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Annotation of marker epitopes for various cell types
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| # This annotation of cell type markers is tailored for surface proteins | |
| # normally profilid with multiplexed imaging (IMC, CODEX). | |
| # It is a simple reference for myself and may be more detailed in some parts than others. | |
| # This reference is hierarchical. | |
| # This annotation is generally pan-tissue. | |
| # Author: Andre Rendeiro | |
| # License: CC BY-SA 2.0 | |
| cell_types: | |
| structural: | |
| basal: | |
| markers: | |
| - KRT5 | |
| - KRT14 | |
| - p63 | |
| - TP63 | |
| - PDPN | |
| epithelium: | |
| markers: | |
| - Cytokeratins | |
| - Keratin818 | |
| - K818 | |
| # Lung: | |
| club: | |
| markers: | |
| - KRT15 | |
| - CD74 | |
| - CC16 | |
| - SCGB1A1 | |
| hillock: | |
| markers: | |
| - KRT4 | |
| - KRT13 | |
| ciliated: | |
| markers: | |
| - FOXJ1 | |
| - TUBB1 | |
| - p73 | |
| - TP73 | |
| tuft: | |
| markers: | |
| - | |
| goblet: | |
| markers: | |
| - MUC5A | |
| - MUC5AC | |
| - MUC5B | |
| - SPDEF | |
| aleveolar: | |
| markers: | |
| - CD44 | |
| - Keratin818 | |
| - K818 | |
| typeI: | |
| markers: | |
| - SFTPB | |
| - PDPN | |
| - Keratin818 | |
| - K818 | |
| - AGER | |
| - AQP5 | |
| - PDPN | |
| typeII: | |
| markers: | |
| - SFTPC | |
| - SFTPA | |
| - Keratin818 | |
| - K818 | |
| endothelial: | |
| markers: | |
| - EpCAM | |
| - CD31 | |
| - AQ1 | |
| - Periostin | |
| lymphatic: | |
| markers: | |
| - PDPN | |
| mesenchymal: | |
| markers: | |
| - Vimentin | |
| - VIM | |
| fibroblast: | |
| markers: | |
| - AlphaSMA | |
| - aSMA | |
| - CollagenTypeI | |
| - ColTypeI | |
| cancer-associated fibroblast: | |
| markers: | |
| - | |
| myofibroblast: | |
| markers: | |
| - ACTA2 | |
| smooth_muscle: | |
| markers: | |
| - aSMA | |
| - AlphaSMA | |
| skeletal_muscle: | |
| markers: | |
| - CD56 | |
| chondrocytes: | |
| markers: | |
| - SOX9 | |
| immune: | |
| lymphoid: | |
| b_cell: | |
| markers: | |
| - CD45 | |
| - CD20 | |
| T_cell: | |
| markers: | |
| - CD45 | |
| - CD3 | |
| CD4: | |
| markers: | |
| - CD4 | |
| Treg: | |
| markers: | |
| - FoxP3 | |
| - FOXP3 | |
| CD8: | |
| markers: | |
| - CD8a | |
| - CD8A | |
| NKcells: | |
| markers: | |
| - CD45 | |
| - CD56 | |
| - CD57 | |
| - CD11b | |
| - ITGAM | |
| myeloid: | |
| markers: | |
| - CD45 | |
| - CD16 | |
| - CD68 | |
| - CD11b | |
| - CD11c | |
| monocytes: | |
| markers: | |
| - CD14 | |
| - IL1beta | |
| - IL1B | |
| macrophages: | |
| markers: | |
| - Vimentin | |
| - VIM | |
| - CD45 | |
| - CD14 | |
| - CD16 | |
| - CD4 | |
| - CD11b | |
| - CD11c | |
| - ITGAM | |
| - CD163 | |
| sources: | |
| - https://www.cusabio.com/c-20938.html | |
| M1: | |
| phenotype: pro-inflamatory, autoimmune, obesity and diabetes, atherosclerosis | |
| environment: virus, bacteria | |
| differentiating_factors: | |
| - LPS, TLR4, NFKB | |
| - TLR4, NFKB | |
| - IFNG, STAT1 | |
| - IL6, STAT1 | |
| markers: | |
| - CD80 | |
| - CD86 | |
| - CD64 | |
| - CD32 | |
| - CD11c | |
| M2: | |
| phenotype: anti-inflamatory, wound healing, fibrosis, allergy and asthma | |
| environment: cancer | |
| differentiating_factors: | |
| - IL6, STAT3 | |
| - IL10, STAT3 | |
| - IL4, STAT6 | |
| - IL4, PI3K | |
| - TGFBeta, SMAD3 | |
| - IL13 | |
| markers: | |
| - CD206 | |
| - CD68 | |
| - CD163 | |
| - ARG1 | |
| neutrophils: | |
| markers: | |
| - CD11b | |
| - CD11c | |
| - CD15 | |
| - MPO | |
| - S100A9 | |
| - S100A8 | |
| - Periostin | |
| dendritic_cells: | |
| markers: | |
| - CD45 | |
| - CD14 | |
| - CD16 | |
| - FCGR3A | |
| - Cd11c | |
| - ITGAX | |
| cDC1: | |
| sources: | |
| - https://doi.org/10.1016/j.smim.2021.101481 | |
| functions: | |
| - regulates host defense to viruses and other intracellular pathogens and promotes CD8+ T-cell-mediated anti-tumor immunity. | |
| - promote tumor rejection given their specialization in recognition of dead and dying cells, cross-presentation and ability to drive CD8 + T-cell response. | |
