Table 2 Immune response to SARS-CoV-2 infection in lung and other tissues (A), peripheral blood (B) and specific cell types among blood immune cells (C). Pathways, host signature and body districts, subset per specific omics data: host proteomics, bulk and single cell RNAseq (scRNAseq)
From: Multi-omics approach to COVID-19: a domain-based literature review
A. Lung and other tissues | |||
|---|---|---|---|
Pathway | Omics | Body district(s) | Host signature |
Inflammatory cytokines | Proteomics | Lung | DEP* up in fatal COVID-19 [TE96, TE110] |
IFN response IL6 signaling Complement cascade | BULK RNAseq | Nasopharyngeal (NP) swabs BAL | DEG** up in COVID-19[TE99, TE108] |
Monocyte and neutrophil recruitment | BULK RNAseq | Nasopharyngeal (NP) swabs BAL | DEG** up and down in COVID-19[TE99, TE108] |
Morphogenesis and migration of immune cells | BULK RNAseq | BAL | DEG** down in COVID-19[TE108] |
Neutrophils extracellular traps TGF-beta response Extracellular traps | BULK RNAseq | Nasopharyngeal (NP) swabs Lung colon | DEG** up in fatal cases and correlated with SARS-CoV-2 viral load in NP[TE119] |
Anti-inflammatory pathways | scRNAseq/CyTOFF | BAL | DEG** down in CD14 + /CD16 + cells of severe cases[TE99] |
Immune cell activation | scRNAseq/CyTOFF | Colon | DEG** down in fatal COVID-19 cases[TE110] |
B. Peripheral blood | |||
|---|---|---|---|
Pathways | Omics | ||
Proteomics | Bulk RNAseq | Metabolomics | |
Inflammation and immune response Neutrophil activation Acute phase response Platelet degranulation Antimicrobial response Tissue damage Coagulation and complement activation | Soluble mediators DEP* up in COVID-19 [TE87,TE88,TE89] | ||
Platelet degranulation Coagulation and complement activation | Soluble mediators DEP* down in COVID-19 [TE89,TE94, TE95] | ||
Inflammation and immune response Neutrophil activation Acute phase response Tissue damage | Soluble mediators DEP* up in severe COVID-19 vs mild [TE89, TE90, TE94]; | ||
Inflammation and immune response Lipid metabolism Coagulation Tissue damage | Soluble mediators DEP* down in severe COVID-19 vs mild [TE89, TE90, TE94]; | ||
Acute phase response Coagulation and complement activation Inflammation and immune response | Soluble mediators DEP* up in severe COVID-19 vs mild DEP* up in fatal COVID-19 DEP* up in poor prognosis for COVID-19 DEP* up in COVID-19 vs influenza [TE88, TE96]; | ||
Inflammatory cytokines and chemokines IFN response | DEG* up and down in COVID-19 [TE90] | ||
Inflammation Immune response Lipid hormones Lipid metabolism Tissue damage | Metabolites up and down in COVID-19 [TE129] | ||
Amino acid metabolism Inflammation and Immune response Lipid metabolism Oxidative Pathways of Cellular Energy Production REDOX homeostasis Tissue damage Urea cycle Xenobiotic metabolism | Metabolites up and down in severe COVID-19 vs. mild [TE101, TE102, TE103, TE104] | ||
Inflammatory response Neutrophil activation generation of NETs Negative regulators of innate immune signaling TCR signaling | DEG** up in severe COVID-19 vs. mild [TE97] | ||
Negative regulators of innate immune signaling TCR signaling | DEG** down in severe COVID-19 vs. mild [TE89] | ||
IFN response | DEG** up in mild COVID-19 [TE89] | ||
Inflammatory response | DEG** up in fatal COVID-19 vs. mild [TE89] | ||
IFN response IL1 IL6, IL10 signaling Complement/coagulation cascade | DEG** up and down in moderate COVID-19 vs coronaviruses, influenza or bacterial pneumonia [TE98] | ||
C. Specific cell types among blood immune cells (CyTOF/scRNAseq) | |||
|---|---|---|---|
Innate cell compartment | Adaptive cell compartment | ||
Pathways | Modulation | Pathways | Modulation |
Dysregulation of innate cells | DEG** up and down in COVID-19 [TE96, TE112] | Gene expression related to T cell apoptosis T cells activation, Th1, Th2 and Th17 | DEG** up and down in COVID-19 [TE89, TE110, TE112, TE144] |
Classical and non-classical Monocytes activation and recruitment Suppressive low density neutrophils NETs formation Dendritic cells function | DEG** up and down in severe COVID-19 vs. mild [TE89, TE105, TE112, TE113] | Negative T cell signaling T cell activation Antibodies production T cell exhaustion Cytotoxic effector cells CD8 polyfunctionality | DEG** up and down in mild, moderate, survivor COVID-19, severe vs mild, survivors vs fatal, COVID-19 vs seasonal coronavirus, influenza or bacterial pneumonia). [TE98, TE105, TE111] |