Multi-level proteomics profiling of virus-restrictive and -permissive cellular environments reveal novel regulators of virus infection

ABSTRACT: Virus proliferation inside host cells relies on a diverse range of host machineries and is also restricted by the host through expressions of antiviral factors. The configuration of virus-dependency and antiviral factors determine the permissiveness of host cells to virus infection, however, overall differences between highly permissive and restrictive cellular states remain largely unexplored. Here we employed an integrated omics analysis combining RNA-seq, proteomics, and phosphoproteomics to study determinants of virus permissiveness across cellular states. We focused on a model system comprising highly permissive cells (HEK293T), steady-state cells (HEK293), and highly restrictive cells (interferon alpha (IFN-a) stimulated HEK293) due to their similar genetic background and distinct virus permissiveness. Our dataset provides an in-depth proteomics map across these cellular states, which revealed pathway-level depletion of innate immune response and enrichment of anabolic processes in HEK293T cell. RNA-seq and proteomics results depicted dynamic regulations of IFN-a response across early/late timepoints and highlighted a group of robustly upregulated antiviral factors. In addition, phosphoproteomics uncovered extensive alterations of phosphorylation in IFN-a response. Integrated analysis of multi-level omics results identified putative regulators of infection that are previously under-described, and we experimentally verified 13 proteins with their regulatory roles in virus infection.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

SUBMITTER: Honglin Chen  

LAB HEAD: Alfredo Castello

PROVIDER: PXD052223 | Pride | 2025-06-16

REPOSITORIES: Pride