Targeted detection of secretion pathway protein interactions for therapeutic production and cellular engineering

Mammalian cells synthesize and secrete thousands of versatile proteins to interact with their environment. Over the past decades, this ability has been harnessed to produce a variety of lifesaving biotherapeutics to treat complex diseases, provide vaccines, or replace enzyme and hormone deficiencies— making the mammalian secretory pathway essential to protein biomanufacturing. In 2018, eleven of the top fifteen drugs by sales were recombinant proteins, produced almost exclusively in mammalian cells, mostly Chinese hamster ovary (CHO) cells. These therapeutics may use the mammalian secretory pathway as an assembly line; however, the detailed pathway mechanisms remain poorly characterized. As such, there continues to exist bottlenecks in the secretory pathway such as machinery deficiencies that throttle protein secretion. First, we must better understand the protein interactions responsible for structure-specific post-translational modifications, and second, determine the interactions that contribute to high recombinant protein yields. Employing systems-wide labeling of protein interactions within the mammalian secretory pathway using proximity-based biotinylation and mass spectrometry analysis, we validate the ability to identify interactions that occur within the endomembrane system and their potential as targets for cellular engineering for improved recombinant protein secretion