Thymic stromal cell types and subtypes with identifying markers from single-cell omic studies
| Study . | Cell type . | Subtype . | Markers . |
|---|---|---|---|
| Park et al., 2020 | TEC | cTEC | EPCAM, FOXN1, PSMB11 |
| mcTEC | EPCAM, DLK2 | ||
| mTECI | EPCAM, KRT14 | ||
| mTECII | EPCAM, AIRE | ||
| mTECIII | EPCAM, KRT1 | ||
| mTECIV | EPCAM, FOXJ1 | ||
| TEC(myo) | EPCAM, MYOD, CHRNA1 | ||
| TEC(neuro) | EPCAM, NEUROD1, CHGA | ||
| Fibroblast | Fib_1 | PDGFRA, COLEC11, ALDH1A2, GDF10 | |
| Fib_2 | PDGFRA, FBN1, PI16, SEMA3D | ||
| Fb_cycling | PDGFRA, PCNA | ||
| Vascular smooth muscle cells (VSMC) | PDGFRB, ACTA2, RGS5 | ||
| Endothelial | Endo | PECAM1, CDH5 | |
| Lymph | PECAM1, LYVE1 | ||
| Campinoti et al., 2020 | TEC | cTEC I | CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA, TP53AIP1 |
| cTEC II | |||
| cTEC III | |||
| mTEC-Myo I | CD24, HES6, EPCAM, CDH1, CLDN3 | ||
| mTEC-Myo II | |||
| mTEC-Neuro I | |||
| mTEC-Neuro II | |||
| mTEC-Diff | |||
| Common (com)TECEMT | CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1, ZEB1 | ||
| comTEC-Proliferating | |||
| comTEC-Polykeratins | |||
| comTEC-Ionocytes | |||
| Bautista et al., 2021 | TEC | cTEChi | EPCAM, FOXN1, PSMB11, CCL25, HLA-DQB1 |
| cTEClo | EPCAM, FOXN1, PSMB11 | ||
| Immature TEC-1 | EPCAM, KRT8, KRT5, SOCS3, KRT17 | ||
| Immature TEC-2 | EPCAM, KRT8, KRT5, IGFBP5, SAA1, CDH13 | ||
| mTEClo | EPCAM, CLDN4, CCL21, KRT15 | ||
| Aire+ mTEChi | EPCAM, SPIB, AIRE, FEZF2 | ||
| Corneo-like mTEC | EPCAM, KRT1, IVL | ||
| Neuroendocrine | EPCAM, NEUROD1, BEX1 | ||
| Myoid | EPCAM, MYOD1, DES | ||
| Myelin+ | EPCAM, SOX10, MPZ | ||
| Mesenchyme | PDGFRA, LUM, LAMA2 | ||
| Pericytes | PDGFRB, MCAM, CPSG4, FST | ||
| Endothelial | Endo-1 | PECAM1, ACKR1, SELE, APLNR, LGALS3 | |
| Endo-2 | PECAM1, VEGFC, GJA4 | ||
| Endo-3 | PECAM1, ACKR1, APLNR, FN1 | ||
| Endo-4 | LYVE1, PROX1, CCL21 | ||
| Mesothelium | MSLN, UPK3B, PRG4 | ||
| Heimli et al., 2023 | TEC | cTEC | EPCAM, PSMB11, PRSS16, CCL25 |
| NEURL2+ TEC | EPCAM, PRSS16, NEURL2, DLL4 | ||
| mcTEC | EPCAM, DLK2, CCL2, KRT15 | ||
| mTECI | EPCAM, DLK2, CCL2, KRT15, CCL19, CXCL14 | ||
| mTECII | EPCAM, AIRE, HLA-DRA, NTHL1 | ||
| mTECIII | EPCAM, IVL, ANXA1, ANXA9 | ||
| mTEC(myo) | EPCAM, MYOG, MYOD1, DES | ||
| mTEC(neuro) | EPCAM, NEUROD1, BEX1 | ||
| Ciliated | EPCAM, ATOH1, GFI1, LHX3, FOXJ1 | ||
| Ionocyte-like | EPCAM, FOXI1,ASCL3, CFTR, CLCNKB | ||
| Fibroblast | Fibro_1 | COL15A1, SFRP2 | |
| Fibro_2 | IL33, CCL19 | ||
| Fibro_3 | CCL19, CXCL9, CXCL10, CD40, HLA-DRA | ||
| Fibro_4 | DPP4, PI16, SEMA3C, MFAP5,FBN1 | ||
| Endothelial | Endo_1 | PECAM1, ACKR1, ICAM1, SELE | |
| Endo_2 | PECAM1, ACKR1 | ||
