Virus-Host Interactome and Proteomic Survey Reveal Potential Virulence Factors Influencing SARS-CoV-2 Pathogenesis

Abstract

Summary Background The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a global public health concern due to relatively easy person-to-person transmission and the current lack of effective antiviral therapy. However, the exact molecular mechanisms of SARS-CoV-2 pathogenesis remain largely unknown. Methods Genome-wide screening was used to establish intraviral and viral-host interactomes. Quantitative proteomics was used to investigate the peripheral blood mononuclear cell (PBMC) proteome signature in COVID-19. Findings We elucidated 286 host proteins targeted by SARS-CoV-2 and >350 host proteins that are significantly perturbed in COVID-19-derived PBMCs. This signature in severe COVID-19 PBMCs reveals a significant upregulation of cellular proteins related to neutrophil activation and blood coagulation, as well as a downregulation of proteins mediating T cell receptor signaling. From the interactome, we further identified that non-structural protein 10 interacts with NF-κB-repressing factor (NKRF) to facilitate interleukin-8 (IL-8) induction, which potentially contributes to IL-8-mediated chemotaxis of neutrophils and the overexuberant host inflammatory response observed in COVID-19 patients. Conclusions Our study not only presents a systematic examination of SARS-CoV-2-induced perturbation of host targets and cellular networks but it also reveals insights into the mechanisms by which SARS-CoV-2 triggers cytokine storms, representing a powerful resource in the pursuit of therapeutic interventions. Funding National Key Research and Development Project of China, National Natural Science Foundation of China, National Science and Technology Major Project, Program for Professor of Special Appointment (Eastern Scholar) at Shanghai Institutions of Higher Learning, Shanghai Science and Technology Commission, Shanghai Municipal Health Commission, Shanghai Municipal Key Clinical Specialty, Innovative Research Team of High-level Local Universities in Shanghai, Interdisciplinary Program of Shanghai Jiao Tong University, SII Challenge Fund for COVID-19 Research, Chinese Academy of Sciences (CAS) Large Research Infrastructure of Maintenance and Remolding Project, and Chinese Academy of Sciences Key Technology Talent Program.

SARS-CoV-2 Nucleocapsid protein attenuates stress granule formation and alters gene expression via direct interaction with host mRNAs

“…In addition, Huntington, Parkinson’s and Alzheimer’s disease related pathways were significantly enriched among the identified interaction partners (P-value cut-off 0.05 (FDR)) (Extended Figure 2B). We next compared our protein interaction data with two previously published AP-MS studies that were also performed in HEK293 cells 13,14 . We observed that there is little interaction partner overlap among the different reports, highlighting the variability of the experimental and/or statistical analyses employed in the various studies to catalogue the virus-host PPIs (see discussion) (Figure 1A).…”

“…In this study, we report the biological impact of the SARS-CoV-2 N protein on host cells. Starting from a proteomic workflow, we found that there is little overlap across studies that recently reported virus-host PPIs for SARS-CoV-2 proteins 13,14 . This observation is perhaps not surprising due to varied experimental and statistical analyses employed across different studies.…”

“…Recent proteomic studies have indicated that SARS-CoV-2 N associates with the host stress granule (SG)-nucleating proteins Ras-GTPase-activating protein SH3-domain-binding protein 1 and 2 (G3BP1 and G3BP2) 12–14 . SGs are membrane-less protein-mRNA aggregates that form in the cytoplasm in response to a variety of environmental stressors, such as oxidative stress, osmotic stress, UV irradiation, and viral infection 15,16 .…”

Role of Multiomics Data to Understand Host–Pathogen Interactions in COVID-19 Pathogenesis

“…Another group expressed SARS-CoV-2 proteins in cell lines to elucidate the interactome of the viral proteins with host proteins. 75 The viral proteins were found to interact with almost 256 host cellar proteins affecting multiple pathways related to essential cellar functioning such as ATP biosynthesis mRNA transport, nucleotide-excision repair, translation initiation, and metabolic processes such as cellular amino acid and reactive oxygen species metabolism. Of particular importance was a finding that implicated the interaction between viral nonstructural protein 10 and NF-κB-repressing factor (NKRF), which in turn induces expression of chemokines such as interleukin-8 (IL-8).…”

“…Chemokines like IL-8 trigger neutrophil chemotaxis, where these neutrophils reach on-site and release more pro-inflammatory compounds, and as a result, additional inflammatory signals are activated. 75 , 76 …”