Comprehensive profiling of lipid metabolites in urine of canine patients with liver mass

Urinary lipid production in dogs with urothelial carcinoma

Canine urothelial carcinoma (cUC) is a prevalent and aggressive malignancy in dogs. Current treatments have limited effectiveness, and delays in diagnosis are often a concern. cUC is unique in that it shows high responsiveness to cyclooxygenase (COX) inhibitors and has a high frequency of a single nucleotide mutation in BRAF, known as BRAFV595E. COX is one of the key enzymes involved in the production of lipid mediators, which regulate the progression of various diseases. Although studies have revealed the roles of COX in cUC, the production profiles of lipid mediators remain unknown. In this study, we comprehensively measured the urinary lipid mediator levels of cUC dogs using liquid chromatography-tandem mass spectrometry. We found that lipid production was altered in cUC, with increased amounts of several COX-catalyzed lipids, including prostaglandin E2 and thromboxane B2, and several lipoxygenase-catalyzed lipids, including leukotriene E4. Additionally, we found that the BRAFV595E mutation tended to increase the levels of most enzymatically produced lipids. Our results provide insights into novel therapeutic and diagnostic strategies for cUC and cancers with BRAF mutations.

Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions

Protein-protein interactions (PPIs) and protein-metabolite interactions play a key role in many biochemical processes, yet they are often viewed as being independent. However, the fact that small molecule drugs have been successful in inhibiting PPIs suggests a deeper relationship between protein pockets that bind small molecules and PPIs. We demonstrate that 2/3 of PPI interfaces, including antibody-epitope interfaces, contain at least one significant small molecule ligand binding pocket. In a representative library of 50 distinct protein-protein interactions involving hundreds of mutations, >75% of hot spot residues overlap with small molecule ligand binding pockets. Hence, ligand binding pockets play an essential role in PPIs. In representative cases, evolutionary unrelated monomers that are involved in different multimeric interactions yet share the same pocket are predicted to bind the same metabolites/drugs; these results are confirmed by examples in the PDB. Thus, the binding of a metabolite can shift the equilibrium between monomers and multimers. This implicit coupling of PPI equilibria, termed "metabolic entanglement", was successfully employed to suggest novel functional relationships among protein multimers that do not directly interact. Thus, the current work provides an approach to unify metabolomics and protein interactomics.