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Open Access Publications from the University of California

Scholarly Works (110 results)

  • Thesis
  • Peer Reviewed
UCLA Electronic Theses and Dissertations (2017)

Injectable hydrogels are widely used as in situ scaffolds to support tissue regrowth but suffers from degradation before tissue reformation. As shown in our last paper, microporous Annealed Particle (MAP) gels can provide a stably linked interconnected network for tissue regrowth. While current applications of MAP gel composed of 4-arm poly(ethylene) glycol-vinyl sulphone (PEG-VS) backbone is limited to mimicking soft tissues new backbone material 8-arm PEG-VS increases the range of gel stiffness. Stiffer gel scaffold facilitates cell infiltration rate and expands application to tissues with greater mechanical movement. However, backbone and cross-linker materials can react in the channel and form polymers due to transverse diffusion, which causes jetting in the device and interrupts monodisperse droplet production. Here we present a three-inlet flow-focusing droplet generator which can prevent polymerization in the channel by controlling the width of a middle buffer stream. We have shown that it enables 4 times longer production time for previous material and at least 2 times longer production time for new material. MAP gel with a higher stiffness and annealing force is achieved using the 3-inlet device. The 3-inlet device empowers mass production of MAP gel, leading to higher reproducibility of MAP gel related research studies. The study of the middle buffer stream gives ideas to other flow-focusing microfluidics system where two reactants need to be separated before encapsulation in droplets.

    Cover page: 3-inlet Flow-Focusing Droplet Generator Enables Longtime Production of Microporous Annealed Particle Gel with A Range of Stiffness and Size
    • Thesis
    • Peer Reviewed
    UC San Diego Electronic Theses and Dissertations (2023)

    Neurotrophic receptor tyrosine kinases (NTRKs) belong to the receptor tyrosine kinase (RTK) family. NTRKs are responsible for the activation of multiple downstream signaling pathways that regulate cell growth, proliferation, differentiation, and apoptosis. NTRK-associated mutations lead to aberrant activation of these downstream pathways and often result in oncogenesis. This study characterizes the NACC2-NTRK2 oncogenic fusion protein that leads to pediatric astrocytoma and glioblastoma. This fusion joins the broad-complex, tramtrack, and bric-a-brac (BTB) domain of Nucleus Accumbens-associated protein 2 (NACC2) with the transmembrane helix and tyrosine kinase domain of NTRK2. This work focuses on identifying domains critical to the fusion protein activity and possible methods to deactivate the fusion. NACC2-NTRK2 is able to transform NIH3T3 cells. Such activity depends on the NTRK2 kinase domain phosphorylation that activates signaling pathways including MAPK, JAK/STAT, and PLCγ. The activation of the NTRK2 kinase domain relies on the multimerization of the NACC2 BTB domain. A BTB domain charged pocket mutation and a monomer core mutation result in deactivation of the kinase domain and abrogates the ability to transform NIH3T3 cells, suggesting that BTB domain inhibition could be a potential treatment for the NACC2-NTRK2 induced cancer. The undefined region of NACC2 at residues 120-418 is responsible for forming stronger multimers. Once removed, the NACC2-NTRK2 multimer is vulnerable to SDS denaturation and leads to reduced activity of the fusion. Lastly, the removal of the transmembrane helix leads to higher activation of the NACC2-NTRK2 fusion. A protein stability assay indicates that transmembrane deletion prevents NACC2-NTRK2 degradation.

