UC San Diego

The metabolic network has evolved over millennia into an intricate system of reactions which maintain cellular homeostasis. Highly proliferative cells, including cancers, reprogram the network to sustain elevated biomass accumulation. Lipid metabolism, in particular, is critical to support growth as these complex molecules serve numerous essential roles in cell biology. The chapters of this thesis are all independent bodies of work which explore mechanisms of fatty acid reprogramming in mammalian cells as well as present software tools which expedite analysis of metabolic studies. Chapter 1, titled “Profiling fatty acid metabolism in cancer cells using stable isotope tracing” is a review of relevant literature concerning the rewiring of central carbon and lipid metabolism under highly proliferative disease states as well as the utility of stable isotope tracing and metabolic modeling. Chapter 2, titled “NaCT/SLC13A5 facilitates citrate import and metabolism under nutrient-limited conditions” quantifies the contribution of NaCT-mediated citrate uptake to central carbon metabolism in multiple cell systems. The findings demonstrated that citrate uptake promoted lipogenesis and proliferation in glutamine deprived conditions, as well as increased tolerance to zinc-induced toxicity. Chapter 3, titled “ATP-citrate lyase deficiency highlights critical sources of lipogenic acetyl-CoA in cancer cells” describes how multiple layers of redundancy support lipogenic acetyl-CoA synthesis. Cells were found to rely on non-canonical sources of acetyl-CoA including de novo acetate synthesis, and peroxisomal b-oxidation when deficient in functional ATP-citrate lyase (ACLY). Chapter 4, titled “Escher-Trace: A Web Application for Pathway-Based Visualization of Stable Isotope Tracing Data” describes a web-based visualization platform for analyzing stable isotope tracing data with the context of metabolic pathway architecture. The software simplifies the analytical pipeline for nominal resolution stable isotope tracing measurements, by automating multiple intermediary steps including natural isotope correction and data plotting. Chapter 5, titled “Analysis of high-resolution lipidomic data with Escher-Trace” details an analytical pipeline for analysis of high-resolution mass spectrometry (HRMS) data which incorporates the Escher-Trace platform. By expanding the feature set of Escher-Trace and introducing an intermediary script connecting the platform to existing HRMS analysis software, the pipeline is found to expedite analysis of complex HRMS datasets. Overall, these findings reveal compensatory mechanisms employed upon disruption of canonical lipogenesis as well as provide tools which contextualize stable isotope tracing data and facilitate analysis of metabolic studies.