TABLE 4.
Single-cell Cluster Expression of Innate Immune Genes.
| Gene | Protein | Innate immune function |
| Cluster 0 (Epithelial cells) | ||
| Lbp | LPS Binding Protein | Endotoxin receptor component |
| Hmgb2 | High mobility group box 2 | Innate immune DNA/RNA receptor |
| Csf1 | Colony stimulating factor 1 | Macrophage differentiation |
| Cxcl16 | Chemokine CXCL16 | T-cell recruitment |
| Ptpn2 | PTP2 | T-cell activitation, tissue growth |
| Cadm1 | CADM1 | NK and T-cell regulation by other cell types |
| Cd24a | CD24A | B-cell differentiation, tissue growth |
| Lcn2 | Lipocalin2 | Antibacterial |
| Sftpd | surfactant D | Antibacterial, surfactant |
| Xrcc5 | DNA repair XRCC5 | Antiviral |
| Cd55 | DAF | Negative complement regulator |
| Cluster 1 (Epithelial cells) | ||
| Cd25 | IL2 receptor α | Control of regulatory T-cell, tissue growth |
| Ppp1r1b | PPP1R1B | Regulatory T-cell activation, cell survival |
| Ltf | Lactoferrin | Antimicrobial |
| Reg3γ | REG3γ | Antimicrobial |
| Isg20 | ISG20 | IFN-stimulated antiviral |
| Cluster 6 (Epithelial cells) | ||
| Sftpd | surfactant D | antibacterial, surfactant |
| Cluster 2 (Basal epithelial cells) | ||
| Lbp | LPS Binding | endotoxin receptor component |
| Hmgb2 | High mobility group box 2 | innate immune DNA/RNA receptor |
| Cadm1 | CADM1 | NK and T-cell regulation by other cell types |
| Gata3 | GATA3 | Immune cell differentiation, tissue growth |
| Rab20 | RAB20 | endocytosis, antibacterial responses |
| Xrcc5 | DNA repair XRCC5 | antiviral response |
| Ifitm1 | IFITM1 | Inhibition of viral entry |
| Rpl39 | Ribosomal protein L39 | Viral gene transcription |
| Rpl13a | Ribosomal | Suppression of inflammation |
| Rps19 | Ribosomal | Suppression of interferon |
| Axl | AXL receptor tyrosine kinase | TLR inhibition |
| Cd55 | DAF | negative complement regulator |
| Cluster 11 (Ciliated epithelial cells) | ||
| Adam8 | ADAM8 | leukocyte migration |
| Cd24a | CD24A | B-cell differentiation, tissue growth |
| Ifitm1 | IFITM1 | inhibition of viral entry |
| Aqp4 | Aquaporin4 | water permeability, response to inflammation |
| Clusters 3, 4, 5 (All stromal cells) | ||
| Gsn | Gelsolin | TLR endocytosis |
| Rarres2 | Chemerin | Chemotactic, anti-inflammatory |
| C1ra | Complement C1 component | Complement response |
| Colec12 | Collectin-12 | Antimicrobial responses |
| Serping1 | Serpin G1 | Negative complement regulator |
| Axl | AXL receptor tyrosine kinase | TLR inhibition |
| Cluster 3 (Stromal cells) | ||
| C1s1 | Complement C1 component | Complement response |
| Cr1l | C1 receptor like | Complement activation |
| Samhd1 | SAMHD1 | Mediates TNF inflammatory responses |
| Lgals9 | Galactin9 | Negative regulation of T- and NK-cells |
| Ifitm1 | IFITM1 | Inhibition of viral entry |
| Clec2d | CLEC2D | Protection against NK cell lysis |
| Cluster 4 (Stromal cells) | ||
| C1s1 | Complement C1 component | Complement response |
