A Combined Proteomics/Genomics Approach Links Hepatitis C Virus Infection with Nonsense-Mediated mRNA Decay

Abstract

SUMMARY Hepatitis C virus (HCV) is a leading cause of liver disease, but insight into virus-host interactions remains limited. We systematically used affinity purification/mass spectrometry to define the host interactions of all 10 HCV proteins in hepatoma cells. We combined these studies with RNAi knockdown of corresponding genes using a two-step scoring approach to generate a map of 139 high-confidence HCV-host protein-protein interactions. We found mitochondrial proteins highly involved in HCV infection and characterized a new interaction between the viral core protein and host protein within bgcn homolog (WIBG). Expression of core prevents WIBG from binding its regular interaction partners Y14 and Magoh, two known mediators of the nonsense-mediated mRNA decay pathway. We discovered that this surveillance pathway is disrupted in HCV-infected cells, causing potentially harmful transcripts to accumulate. Our study provides the first comprehensive view of HCV-host interactions and uncovers new mechanisms for how HCV perturbs host functions during infection.

Global Mapping of the Inc-Human Interactome Reveals that Retromer Restricts Chlamydia Infection

“…To determine whether diverse intracellular pathogens target similar host processes, we compared our Inc-human interactome to three recently assembled virus-human interactomes: HIV (Jager et al, 2011), KSHV (Davis et al, 2014) and HCV (Ramage et al, 2015). These viral interactomes were derived using the same pipeline that we employed, providing an opportunity for cross-pathogen analyses.…”

“…(C) Overlap of Chlamydia prey with previously published AP-MS interactomes of HIV (Jager et al, 2011), HCV (Ramage et al, 2015), and KSHV (Davis et al, 2014). p -values determined by the hyper-geometric test.…”

“…Inc-human interactions (blue lines) were identified by AP-MS. Interactions between human proteins (dark grey lines) were curated from CORUM and STRING databases. Inc human prey in common with HIV, KSHV, or HCV prey (Davis et al, 2014; Jager et al, 2011; Ramage et al, 2015) are outlined in red. A subset of identified host complexes or proteins with similar functions are labeled.…”

Relevance Rank Platform (RRP) for Functional Filtering of High Content Protein–Protein Interaction Data*

“…Importantly, the relevance of modular nature of RRP is emphasized by the result that the majority of the top ten RRP ranked proteins from both interactomes would have had much lower ranks if only the RNAi screen from the PC3 cell line would have been used as a functional filter (Supplemental Table 11). Therefore, RRP clearly offers an added value beyond the already existing bioinformatics (3,4,8) and RNAi approaches (38,39). Based on the vast amount of gene expression data covering also all functionally nonannotated genes, RRP could in principle be used for any gene whose function can be addressed by an siRNA-based screening assay, including not only cell survival analysis but also a variety of high-content imaging based phenotypic screens.…”

Lineage-Specific Viral Hijacking of Non-canonical E3 Ubiquitin Ligase Cofactors in the Evolution of Vif Anti-APOBEC3 Activity

“…This approach has been used to map global host-pathogen PPIs for HIV-1 (Jäger et al, 2012a), Herpes (Davis et al, 2015), and Hepatitis C (Ramage et al, 2015), as well as to study the PPIs of individual viral proteins in HPV (Tan et al, 2012; White et al, 2012a, 2012b), influenza (York et al, 2014), and picornaviruses (Greninger et al, 2012). Historically, these types of proteomic analyses have focused on a single virus or closely related sets of viruses, and typically from the same (human) host.…”