies to prevent retinal degeneration and also enabled in vivo investigation of cellular and molecular mechanisms responsible for photoreceptor cell death. Here, we examine and compare the contribution of endoplasmic reticulum stress to retinal degeneration in several vertebrate models of RP generated through expression of mutant rhodopsins.
            Cover page: Endoplasmic Reticulum Stress in Vertebrate Mutant Rhodopsin Models of Retinal Degeneration
            • Article
            • Peer Reviewed
            UC San Francisco Previously Published Works (2009)
            Maintenance of endoplasmic reticulum (ER) function is achieved in part through Ire1 (inositol-requiring enzyme 1), a transmembrane protein activated by protein misfolding in the ER. The cytoplasmic nuclease domain of Ire1 cleaves the messenger RNA (mRNA) encoding XBP-1 (X-box-binding protein 1), enabling splicing and production of this active transcription factor. We recently showed that Ire1 activation independently induces the rapid turnover of mRNAs encoding membrane and secreted proteins in Drosophila melanogaster cells through a pathway we call regulated Ire1-dependent decay (RIDD). In this study, we show that mouse fibroblasts expressing wild-type Ire1 but not an Ire1 variant lacking nuclease activity also degrade mRNAs in response to ER stress. Using a second variant of Ire1 that is activated by a small adenosine triphosphate analogue, we show that although XBP-1 splicing can be artificially induced in the absence of ER stress, RIDD appears to require both Ire1 activity and ER stress. Our data suggest that cells use a multitiered mechanism by which different conditions in the ER lead to distinct outputs from Ire1.
              Cover page: Regulated Ire1-dependent decay of messenger RNAs in mammalian cells
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2018)
              A 52 year-old man with Erdheim-Chester Disease (ECD) (a non-Langerhans polyostotic sclerosing histiocytosis) had next-generation sequencing (NGS) performed as part of his diagnostic workup. In addition to the tissue BRAF V600E mutation that is found in over 50% of ECD cases, he was also found to have a JAK2 V617F alteration in cell-free circulating tumor DNA (ctDNA) (liquid biopsy). The latter was thought to be an "incidental" finding, perhaps due to clonal hematopoiesis (though this usually occurs in older individuals), as his blood counts were normal and he had no splenomegaly. Approximately 13 months after the ctDNA test showing JAK2 V617F, he developed anemia, thrombocytopenia, and splenomegaly. Marrow biopsy then showed megakaryocytic atypia and markedly increased marrow fibrosis, consistent with WHO grade 2 of 3 myelofibrosis. Therefore, the patient was determined to have ECD with a typical BRAF V600E mutation, as well as primary myelofibrosis, with the latter diagnosis manifesting clinically over one year after the JAK2 V617F was first detected in ctDNA. He recently was started on the JAK2 inhibitor ruxolitinib. This case demonstrates that genomic alterations detected by liquid biopsy for evaluation of specific malignancies already present may serve as an early harbinger of hematological disease.
                • Article
                • Peer Reviewed
                UC San Diego Previously Published Works (2015)
                Eukaryotic cells fold and assemble membrane and secreted proteins in the endoplasmic reticulum (ER), before delivery to other cellular compartments or the extracellular environment. Correctly folded proteins are released from the ER, and poorly folded proteins are retained until they achieve stable conformations; irreparably misfolded proteins are targeted for degradation. Diverse pathological insults, such as amino acid mutations, hypoxia, or infection, can overwhelm ER protein quality control, leading to misfolded protein buildup, causing ER stress. To cope with ER stress, eukaryotic cells activate the unfolded protein response (UPR) by increasing levels of ER protein-folding enzymes and chaperones, enhancing the degradation of misfolded proteins, and reducing protein translation. In mammalian cells, three ER transmembrane proteins, inositol-requiring enzyme-1 (IRE1; official name ERN1), PKR-like ER kinase (PERK; official name EIF2AK3), and activating transcription factor-6, control the UPR. The UPR signaling triggers a set of prodeath programs when the cells fail to successfully adapt to ER stress or restore homeostasis. ER stress and UPR signaling are implicated in the pathogenesis of diverse diseases, including neurodegeneration, cancer, diabetes, and inflammation. This review discusses the current understanding in both adaptive and apoptotic responses as well as the molecular mechanisms instigating apoptosis via IRE1 and PERK signaling. We also examine how IRE1 and PERK signaling may be differentially used during neurodegeneration arising in retinitis pigmentosa and prion infection.
                  Cover page: Multiple Mechanisms of Unfolded Protein Response–Induced Cell Death
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2019)

