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Hyunmin Kim edited this page Jan 31, 2021 · 8 revisions

##Todo

Regulation of immune responses by the airway epithelial cell landscape

NatRevImm2021

Table 1

cell_type gene PMID
Basal cells KRT5, TP63, KRT14, PDPN, NGFR, LGALS1, ITGA6, ITGB4, LAMA3, LAMB3, KRT15, S100A2, NPPC, BCAM, DST Main airway stem cells — regeneration, repair of epithelial lining
Suprabasal cells KRT5, TP63 low, KRT19, NOTCH3 Intermediate between basal and club cells
Secretory — club and goblet cells SCGB1A1 (club cells), MUC5AC (goblet cells), MUC5B, TFF3, SCGB3A1, BPIFB1, MSMB, SLPI, WFDC2 Secretion of mucus, antimicrobial and anti-inflammatory peptides
Deuterosomal cells DEUP1/CCDC67, FOXJ1, FOXN4, CDC20B Precursor of ciliated cell characterized by genes critical to centriole amplification
Ciliated cells FOXJ1, PIFO, TPPP3, SNTN, FAM183A, LRRIQ1, DNAH12, C20orf85, SNTN, CAPS, TUBB4B, DNAH5, TSPAN1 Clearance of mucus and debris
Mucous-ciliated cells FOXJ1, MUC5AC Differentiation intermediate between goblet and ciliated cells in homeostatic and diseased airways
Ionocyte FOXI1, CFTR, ASCL3, RARRES2 Ion transport, fluid and pH regulation
Pulmonary neuroendocrine cells ASCL1, CHGA, CGRP, INSM1, HOXB5 Environmental sensor — signals to CNS
Tuft/brush cells DCLK1, RGS13, POU2F3, ASCL2, LRMP Immune and taste sensor, leukotriene synthesis, links to type 2 immunity
Hillock cells KRT13, KRT4 Transitional cell type between basal and secretory; located in stratified, non-ciliated structures with high cell turnover; postulated to play a role in squamous barrier function and immunomodulation