      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2018)
      Clinical differentiation of atypical breast abscesses from necrotic tumour in premenopausal women is challenging and may delay appropriate therapy. In this case report, we present a 36-year-old woman with signs, symptoms and conventional imaging features of malignancy who underwent breast MRI. On diffusion-weighted imaging (DWI), profoundly low apparent diffusion coefficient values were a distinguishing sign of breast abscess from necrotic breast cancer, and helped manage the patient conservatively. We present a companion case of necrotic breast tumour highlighting significant differences in DWI.
        Cover page: Diffusion-weighted imaging is helpful in the accurate non-invasive diagnosis of breast abscess: correlation with necrotic breast cancer
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2014)
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2017)
          Accurate prediction of Alzheimer's disease (AD) is important for the early diagnosis and treatment of this condition. Mild cognitive impairment (MCI) is an early stage of AD. Therefore, patients with MCI who are at high risk of fully developing AD should be identified to accurately predict AD. However, the relationship between brain images and AD is difficult to construct because of the complex characteristics of neuroimaging data. To address this problem, we present a longitudinal measurement of MCI brain images and a hierarchical classification method for AD prediction. Longitudinal images obtained from individuals with MCI were investigated to acquire important information on the longitudinal changes, which can be used to classify MCI subjects as either MCI conversion (MCIc) or MCI non-conversion (MCInc) individuals. Moreover, a hierarchical framework was introduced to the classifier to manage high feature dimensionality issues and incorporate spatial information for improving the prediction accuracy. The proposed method was evaluated using 131 patients with MCI (70 MCIc and 61 MCInc) based on MRI scans taken at different time points. Results showed that the proposed method achieved 79.4% accuracy for the classification of MCIc versus MCInc, thereby demonstrating very promising performance for AD prediction.
            Cover page: Longitudinal measurement and hierarchical classification framework for the prediction of Alzheimer’s diseaseCreative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2024)
            Neurotrophic receptor tyrosine kinases (NTRKs) belong to the receptor tyrosine kinase (RTK) family. NTRKs are responsible for the activation of multiple downstream signaling pathways that regulate cell growth, proliferation, differentiation, and apoptosis. NTRK-associated mutations often result in oncogenesis and lead to aberrant activation of downstream signaling pathways including MAPK, JAK/STAT, and PLCγ1. This study characterizes the NACC2-NTRK2 oncogenic fusion protein that leads to pilocytic astrocytoma and pediatric glioblastoma. This fusion joins the BTB domain (Broad-complex, Tramtrack, and Bric-a-brac) domain of NACC2 (Nucleus Accumbens-associated protein 2) with the transmembrane helix and tyrosine kinase domain of NTRK2. We focus on identifying critical domains for the biological activity of the fusion protein. Mutations were introduced in the charged pocket of the BTB domain or in the monomer core, based on a structural comparison of the NACC2 BTB domain with that of PLZF, another BTB-containing protein. Mutations were also introduced into the NTRK2-derived portion to allow comparison of two different breakpoints that have been clinically reported. We show that activation of the NTRK2 kinase domain relies on multimerization of the BTB domain in NACC2-NTRK2. Mutations which disrupt BTB-mediated multimerization significantly reduce kinase activity and downstream signaling. The ability of these mutations to abrogate biological activity suggests that BTB domain inhibition could be a potential treatment for NACC2-NTRK2-induced cancers. Removal of the transmembrane helix leads to enhanced stability of the fusion protein and increased activity of the NACC2-NTRK2 fusion, suggesting a mechanism for the oncogenicity of a distinct NACC2-NTRK2 isoform observed in pediatric glioblastoma.
              Cover page: Critical domains for NACC2-NTRK2 fusion protein activation.
              • Article
              • Peer Reviewed
              UC San Diego Previously Published Works (2024)
              AIM OF STUDY: Chromosomal translocations involving neurotrophic receptor tyrosine kinases (NTRKs) have been identified in 20 % of soft tissue sarcomas. This work focuses on the EML4-NTRK3 translocation identified in cases of Infantile Fibrosarcoma, which contains the coiled-coil multimerization domain of Echinoderm Microtubule-like protein 4 (EML4) fused with the tyrosine kinase domain of Neurotrophic Receptor Tyrosine Kinase 3 (NTRK3). The aim of the study was to test the importance of tyrosine kinase activity and multimerization for the oncogenic activity of EML4-NTRK3. METHODS: These studies examined EML4-NTRK3 proteins containing a kinase-dead or WT kinase domain, together with mutations in specific salt bridge residues within the coiled-coil domain. Biological activity was assayed using focus assays in NIH3T3 cells. The MAPK/ERK, JAK/STAT3 and PI3K/AKT pathways were analyzed for downstream activation of signaling pathways. Localization of EML4-NTRK3 proteins was examined by immunofluorescence microscopy, and the ability of the EML4 coiled-coil domain to drive protein multimerization was examined by biochemical assays. RESULTS: Activation of EML4-NTRK3 relies on both the tyrosine kinase activity of NTRK3 and salt-bridge stabilization within the coiled-coil domain of EML4. The tyrosine kinase activity of NTRK3 is essential for the biological activation of EML4-NTRK3. Furthermore, EML4-NTRK3 activates downstream signaling pathways MAPK/ERK, JAK/STAT3 and PKC/PLCγ. The disruption of three specific salt bridge interactions within the EML4 coiled-coil domain of EML4-NTRK3 blocks downstream activation, biological activity, and the ability to hetero-multimerize with EML4. We also demonstrate that EML4-NTRK3 is localized in the cytoplasm and fails to associate with microtubules. CONCLUDING STATEMENT: These data suggest potential therapeutic strategies for Infantile Fibrosarcoma cases bearing EML4-NTRK3 fusion through inhibition of salt bridge interactions and disruption of multimerization.
                Cover page: The oncogenic fusion protein EML4-NTRK3 requires three salt bridges for stability and biological activity.
                • Article
                • Peer Reviewed
                UC Berkeley Previously Published Works (2019)
                Cleft lip with/without cleft palate (CLP) is a common craniofacial malformation with complex etiologies, reflecting both genetic and environmental factors. Most of the suspected genetic risk for CLP has yet to be identified. To further classify risk loci and estimate the contribution of rare variants, we sequenced the exons in 49 candidate genes in 323 CLP cases and 211 nonmalformed controls. Our findings indicated that rare, protein-altering variants displayed markedly higher burdens in CLP cases at relevant loci. First, putative loss-of-function mutations (nonsense, frameshift) were significantly enriched among cases: 13 of 323 cases (~4%) harbored such alleles within these 49 genes, versus one such change in controls (p = 0.01). Second, in gene-level analyses, the burden of rare alleles showed greater case-association for several genes previously implicated in cleft risk. For example, BHMT displayed a 10-fold increase in protein-altering variants in CLP cases (p = .03), including multiple case occurrences of a rare frameshift mutation (K400 fs). Other loci with greater rare, coding allele burdens in cases were in signaling pathways relevant to craniofacial development (WNT9B, BMP4, BMPR1B) as well as the methionine cycle (MTRR). We conclude that rare coding variants may confer risk for isolated CLP.
                  Cover page: Accumulation of rare coding variants in genes implicated in risk of human cleft lip with or without cleft palate
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2018)
                  The capsaicin receptor TRPV1 has been intensively studied by cryo-electron microscopy and functional tests. However, though the apo and capsaicin-bound structural models are available, the dynamic process of capsaicin activation remains intangible, largely due to the lack of a capsaicin-induced open structural model and the low occupancy of the transition states. Here we report that reducing temperature toward the freezing point substantially increased channel closure events even in the presence of saturating capsaicin. We further used a combination of fluorescent unnatural amino acid (fUAA) incorporation, computational modeling, and rate-equilibrium linear free-energy relationships analysis (Φ-analysis) to derive the fully open capsaicin-bound state model, and reveal how the channel transits from the apo to the open state. We observed that capsaicin initiates a conformational wave that propagates through the S4-S5 linker towards the S6 bundle and finally reaching the selectivity filter. Our study provides a temporal mechanism for capsaicin activation of TRPV1.
                    Cover page: The conformational wave in capsaicin activation of transient receptor potential vanilloid 1 ion channel.
                    • Article
                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2013)

