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Open Access Publications from the University of California

Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Irvine Electronic Theses and Dissertations (2023)

This thesis presents a user-friendly pipeline for analyzing data from evolving mass spectrometry techniques, developed in response to the growing volume and complexity of data in the field of proteomics. While offering a comprehensive review of current methods for isolating and identifying interacting proteins using MS analysis, the pipeline also highlights areas for integrating other -omic resources to enhance data interpretation. This pipeline was utilized to identify novel regulators within the Hippo pathway, a central regulator of cell proliferation and organ size. A unique 9-amino acid sequence was identified, vital for interactions between WW-PxY motif containing proteins in the Hippo pathway. Furthermore, the pipeline aided in the discovery of a new YAP inhibitor, Syntaxin binding protein 4 (STXBP4), harboring this conserved sequence. The pipeline was also employed to investigate potential regulators in the PLD-PA-Hippo axis. Although no Hippo pathway regulators were found within the PLD family, the analysis unveiled significant Hippo-independent interactions. Among the interactors of six PLD members, the E3 ubiquitin-protein ligase, PJA2, was found to bind specifically to PLD1, an oncogene. Furthermore, Phosphatidic Acid (PA) was shown to bind, co-localize, and regulate Sphingosine Kinase1 (SPHK1), linked to cell growth, proliferation, and survival. This thesis underscores the importance of continually updating bioinformatic resources to keep up with advances in data generation techniques, thus allowing the extraction of relevant biological information from intricate datasets. The studies driven by this pipeline signify just the inception, and further tools, such as additional disease -omic resources, can be integrated for comprehensive insights into many biological processes.

  • 7 supplemental ZIPs
Cover page: Pipeline Development for Hippo Pathway Related Protein Interactome Analysis
  • Article
  • Peer Reviewed
UC Irvine Previously Published Works (2023)
During intracellular signal transduction, protein-protein interactions (PPIs) facilitate protein complex assembly to regulate protein localization and function, which are critical for numerous cellular events. Over the years, multiple techniques have been developed to characterize PPIs to elucidate roles and regulatory mechanisms of proteins. Among them, the mass spectrometry (MS)-based interactome analysis has been increasing in popularity due to its unbiased and informative manner towards understanding PPI networks. However, with MS instrumentation advancing and yielding more data than ever, the analysis of a large amount of PPI-associated proteomic data to reveal bona fide interacting proteins become challenging. Here, we review the methods and bioinformatic resources that are commonly used in analyzing large interactome-related proteomic data and propose a simple guideline for identifying novel interacting proteins for biological research.
    Cover page: Analysis of affinity purification-related proteomic data for studying protein–protein interaction networks in cells
    • Article
    • Peer Reviewed
    UC Irvine Previously Published Works (2022)
    Mammalian phospholipase D (PLD) enzyme family consists of six members. Among them, PLD1/2/6 catalyzes phosphatidic acid (PA) production, while PLD3/4/5 has no catalytic activities. Deregulation of the PLD-PA lipid signaling has been associated with various human diseases including cancer. However, a comprehensive analysis of the regulators and effectors for this crucial lipid metabolic pathway has not been fully achieved. Using a proteomic approach, we defined the protein interaction network for the human PLD family of enzymes and PA and revealed diverse cellular signaling events involving them. Through it, we identified PJA2 as a novel E3 ubiquitin ligase for PLD1 involved in control of the PLD1-mediated mammalian target of rapamycin signaling. Additionally, we showed that PA interacted with and positively regulated sphingosine kinase 1. Taken together, our study not only generates a rich interactome resource for further characterizing the human PLD-PA lipid signaling but also connects this important metabolic pathway with numerous biological processes.
      Cover page: Interactome Analysis of Human Phospholipase D and Phosphatidic Acid-Associated Protein Network
      • Article
      • Peer Reviewed
      UC Irvine Previously Published Works (2023)
      The Hippo pathway is known for its crucial involvement in development, regeneration, organ size control, and cancer. While energy stress is known to activate the Hippo pathway and inhibit its effector YAP, the precise role of the Hippo pathway in energy stress response remains unclear. Here, we report a YAP-independent function of the Hippo pathway in facilitating autophagy and cell survival in response to energy stress, a process mediated by its upstream components MAP4K2 and STRIPAK. Mechanistically, energy stress disrupts the MAP4K2-STRIPAK association, leading to the activation of MAP4K2. Subsequently, MAP4K2 phosphorylates ATG8-family member LC3, thereby facilitating autophagic flux. MAP4K2 is highly expressed in head and neck cancer, and its mediated autophagy is required for head and neck tumor growth in mice. Altogether, our study unveils a noncanonical role of the Hippo pathway in energy stress response, shedding light on this key growth-related pathway in tissue homeostasis and cancer.
        Cover page: The Hippo pathway noncanonically drives autophagy and cell survival in response to energy stress
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