| C2 | Complement C2 | Complement response |
| C3 | Complement C3 | Complement response |
| Apoe | Apolipoprotein E | Leukocyte regulation, lipid metabolism |
| Zyx | Zyxin | Viral pathogen receptor signaling |
| Bst2 | Tetherin | Antiviral |
| Serinc3 | Serine incorporator 3 | Antiviral |
| Trp53 | P53 | Antiviral |
| Ifitm1 | IFITM1 | Inhibition of viral entry |
| Lgals9 | Galectin 9 | Negative regulator of T- and NK-cells |
| Cluster 5 (Stromal cells) | ||
| Lgals3 | Galectin 3 | Acute inflammation activator |
| Csf1 | Colony stimulating factor 1 | Macrophage differentiation |
| Trp53 | P53 | Antiviral |
| Tgfb1 | TGFβ1 | Multifunctional, immunocyte inhibition |
| Tspan6 | Tetraspanin 6 | Negative innate immune regulator |
| Cluster 7 (Vascular endothelial cells) | ||
| Vim | Vimentin | Viral and bacterial attachment |
| Samhd1 | SAMHD1 | Mediates TNF inflammatory responses |
| Dab2ip | DAB2 interacting protein | TNF, IFN and LPS signaling pathways |
| Irf1 | IFN response factor | IFN production |
| Adam15 | ADAM15 | Epithelial−T-cell interaction |
| Cav1 | Caveolin 1 | T-cell activation, TGFß1 inhibition |
| Iigp1 | IFN-inducible G Protein 1 | IFN-inducible antimicrobial |
| Cebpg | CEBPG | IL4 gene activation |
| Irgm1 | IRGM1 | Mucosal immune response inhibition |
| Cluster 12 (Lymphatic endothelial cells) | ||
| Mrc1 | Mannose receptor C1 | Pathogen neutralization |
| Ptx3 | Pentraxin 3 | Positive regulation of innate immunity |
| Ccl21 | Chemokine CCL21 | T-cell chemotaxis |
| Arrb2 | Arrestin β2 | Cytokine/chemokine signaling pathways |
| Bst2 | Tetherin | Anti-viral |
| Serinc3 | Serine incorporator 3 | Antiviral |
| Tspan6 | Tetraspanin 6 | Negative innate immune regulator |
| Cluster 13 (Pericytes) | ||
| C1s1 | Complement C1 component | Complement response |
| Cav1 | Caveolin 1 | T-cell activation, TGFß1 inhibition |
| Ifitm1 | IFITM1 | Inhibition of viral entry |
| Cluster 8 (Macrophages) | ||
| Tlr2 | Toll-like receptor 2 | Pathogen receptor |
| Cd14 | CD14 | LPS receptor component |
| Ly86 | MD-1 | LPS receptor component |
| Nlrp3 | NALP3 | Pathogen receptor, inflammasome |
| MyD88 | MYD88 | TLR signaling adaptor |
| Mrc1 | Mannose receptor C1 | Pathogen neutralization |
| Unc93b1 | UNC93B1 | Required for TLR DNA recognition |
| Cfp | Complement factor P | Alternative complement response |
| C1qa,b,c | Three C1q A-chains | Complement response |
| Irf5, Irf8 | IFN response factors | IFN production |
| Cd86 | CD86 | T-cell activation, IL2 production |
| Actr3 | ACTR3 | Phagocytosis |
| Trem2 | TREM2 | Immune activation in phagocytes |
| Cd74 | CD74 | MHC class II antigen processing |
| Clec4a2 | Lectin-like immunoreceptor | Antigen presentation |
| Apoe | Apolipoprotein E | Macrophage, T- and NK-cell regulation |
| Arrb2 | Arrestin β2 | Cytokine/chemokine signaling pathways |
| Ccl2 | Chemokine CCL2 | Macrophage chemotaxis |