NatCom2020

Obtained from TableS2 of googledrive

Cell types Genes PMID
Epithelial cells EPCAM, KRT19, CDH1, KRT18 28474673, 31067475
T lymphocytes CD3D, CD3E, CD3G, TRAC 28475900, 31209336
B lymphocytes CD79A, IGHM, IGHG3, IGHA2 31712411, 30523328
Myeloid cells CD68, MARCO, FCGR3A (CD16), LYZ 28475900, 29967419
NK cells NCAM1 (CD56), NKG7, GNLY, KLRD1 28475900, 31477722
MAST cells KIT, MS4A2,GATA2 30979687
Fibroblasts DCN, COL1A1, COL1A2, THY1 31209336, 29198524
Endothelial cells PECAM1, CLDN5, FLT1, RAMP2 30674341, 21460247, 23355623
Oligodendrocytes OLIG1, OLIG2, MOG, CLDN11 29615592, 26628089
AT1 AGER 30554520
AT2 SFTPC, LAMP3 30554520
Club SCGB1A1 30554520
Ciliated FOXJ1, RFX2 30554520
Tip-like ECs RAMP3, RGCC, ADM 29449267
Stalk-like ECs SELP, ACKR1 29449267
Lymphatic ECs CCL21, LYVE1 29449267
EPCs TYROBP, C1QB 29449267
Tumor ECs HSPG2, INSR, VWA1 29988129, 30559346, 10629090
COL13A1+ matrix FBs COL13A1, TCF21, ITGAB, CXCL14, NPNT 29590628
COL14A1+ matrix FBs COL14A1, GSN, PI16, CYGB, PRRX1 29590628
Myofibroblasts ACTA2, MYH11, TAGLN, ACTG2, MYLK 29590628
Smooth muscle cells CNN1, SYNPO2, CRYAB, DES 28564607
Mesothelial cells UPK3B, MSLN, CALB2, WT1 29590628
Pericytes RGS5, CSPG4, ABCC9, KCNJ8 28564607
Perivascular FB-like cells CYP1B1, APOD 29443965
Lipofibroblast FABP4, FABP5, PPARG 29590628
Monocyte CTSS, FCN1, S100A8, S100A9, LYZ, VCAN 29967419
Macrophage LGMN, CTSB, CD14, FCGR3A 29967419
mo-lineage MAFB, MAF, CX3CR1, ITGAM, CSF1R 28257233
Alveolar-Mac MARCO, FABP4, MCEMP1 28257233
Anti-inflammatory CD163, APOE, SEPP1, C1QA, C1QB, C1QC 27381735, 21350196, 26053663, 22523386
Pro-inflammatory CXCL8, IL1B 25339958
Cycling STMN1, MKI67, TOP2A, CDK1 29967419
DC CLEC10A, CD1C, CLEC4C, PTCRA, CCR7, LAMP3 28475900
CD1c+ DCs (LCs) CD1C, ITGAX 24744755
CD141+ DCs CLEC9A, XCR1 24744755
CD207+CD1a+ LCs CD207, CD1A 24744755
Activated DCs CCR7, LAMP3 17312119
pDCs IL3RA, CLEC4C 28428369
CD163+CD14+ DCs CD14, CD163 31474513
GC B cells in the DZ STMN1, AICDA, MKI67, BIRC5 30104629
GC B cells in the LZ LMO2, BCL2A1 30104629
GrB-secreting cells GZMB 21808264
Follicular B cells MS4A1, HLA-DRA 29988129
MALT B cells JCHAIN, IGHA1 29988129
Plasma cells IGHG1 29988129
CD4+ T Il7R, CD4 14662907, 28475900
CD8+ T CD8A, CD8B 28475900
Naïve TCF7, SELL, LEF1, CCR7 29942094
Exhausted LAG3, TIGIT, PDCD1, HAVCR2 29942094
Cytotoxic IL2, GZMA, GNLY, PRF1, GZMB, GZMK, IFNG, NKG7 29942094
Treg IL2RA, FOXP3, IKZF2, TGFB1, TGFB3, TGFBI, TGFBR1 29942094, 28474673
T follicular helper MAF, CXCR5, PDCD1, CXCL13 28265271, 28570278
T helper 17 IRF4, CREM, NR4A2 21381156, 27680869, 23437182
T helper 1 STAT4, IFNG, IL12RB2 24987392, 21685955
T helper 2 GATA3, STAT6, IL4 24987392
gamma delta T TRDC, TRGC2, TRGC1 31118283
NK XCL1, FCGR3A, KLRD1, KLRF1 31477722
id name feature
TRM tissue-resident memory T cell CD8A CD69 ITGAE(CD103) ITGA1(CD49a)
TPM peripheral memory T cell -
TEM effector memory T cell -
B resident memory B cell CD69 CXCR3
ILC innate lymphoid cells -
id name feature link
TRM tissue-resident memory T cell CD8A CD69 ITGAE(CD103) ITGA1(CD49a) 1
TCM central memory T cell CD8A CD62L CCR7 1
TH1 T helper 1 cell 1
TH2 T helper 2 cell 1
TH17 T helper 17 cell 1
TREG regulatory T cell CD4 IL2RA(CD25) FOXP3 a
TFH T follicular helper cell CD4 CXCR5 1
Neutrophile Neutrophile CEACAM8(CD66b) CXCL5 1
NK Natural killer cell CD96 1
M1 Macrophage 1 IL-12 1
M2 Macrophage 2 IL-10 TGFB 1
TAM Tumor-associated macrophage CD14 CD40 CD68 1
MDSC Myeloid-derived suppressor cells IDO1 1
PMN-MDSC neutrophil-like granulocytic or polymorphonuclear MDSC OLR1 1
M-MDSC more prominent monocytic MDSC 1
B B cell CD20 CD19 CD138 STAT3 1
BREG regulatory B cell IL10 1
TAMC tumor-associated mast cell [NatRevCancer2020]

1: The immune contexture and Immunoscore in cancer prognosis and therapeutic efficacy 2: Single-cell RNA sequencing demonstrates the molecular and cellular reprogramming of metastatic lung adenocarcinoma

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