| Endo_3 | PECAM1, CXCL12, SEMA3G, HEY1, NOTCH4, IL32 | ||
| Endo_4 | LYVE1, PROX1, FLT4 | ||
| Mural | Mural_1 | ATF3, NR4A1, CDKN1A, MYH11, TAGLN | |
| Mural_2 | MYH11 | ||
| Mural_3 | CCL21, CCL19, CXCL12 | ||
| Ragazzini et al., 2023 | TEC | cTEC immediate-early genes | CD274, TBATA, PRSS16, FOXN1, AP-1 |
| cTEC conventional I–III | TBATA, PRSS16, CTSV, KCNIP3 | ||
| cTEC differentiating | TBATA, PRSS16, ATF3, CCL5 | ||
| PolyKRT | KRT5, KRT8, KRT13, KRT14, KRT15, KRT17 | ||
| PolyKRT proliferating | KRT5, KRT8, KRT13, KRT14, KRT15, KRT17, HMGB2 | ||
| mTEC Hassall’s body region | KRT1, KRT6A,KRT10, AIRE, FEZF2 | ||
| mTEC Ionocytes | CFTR, TFCP2L1, ASCL3, FOXI1, KRT7 | ||
| mTEC differentiating | ASCL1, CLDN3-4 | ||
| mTEC Myoid | MYOD, MYOG, TTN, MEFC2 | ||
| mTEC Neuro early | NEUROD1, GNG8, SOX11, NKX6-2, MGP, AVP | ||
| mTEC Neuro intermediate | NEUROD1, GNG8, POUF4F1, HIGD1B, GKAP1 | ||
| mTEC Mechano high | S100A1, POUF4F3, IRX2, SOX2 | ||
| mTEC Mechano low | S100A1, POUF4F3, IRX2, ATOH1 | ||
| Stankiewicz et al., 2023, Preprint | TEC | cTEC | PSMB11, KRT5, KRT8 |
| mTEC | EPCAM, KRT5, KRT8 | ||
| Activated mTEC | EPCAM, CLASS I, CLASS II | ||
| Specialty TEC | EPCAM, NEUROD1, MYOG, POU4F1 | ||
| Fibroblast | DPP4+ capsular (cap) Fibs | PDGFRA, PI16, DPP4 | |
| capFibs | PDGFRA, PI16 | ||
| Medullary Fibs | PDGFRA, CCL19, CLASS I | ||
| Fibs proliferating | PDGFRA, MKI67 | ||
| KRT+ Fibs | PDGFRA, KRT5, KRT8 | ||
| VSMC | MCAM, ACTA2 | ||
| Pericytes | MCAM | ||
| Endothelial | ECs (Notch) | CD31, JAG1, JAG2, DLL1, DLL4 | |
| ECs | CD31 | ||
| Lymphatic endothelial cells | CD31, LYVE1 | ||
| Yayon et al., 2023, Preprint | TEC | cTECI | PSMB11, LY75, CCL25, HLA-DRA |
| cTECII | PSMB11, LY75, CCL25, HLA-DRA, DLL4, FOXN1 | ||
| cTECIII | PSMB11, LY75, CCL25, HLA-DRA, TBATA, TP53AIP1 | ||
| mcTEC | DLK2, IGFBP5, IGFBP6, CCN2, CCL2, ITGA6, KRT15 | ||
| mcTEC-Prolif | DLK2, IGFBP5, IGFBP6, CCN2, CCL2, ITGA6, MKI67 | ||
| mTECI | EPCAM, ASCL1, CCL21 | ||
| mTECI-trans | EPCAM, ASCL1 | ||
| mTECII | EPCAM, AIRE, FEZF2, CRIP1 | ||
| mTECIII | EPCAM, SLPI, IVL, KRT10, CDKN2A | ||
| TEC-neuro | EPCAM, NEUROD1, BEX1, NEUROG1, NEUROD4 | ||
| TEC-ciliated | EPCAM, NEUROD1, BEX1, PCP4, FOXJ1 | ||
| TEC-myo | EPCAM, MYOG, TTN, CHRNA1 | ||
| TEC-tuft | EPCAM, FOXI1, CFTR, POU2F3, PLCB2 | ||
| Fibroblast | PeriloFb | PDGFRA, PDGFRB, VIM, COLEC11, ALDH1A2, GDF10 | |
| PeriloFb-Prolif | PDGFRA, PDGFRB, VIM, COLEC11, ALDH1A2, GDF10, MKI67 | ||
| InterloFb | PDGFRA, PDGFRB, VIM, FBN1, PI16, MFAP5, SEMA3C | ||
| InterloFb-COL9A3 | PDGFRA, PDGFRB, VIM, FBN1, PI16, MFAP5, SEMA3C, COL9A3, COL13A1, WIF1, DHRS3 | ||
| Medullary fibroblasts (medFb) | PDGFRA, PDGFRB, VIM, CCL19, IL33, TNSF10, CXCL9, CXCL10 | ||