| markers: | |
| - IRF8 | |
| - BATF3 | |
| - ID2 | |
| - CLEC9A (DNGR-1) | |
| - XCR1 | |
| - BDCA-3 (CD141) | |
| cDC2: | |
| sources: | |
| - https://doi.org/10.1016/j.smim.2021.101481 | |
| functions: orchestrate host barrier protection as well as immunity to extracellular pathogens and/or allergens largely by promoting CD4+ helper T-cell responses through presentation of soluble antigens via MHC class II (MHC-II). | |
| markers: | |
| - IRF4 (high) | |
| - RELB | |
| - ZEB2 | |
| - KLF4 | |
| - NOTCH | |
| pDC: | |
| sources: | |
| - https://doi.org/10.1016/j.smim.2021.101481 | |
| functions: | |
| - specialized for anti-viral responses and are an important source of IFN-I (and IFN-III) upon viral infection. | |
| - pDC are considered to have a similar role in potentiating anti-tumoral immune responses via IFN-I production, however, pDC may also drive tolerance and immune suppression in the context of malignancy. | |
| - While pDC are able to cross-present antigen to prime CD8 + T-cells, they exhibit inferior cross-presenting capacity relative to their conventional DC counterparts. | |
| markers: | |
| - CD11d | |
| - BDCA-2 (CLEC4C or CD303) | |
| - CD123 | |
| - CD304 | |
| - TCF4 | |
| - IRF8 | |
| - RUNX1 | |
| tDC: | |
| sources: 10.1016/j.celrep.2019.11.042 | |
| comment: also known as AXL+ DC or ASDC | |
| markers: | |
| - AXL | |
| MoDC: | |
| sources: | |
| - https://doi.org/10.1016/j.smim.2021.101481 | |
| functions: | |
| - highly context-dependent DC subset that differentiate in response to inflammatory stimuli and are recruited to sites of inflammation, including the TME, via the CCR2-CCL2 chemokine signaling axis. | |
| - MoDC are heterogeneous and share substantial overlap with certain cDC2 subsets and monocytes, which is reflected in the diverse range of immune actions initiated by MoDC. | |
| markers: | |
| - CD14 | |
| - CD88 | |
| DC3: | |
| sources: | |
| - https://doi.org/10.1016/j.smim.2021.101481 | |
| functions: | |
| - tumor-infiltrating DCs. | |
| - share overlapping phenotypic features with conventional DC, including both cDC1 and cDC2, yet harbor a distinct transcriptional profile. | |
| - DC3 program is signified by the co-existence maturation/activation markers and an immunoregulatory profile that includes markers of DC migration, DC maturation, immune-regulation. | |
| markers: | |
| - | |
| basophiles: | |
| markers: | |
| - | |
| eosinophil: | |
| markers: | |
| - IL5RA | |
| - CCR3 | |
| - PRG2 | |
| - PTGDR2 | |
| - SIGLEC8 | |
| - GATA2 | |
| mast_cell: | |
| markers: | |
| - cKIT | |
| - CD117 | |
| - MastCellTryptase | |
| - TPSAB1 | |
| myeloid-derived suppressor cells: | |
| markers: | |
| - CD11b | |
| - ITGAM | |
| - GranzymeB | |
| - GZMB | |
| cell_states: | |
| proliferative: | |
| markers: | |
| - Ki67 | |
| - PCNA | |
| - MCM2 | |
| - pHH3 | |
| cell death: | |
| markers: | |
| - CleavedCaspase3 | |
| - CC3 | |
| - CleavedPARP | |
| - Survivin | |
| - CitH3 | |
| - SC5b9 | |
| - iNOS | |
| hypoxia: | |
| markers: | |
| - Carbonic anhydrase IX | |
| cytotoxic: | |
| markers: | |
| - GranzymeB | |
| activation: | |
| markers: | |
| - CD27 | |
| - CD39 | |
| - CD84 | |
| # For DCs: | |
| migration: | |
| markers: | |
| - CCR7 | |
| - FSCN1 | |
| maturation: | |
| markers: | |
| - LAMP3 | |
| - CD80 | |
| - CD83 | |
| - CD40 | |
| immune-regulation: | |
| markers: | |
| - PD-L1 | |
| - PD-L2 | |
| - IDO1 | |
| - CD200 | |
| inflammation: | |
| markers: | |
| - pSTAT3 | |
| - pSTAT3Tyr705 | |
| - pNFkbp65 | |
| - IRF2BP2 | |
| - IL6 | |
| - IL1beta | |
| - iNOS | |
| arrest: | |
| markers: | |
| - p21 | |
| - p27 | |
| senescence: | |
| markers: | |
| - uPAR | |
| - p21 | |
| - p16 | |
| - CDKN1A | |
| - CDKN2A | |
| infected: | |
| markers: | |
| - SARSSpikeS1 | |
| # When updating, make sure syntax is correct: | |
| # $ python -c "import yaml; yaml.safe_load(open('markers_to_cell_type_labels.yaml'))" |
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