Multiplexed proteomics and imaging of resolving and lethal SARS-CoV-2 infection in the lung

Abstract

Normal tissue physiology and repair depends on communication with the immune system. Understanding this communication at the molecular level in intact tissue requires new methods. The consequences of SARS-CoV-2 infection, which can result in acute respiratory distress, thrombosis and death, has been studied primarily in accessible liquid specimens such as blood, sputum and bronchoalveolar lavage, all of which are peripheral to the primary site of infection in the lung. Here, we describe the combined use of multiplexed deep proteomics with multiplexed imaging to profile infection and its sequelae directly in fixed lung tissue specimens obtained from necropsy of infected animals and autopsy of human decedents. We characterize multiple steps in disease response from cytokine accumulation and protein phosphorylation to activation of receptors, changes in signaling pathways, and crosslinking of fibrin to form clots. Our data reveal significant differences between naturally resolving SARS-CoV-2 infection in rhesus macaques and lethal COVID-19 in humans. The approach we describe is broadly applicable to other tissues and diseases.

Cell-type-resolved quantitative proteomics map of interferon response against SARS-CoV-2

“…In addition, many of the ISGs such as IFIT1, ISG15, and DDX58 were upregulated in all three cell lines (Figure 6). Induction of type I and type II IFN that was proportional to the viral load was also noted in a proteomics study performed in autopsy lung material of fatal COVID-19 cases and lung tissues obtained from SARS-CoV-2-infected non-human primates in a longitudinal manner (Kalocsay et al, 2020). Another recent study performed on autopsy tissues from various organs observed that COVID-19 patients with coronary heart disease had upregulation of multiple protein belonging to RIG-I signaling pathway, and overall, interferon gamma receptor 1 (IFNGR1) was dysregulated in all the major organs except for the thyroid and testes (Nie et al, 2021).…”

Comparative spatial transcriptomic profiling of severe acute respiratory syndrome coronavirus 2 Delta and Omicron variants infections in the lungs of cynomolgus macaques

“…NanoString GeoMx was used for the spatial transcriptomic analysis of lung tissues from experimentally infected animals, as previously described 22–24 . We prepared 4 μm FFPE (formalin‐fixed paraffin embedded) tissue sections from Delta and Omicron variants‐ and mock‐infected animals.…”

“…NanoString GeoMx was used for the spatial transcriptomic analysis of lung tissues from experimentally infected animals, as previously described. [22][23][24] We prepared 4 μm FFPE (formalin-fixed paraffin embedded) tissue sections from Delta and Omicron variants-and mock-infected animals. The tissue slides were hybridized with probes for the Human Whole Transcriptome Atlas targeting >18 000 genes and then tissue morphology was visualized using immunofluorescence for PanCK, CD45, and CD68 with Syto13 DNA nucleic acid staining.…”

Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology

“…In general, XL-MS techniques are widely used but little has been done yet in the context of ssRNA viruses. Due to the current pandemic, SARS-CoV-2 studies are evoking increased interest, giving rise to chemical crosslinking datasets, especially in the context of protein-RNA binding and host-pathogen association unravelling a more detailed picture in COVID-19 disease response [ 47 , 48 ]. Jack et al [ 49 ] investigated an intrinsically disordered N-terminal region of SARS-CoV-2 nucleoprotein using XL-MS as complementary data to previous cryo-EM structures [ 1 , 49 ].…”