| Ccl3 | Chemokine CCL3, MIP1α | Monocyte, PMN chemotaxis |
| Ccl4 | Chemokine CCL4, MIP1β | NK cell, monocyte chemotaxis |
| Ccl5 | Chemokine CCL5, RANTES | T-cell chemotaxis |
| Ccl9 | Chemokine CCL9, MRP2 | Dendritic cell chemotaxis |
| Cxcl16 | Chemokine CXCL16 | T-cell, NK-cell chemotaxis |
| Coro1a | Coronin 1A | Lytic granule secretion |
| Cx3cr1 | Fractalkine receptor | T-cell, monocyte chemotaxis |
| Fcer1g | FCER1γ | IgE receptor component |
| Lyn | LYN | Diverse immune signaling pathways |
| Nrros | Negative regulator of ROS | TGFβ1 activation in macrophages |
| Ptpn6 | PTPN6 | Hematopoietic cell signaling |
| Rab20 | RAB20 | Endocytosis, antibacterial responses |
| Slc11a1 | SLC11A1 | Iron transporter, antibacterial |
| Bst2 | Tetherin | Anti-viral |
| Sirpa | SIRPA | Dendritic cell activation inhibitor |
| Tgfb1 | TGFβ1 | Multifunctional, immunocyte inhibition |
| Axl | AXL receptor tyrosine kinase | TLR inhibition |
| Rab7b | RAB7B | Negative regulation of TLRs |
| Cluster 9 (Monocytes, Dendritic cells) | ||
| Cluster 9 cells expressed a subset of genes expressed by the macrophages of Cluster 8: Cfp, Tgfb1, Vim, Actr3, Ccl6, Ccl9, Cd74, Coro1a, Cybb, Fcer1g, Ly86, Nrros, Ptpn6 and Unc93b1. However, they also expressed: | ||
| Myo1f | Myosin 1F | Immune cell motility |
| Klrd1 | KLRD1 | MHC recognition by cytotoxic cells |
| Klrk1 | KIRK1 | Cytotoxicity of virus-infected cells |
| Slamf7 | SLAMF7 | NK cell activation |
| Lgals3 | Galectin 3 | Monocyte, macrophage chemotaxis |
| Rnase6 | RNASE6 | Antibacterial |
| Rpl39 | Ribosomal protein L39 | Viral gene translation |
| Rps19 | Ribosomal protein S19 | Viral gene translation |
| Cluster 10 (T-cells, NK cells) | ||
| Hmgb2 | HMGB2 | Innate immune DNA/RNA receptor |
| Txk | TXK tyrosine kinase | Th1 cytokine production |
| Coro1a | Coronin 1A | Lytic granule secretion |
| Klrd1 | KLRD1 | MHC recognition by cytotoxic cells |
| Klrk1 | KIRK1 | Cytotoxicity of virus-infected cells |
| Ccl5 | Chemokine CCL5, RANTES | T-cell chemotaxis |
| Rpl14a | Ribosomal protein 14a | Viral replication and gene translation |
| Cluster 14 (ILC2s) | ||
| Coro1a | Coronin 1A | Lytic granule secretion |
| Samhd1 | SAMHD1 | Mediates TNF inflammatory responses |
| Arg1 | Arginase 1 | Promotes acute type 2 inflammation |
| C1qbp | C1q binding protein | Multiple immune/inflammatory responses |
| Ccl1 | Chemokine CCL1 | Monocyte chemotaxis |
| Cluster 15 (B-cells) | ||
| Ly86 | MD-1 | LPS receptor component |
| Unc93b1 | UNC93B1 | Required for TLR DNA recognition |
| Cd74 | CD74 | MHC class II antigen processing |
| Ptpn6 | PTPN6 | |
| Coro1a | Coronin 1A | Lytic granule secretion |
| Slamf7 | SLAMF7 | NK cell activation |
| Irf8 | IFN response factor 8 | Regulates IFN responses |
| Cluster 16 (Melanocytes) | ||
| Vim | Vimentin | Viral and bacterial attachment |
| Mif | MMIF | Pro-inflammatory mediator |
| Gapdh | GAPDH | Inhibits IFN-induced gene expression |