Lipid Regulation of Protein Functions

Lipids are essential building blocks of all cells and play fundamental roles in mediating cellular signaling pathways, protein localization, and membrane trafficking. Increasing evidence suggests that lipids are critical regulators of protein fate and cellular homeostasis. Imbalances in lipid metabolism have been implicated in various diseases, including cancer and neurodegenerative diseases. However, the molecular mechanisms by which lipid metabolism affect proteome dynamics and protein secretion remain poorly understood. This dissertation explores how lipids affect global proteome responses and protein functions. In the first study, we demonstrated how cells respond to acute inhibition of de novo sphingolipid synthesis using mass spectrometry and bioinformatic analysis. Gene set enrichment analysis unveiled downregulation or upregulation of the proteome across some pathways, especially in membrane fractions, including upregulation of cholesterol homeostasis and lysosome pathways. A combination of cholesterol synthesis and de novo sphingolipid synthesis inhibitors synergistically reduced cancer cell viability. The results reveal the potential metabolic vulnerabilities that may be targeted in cancer combination therapies. In the second study, we developed a method to identify new phospholipid-conjugated proteins at the proteome level using a combination of a click reaction, PLD digestion, and mass spectrometry. We found that secretory proteins are enriched among the newly identified phospholipid-conjugated proteins. Interestingly, more than half of them lack a signal peptide and are secreted via an unconventional secretion pathway. Our data suggests that phospholipid conjugation may enhance the unconventional secretion of leaderless cytosolic proteins, revealing a novel role for phospholipids in protein trafficking. Together, our studies highlight the previously unrecognized links between proteome regulation and lipid metabolism. We found that the lipid metabolic pathway can influence global proteome adaptation and protein trafficking. These findings expand our understanding of cellular regulation of lipid metabolism and may be exploited to target lipid metabolism in lipid-related diseases.