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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2018)
Developmental Pluripotency-Associated-4 (DPPA4) is one of the few core pluripotency genes lacking clearly defined molecular and cellular functions. Here, we used a proteomics screening approach of human embryonic stem cell (hESC) nuclear extract to determine DPPA4 molecular functions through identification of novel cofactors. Unexpectedly, the signaling molecule ERBB3-binding protein 1 (EBP1) was the strongest candidate binding partner for DPPA4 in hESC. EBP1 is a growth factor signaling mediator present in two isoforms, p48 and p42. The two isoforms generally have opposing functions, however their roles in pluripotent cells have not been established. We found that DPPA4 preferentially binds p48 in pluripotent and NTERA-2 cells, but this interaction is largely absent in non-pluripotent cells and is reduced with differentiation. The DPPA4-EBP1 interaction is mediated at least in part in DPPA4 by the highly conserved SAF-A/B, Acinus and PIAS (SAP) domain. Functionally, we found that DPPA4 transcriptional repressive function in reporter assays is significantly increased by specific p48 knockdown, an effect that was abolished with an interaction-deficient DPPA4 ΔSAP mutant. Thus, DPPA4 and EBP1 may cooperate in transcriptional functions through their physical association in a pluripotent cell specific context. Our study identifies EBP1 as a novel pluripotency cofactor and provides insight into potential mechanisms used by DPPA4 in regulating pluripotency through its association with EBP1. Stem Cells 2018;36:671-682.
    Cover page: ERBB3-Binding Protein 1 (EBP1) Is a Novel Developmental Pluripotency-Associated-4 (DPPA4) Cofactor in Human Pluripotent Cells
    • Multimedia
    Symposium 2024 (2024)

    Issues:Neutropenia can be classified based on pathophysiology as severe versus benign based on bone marrow reserve of neutrophil precursors, which determines the risk of serious bacterial infections (SBI). The current guidelines for management of fever in neutropenic patients are reliant on the knowledge gained in the oncology setting. There are no clear guidelines for management of fever in patients with benign neutropenia regarding evaluation or antibiotic administration, despite their lower risk of SBI. This leads to significant practice variation in management of patients with benign neutropenia who present with fever and may result in unnecessary hospital visits or antibiotic administration, leading to poor quality of life for these patients and avoidable use of healthcare resources. We initiated a quality improvement project to address this issue at Rady Children’s Hospital, San Diego, (RCHSD) with the goal of decreasing the percentage of emergency department (ED) visits for patients with benign neutropenia from a baseline of 60% febrile events to 30% febrile events by May 31, 2025.

     

    Description: We collected baseline data via manual chart review from Jan 2023 to Nov 2023 to identify how febrile events were managed in patients with benign neutropenia at RCHSD (Table 1). None of the patients were identified as having a serious bacterial infection. We then sent a survey to all hematology providers at our institution to identify their practice of managing fever in patients with benign neutropenia. Based on the survey results, we created an Ishikawa chart (Figure 1) to identify barriers, and a key driver diagram (Figure 2) to identify possible interventions. We created an ideal process map based on the input from the hematology providers and the proposed algorithm (Figure 3) was agreed upon by the hematology providers.

     

    Lessons Learned/Expected Outcomes: Some of the main barriers identified were variation in practices and lack of uniform guidelines in management of fever in patients with benign neutropenia. We plan to use the model of improvement methodology with the key driver diagram to guide improvement efforts.

     

    Recommendations: Next steps include presenting the proposed algorithm to the fellows and other providers in the department of hematology-oncology, and to the ED providers before going live with the project. We also plan to present it to general pediatricians at the CPMG (Children’s Physician Medical Group) conference. We will post the algorithm in the inpatient and hematology/oncology clinic workroom and make it easily accessible to all providers on division shared folder. We plan to create a Smart Phrase on EPIC to have a standardized plan in the notes of all patients with a diagnosis of suspected or established benign neutropenia. We will discuss our progress and gain feedback in subsequent QI and division meetings.

