Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has become a global health pandemic. COVID-19 severity ranges from an asymptomatic infection to a severe multiorgan disease. Although the inflammatory response has been implicated in the pathogenesis of COVID-19, the exact nature of dysregulation in signaling pathways has not yet been elucidated, underscoring the need for further molecular characterization of SARS-CoV-2 infection in humans. Here, we characterize the host response directly at the point of viral entry through analysis of nasopharyngeal swabs. Multiplexed high-resolution MS-based proteomic analysis of confirmed COVID-19 cases and negative controls identified 7582 proteins and revealed significant upregulation of interferon-mediated antiviral signaling in addition to multiple other proteins that are not encoded by interferon-stimulated genes or well characterized during viral infections. Downregulation of several proteasomal subunits, E3 ubiquitin ligases, and components of protein synthesis machinery was significant upon SARS-CoV-2 infection. Targeted proteomics to measure abundance levels of MX1, ISG15, STAT1, RIG-I, and CXCL10 detected proteomic signatures of interferon-mediated antiviral signaling that differentiated COVID-19-positive from COVID-19-negative cases. Phosphoproteomic analysis revealed increased phosphorylation of several proteins with known antiviral properties as well as several proteins involved in ciliary function (CEP131 and CFAP57) that have not previously been implicated in the context of coronavirus infections. In addition, decreased phosphorylation levels of AKT and PKC, which have been shown to play varying roles in different viral infections, were observed in infected individuals relative to controls. These data provide novel insights that add depth to our understanding of SARS-CoV-2 infection in the upper airway and establish a proteomic signature for this viral infection. Graphical Abstract Highlights • Nasopharyngeal swabs are an excellent sample to study host response in COVID-19. • Proteins encoded by interferon-stimulated genes were robustly upregulated. • Novel host response proteins were revealed by proteomics and phosphoproteomics. • Host phosphoproteome is substantially altered upon SARS-CoV-2 infection. In Brief Dysregulated immune response to SARS-CoV-2 infection underlies severe diseases; however, the precise underlying mechanisms have not yet been elucidated. To establish a proteomic signature of SARS-CoV-2 infection in the upper airway, the authors of this study performed a deep proteomic and phosphoproteomic analysis of nasopharyngeal swabs. This study is a valuable resource for investigators interested in studying host response to SARS-CoV-2 infection.
【저자키워드】 COVID-19, Infection, interferon, COVID-19, Coronavirus disease 2019, SARS-CoV-2, Severe acute respiratory syndrome coronavirus 2, host response, virus, Phosphoproteomics, FDR, false discovery rate, MERS-CoV, Middle East respiratory syndrome coronavirus, IFN, interferon, PRM, parallel reaction monitoring, upper airway, AGC, automatic gain control, ISGs, interferon-stimulated genes, MPB, mobile phase B, NHBE, normal human bronchial epithelial, NP, nasopharyngeal, OGFR, opioid growth factor receptor, OPRPN, Opiorphin prepropeptide, PPIase, peptidyl-prolyl