                  Background

                  Critical limb ischemia remains a difficult disease to treat, with limited level one data. The BEST-CLI trial (Best Endovascular vs Best Open Surgical Therapy in Patients with Critical Limb Ischemia) is attempting to answer whether initial treatment with open surgical bypass or endovascular therapy improves outcomes, although it remains in enrollment. This study aims to compare amputation-free survival and reintervention rates in patients treated with initial open surgical bypass or endovascular intervention for ischemic ulcers of the lower extremities.

                  Methods and results

                  Using California nonfederal hospital data linked to statewide death data, all patients with lower extremity ulcers and a diagnosis of peripheral artery disease who underwent a revascularization procedure from 2005 to 2013 were identified. Propensity scores were formulated from baseline patient characteristics. Inverse probability weighting was used with Kaplan-Meier analysis to determine amputation-free survival and time to reintervention for open versus endovascular treatment. Mixed-effects Cox proportional hazards modeling was used to adjust for patient ability to manage their disease and hospital revascularization volume. A total of 16 800 patients were identified. Open surgical bypass was the initial treatment in 5970 (36%) while 10 830 (64%) underwent endovascular interventions. Patients in the endovascular group were slightly younger compared with the open group (70 versus 71 years, ±12 years; P<0.001). Endovascular-first patients were more likely to have comorbid renal failure (36% versus 24%), coronary artery disease (34% versus 32%), congestive heart failure (19% versus 15%), and diabetes mellitus (65% versus 58%; all P values <0.05). After inverse propensity weighting as well as adjustment for patient ability to manage their disease and hospital revascularization experience, open surgery first was associated with a worse amputation-free survival (hazard ratio, 1.16; 95% CI, 1.13-1.20) with no difference in mortality (hazard ratio, 0.94; 95% CI, 0.89-1.11). Endovascular first was associated with higher rates of reintervention (hazard ratio, 1.19; 95% CI, 1.14-1.23).

                  Conclusions

                  Patients with critical limb ischemia have multiple comorbidities, and initial surgical bypass is associated with poorer amputation-free survival compared with an endovascular-first approach, perhaps due to increased severity of wounds at the time of presentation.
                    Cover page: Endovascular-First Treatment Is Associated With Improved Amputation-Free Survival in Patients With Critical Limb Ischemia
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2009)
                    Protein misfolding in the endoplasmic reticulum (ER) activates a set of intracellular signaling pathways, collectively termed the Unfolded Protein Response (UPR). UPR signaling promotes cell survival by reducing misfolded protein levels. If homeostasis cannot be restored, UPR signaling promotes cell death. The molecular basis for the switch between prosurvival and proapoptotic UPR function is poorly understood. The ER-resident proteins, PERK and IRE1, control two key UPR signaling pathways. Protein misfolding concomitantly activates PERK and IRE1 and has clouded insight into their contributions toward life or death cell fates. Here, we employed chemical-genetic strategies to activate individually PERK or IRE1 uncoupled from protein misfolding. We found that sustained PERK signaling impaired cell proliferation and promoted apoptosis. By contrast, equivalent durations of IRE1 signaling enhanced cell proliferation without promoting cell death. These results demonstrate that extended PERK and IRE1 signaling have opposite effects on cell viability. Differential activation of PERK and IRE1 may determine life or death decisions after ER protein misfolding.
                      Cover page: Divergent Effects of PERK and IRE1 Signaling on Cell Viability
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