                    Objective

                    We sought to investigate the impact of 22q11.2 deletion on perioperative outcome in tetralogy of Fallot.

                    Methods

                    We conducted a retrospective review of patients with tetralogy of Fallot who underwent complete surgical reconstruction at The Children's Hospital of Philadelphia between 1995 and 2006. Inclusion criteria included diagnosis of tetralogy of Fallot and known genotype. Fisher exact and Mann-Whitney tests were used for categoric and continuous variables, respectively. Regression analysis was used to determine whether deletion status predicts outcome.

                    Results

                    We studied 208 subjects with tetralogy of Fallot, 164 (79%) without and 44 (20%) with 22q11.2 deletion syndrome. There were no differences in sex, race, gestational age, age at diagnosis, admission weight, and duration of mechanical ventilation. Presenting anatomy, survival, complications and reoperations were also comparable between patients with and without 22q11.2 deletion syndrome. Those with 22q11.2 deletion syndrome had more aortopulmonary shunts preceding complete surgical repair (21% vs 7%, P = .02). This association was present after adjustment for presenting anatomy (stenosis, atresia, or absence of pulmonary valve and common atrioventricular canal) and surgical era. In addition, those with 22q11.2 deletion syndrome had longer cardiopulmonary bypass time (84 vs 72 minutes, P = .02) and duration of intensive care (6 vs 4 days, P = .007).

                    Conclusions

                    Genotype affects early operative outcomes in tetralogy of Fallot resulting, in particular, in longer duration of intensive care. Future studies are required to determine factors contributing to such differences in this susceptible population.
                      Cover page: 22q11.2 Deletion syndrome is associated with perioperative outcome in tetralogy of Fallot
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