    • 1 supplemental ZIP
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2023)
    Histone variant H3.3 is encoded by two genes, H3f3a and H3f3b, which can be expressed differentially depending on tissue type. Previous work in our lab has shown that knockout of H3f3b causes some neonatal lethality and infertility in mice, and chromosomal defects in mouse embryonic fibroblasts (MEFs). Studies of H3f3a and H3f3b null mice by others have produced generally similar phenotypes to what we found in our H3f3b nulls, but the relative impacts of the loss of either H3f3a or H3f3b have varied depending on the approach and genetic background. Here we used a knockout-first approach to target the H3f3a gene for inactivation in C57BL6 mice. Homozygous H3f3a targeting produced a lethal phenotype at or before birth. E13.5 null embryos had some potential morphological differences from WT littermates including smaller size and reduced head size. An E18.5 null embryo was smaller than its control littermates with several potential defects including small head and brain size as well as small lungs, which would be consistent with a late gestation lethal phenotype. Despite a reduction in H3.3 and total H3 protein levels, the only histone H3 post-translational modification in the small panel assessed that was significantly altered was the unique H3.3 mark phospho-Serine31, which was consistently increased in null neurospheres. H3f3a null neurospheres also exhibited consistent gene expression changes including in protocadherins. Overall, our findings are consistent with the model that there are differential, cell-type-specific contributions of H3f3a and H3f3b to H3.3 functions in epigenetic and developmental processes.
      Cover page: A knockout‐first model of H3f3a gene targeting leads to developmental lethality
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2013)
      Abstract Background The histone variant H3.3 plays key roles in regulating chromatin states and transcription. However, the role of endogenous H3.3 in mammalian cells and during development has been less thoroughly investigated. To address this gap, we report the production and phenotypic analysis of mice and cells with targeted disruption of the H3.3-encoding gene, H3f3b. Results H3f3b knockout (KO) mice exhibit a semilethal phenotype traceable at least in part to defective cell division and chromosome segregation. H3f3b KO cells have widespread ectopic CENP-A protein localization suggesting one possible mechanism for defective chromosome segregation. KO cells have abnormal karyotypes and cell cycle profiles as well. The transcriptome and euchromatin-related epigenome were moderately affected by loss of H3f3b in mouse embryonic fibroblasts (MEFs) with ontology most notably pointing to changes in chromatin regulatory and histone coding genes. Reduced numbers of H3f3b KO mice survive to maturity and almost all survivors from both sexes are infertile. Conclusions Taken together, our studies suggest that endogenous mammalian histone H3.3 has important roles in regulating chromatin and chromosome functions that in turn are important for cell division, genome integrity, and development.
        Cover page: Endogenous mammalian histone H3.3 exhibits chromatin-related functions during development
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2021)

        Background

        Vitamin D deficiency and insufficiency have been associated with poorer health outcomes. Children with cancer are at high risk for vitamin D deficiency and insufficiency. At our institution, we identified high variability in vitamin D testing and supplementation in this population. Of those tested, 65% were vitamin D deficient/insufficient. We conducted a quality improvement (QI) initiative with aim to improve vitamin D testing and supplementation among children aged 2-18 years with newly diagnosed cancer to ≥80% over 6 months.

        Methods

        An inter-professional team reviewed baseline data, then developed and implemented interventions using Plan-Do-Study-Act (PDSA) cycles. Barriers were identified using QI tools, including lack of automated triggers for testing and inconsistent supplementation criteria and follow-up testing post supplementation. Interventions included an institutional vitamin D guideline, clinical decision-making tree for vitamin D deficiency, insufficiency and sufficiency, electronic medical record triggers, and automated testing options.

        Results

        Baseline: N = 26 patients, four (15%) had baseline vitamin D testing; two (8%) received appropriate supplementation. Postintervention: N = 33 patients; 32 (97%) had baseline vitamin D testing; 33 (100%) received appropriate supplementation and completed follow-up testing timely (6-8 weeks post supplementation). Change was sustained over 24 months.

        Conclusions

        We achieved and sustained our aim for vitamin D testing and supplementation in children with newly diagnosed cancer through inter-professional collaboration of hematology/oncology, endocrinology, hospital medicine, pharmacy, nursing, and information technology. Future PDSA cycles will address patient compliance with vitamin D supplementation and impact on patients' vitamin D levels.
          Cover page: Improving vitamin D testing and supplementation in children with newly diagnosed cancer: A quality improvement initiative at Rady Children's Hospital San Diego
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2020)
          Histone H3.3 mutations are a hallmark of pediatric gliomas, but their core oncogenic mechanisms are not well-defined. To identify major effectors, we used CRISPR-Cas9 to introduce H3.3K27M and G34R mutations into previously H3.3-wildtype brain cells, while in parallel reverting the mutations in glioma cells back to wildtype. ChIP-seq analysis broadly linked K27M to altered H3K27me3 activity including within super-enhancers, which exhibited perturbed transcriptional function. This was largely independent of H3.3 DNA binding. The K27M and G34R mutations induced several of the same pathways suggesting key shared oncogenic mechanisms including activation of neurogenesis and NOTCH pathway genes. H3.3 mutant gliomas are also particularly sensitive to NOTCH pathway gene knockdown and drug inhibition, reducing their viability in culture. Reciprocal editing of cells generally produced reciprocal effects on tumorgenicity in xenograft assays. Overall, our findings define common and distinct K27M and G34R oncogenic mechanisms, including potentially targetable pathways.
            Cover page: Reciprocal H3.3 gene editing identifies K27M and G34R mechanisms in pediatric glioma including NOTCH signaling
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