UC Irvine

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.