Unraveling the mammalian secretory pathway through systems biology and algorithm development

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ABSTRACT The mammalian secretory pathway regulates a cell’s extracellular interactions by making most signals and receptors that moderate communication and most proteins needed for a cell to interact with its extracellular environment, which includes ~⅓ of their protein-coding genes in the human genome. Furthermore, it is frequently harnessed by pathogens, including all enveloped viruses to aid in their synthesis. To synthesize and transport these thousands of secreted, membrane, and pathogen proteins, the pathway has hundreds of machinery proteins, each with their unique role in the process. However, the regulation of this pathway is poorly understood, especially how it is tailored to the needs of each protein it produces. The parent grant is elucidating these processes by identifying all secretory pathway machinery proteins and detailing their functions, with a particular focus on liver-secreted proteins, and liver diseases. Functional genomics and systems biology techniques are deciphering the regulatory mechanisms controlling the pathway. In this supplement, we build upon the parent grant to decipher the regulatory processes that are hijacked by enveloped viruses, in particular, the Hepatitis C Virus (HCV), to facilitate the rapid synthesis, folding and post-translational modification of its coat proteins. Furthermore, the virus successfully manipulates the host cell to produce their proteins at very high levels, requiring extensive use of host cell resources and machinery. HCV, for example, primarily infects hepatocytes, and is the leading cause of liver disease including cirrhosis. To decipher how HCV regulates the host cell secretory pathway, we will leverage the Biotinylation by Antibody Recognition (BAR) method to measure protein-protein interactions between the E1E2 HCV coat protein, expressed and secreted from hepatocytes. Next we will simultaneously measure the protein secretion rates and the transcriptome for single cells. These data will be used to identify the essential host cell machinery needed for virus protein synthesis and allow the use of gene regulatory network analyses and systems biology modeling to identify how these processes are controlled by the virus. An understanding of how the HCV regulates the host secretory pathway could yield new targets for direct-acting antivirals, or even inform how to engineer cells that can produce subunit vaccines to avoid viral damage and reduce transmission.