| medFb-RGS5 | PDGFRA, PDGFRB, VIM, CCL19, IL33, TNSF10, CXCL9, CXCL10, RGS5 | ||
| medFB-MHCIIh | PDGFRA, PDGFRB, VIM, CCL19, IL33, TNSF10, CXCL9, CXCL10, HLA-DRA, SBSPON, HEY1, LTBP1 | ||
| fetFB-CCL21 | PDGFRA, PDGFRB, VIM, CCL21, FDCSP, CXCL13 | ||
| fetFB-NKX2-5 | PDGFRA, PDGFRB, VIM, TNNT1, NKX2-5, KRT8 | ||
| fetFB-RSPO2 | PDGFRA, PDGFRB, VIM, CES1, RSPO2 | ||
| Endothelial | EC-Art | PECAM1, CDH5, CLDN5, CXCL12, SEMA3G, HEY1 | |
| EC-Art-ELN | PECAM1, CDH5, CLDN5, SULF1, ELN, CXCL12, SEMA3G, HEY1 | ||
| EC-Cap | PECAM1, CDH5, CLDN5, RGCC, PLVAP | ||
| EC-Cap-Prolif | PECAM1, CDH5, CLDN5, RGCC, PLVAP, MKI67 | ||
| EC-Ven | PECAM1, CDH5, CLDN5, PLVAP, ACKR1, ICAM1, CCL2, SELE | ||
| EC-Ven-ELN | PECAM1, CDH5, SULF1, ELN, PLVAP, ACKR1, ICAM1, CCL2, SELE | ||
| EC-Lymphatic | CLDN5, PROX1, TFF3, CCL21 | ||
| Pericytes | SMC | ACTA2, MYH11, RERGL, CASQ2, ELN | |
| Pericyte | RGS5, PDGFRB, ABCC9, KCNJ8 | ||
| Pericyte_CCL19 | RGS5, PDGFRB, ABCC9, KCNJ8, CCL19, CCL21 | ||
| Pericyte_COL1A1 | ACTA2, COL1A1, ELN | ||
| ProlifPericyte | ACTA2, RGS5, PDGFRB, ABCC9, KCNJ8, MKI67, TOP2A |
| Study . | Cell type . | Subtype . | Markers . |
|---|---|---|---|
| Park et al., 2020 | TEC | cTEC | EPCAM, FOXN1, PSMB11 |
| mcTEC | EPCAM, DLK2 | ||
| mTECI | EPCAM, KRT14 | ||
| mTECII | EPCAM, AIRE | ||
| mTECIII | EPCAM, KRT1 | ||
| mTECIV | EPCAM, FOXJ1 | ||
| TEC(myo) | EPCAM, MYOD, CHRNA1 | ||
| TEC(neuro) | EPCAM, NEUROD1, CHGA | ||
| Fibroblast | Fib_1 | PDGFRA, COLEC11, ALDH1A2, GDF10 | |
| Fib_2 | PDGFRA, FBN1, PI16, SEMA3D | ||
| Fb_cycling | PDGFRA, PCNA | ||
| Vascular smooth muscle cells (VSMC) | PDGFRB, ACTA2, RGS5 | ||
| Endothelial | Endo | PECAM1, CDH5 | |
| Lymph | PECAM1, LYVE1 | ||
| Campinoti et al., 2020 | TEC | cTEC I | CCL25, CD274, CFC1, CTSV, FOXN1, KCNIP3, LY75, PRSS16, PSMB11, SCX, SLC46A2, TBATA, TP53AIP1 |
| cTEC II | |||
| cTEC III | |||
| mTEC-Myo I | CD24, HES6, EPCAM, CDH1, CLDN3 | ||
| mTEC-Myo II | |||
| mTEC-Neuro I | |||
| mTEC-Neuro II | |||
| mTEC-Diff | |||
| Common (com)TECEMT | CCL19, CFTR, COL1A1, DAB2, FN1, GLIPR2, HAS2, HGF, KRT14, KRT15, LOXL2, MKI67, MMP2, S100A4, SNAI1, SNAI2, TFCP2L1, TGFB3, TGFBR2, THY1, TP63, TWIST1, ZEB1 | ||
| comTEC-Proliferating | |||
| comTEC-Polykeratins | |||
| comTEC-Ionocytes | |||
| Bautista et al., 2021 | TEC | cTEChi | EPCAM, FOXN1, PSMB11, CCL25, HLA-DQB1 |
| cTEClo | EPCAM, FOXN1, PSMB11 | ||
| Immature TEC-1 | EPCAM, KRT8, KRT5, SOCS3, KRT17 | ||
| Immature TEC-2 | EPCAM, KRT8, KRT5, IGFBP5, SAA1, CDH13 | ||
| mTEClo | EPCAM, CLDN4, CCL21, KRT15 | ||
| Aire+ mTEChi | EPCAM, SPIB, AIRE, FEZF2 | ||
| Corneo-like mTEC | EPCAM, KRT1, IVL | ||
| Neuroendocrine | EPCAM, NEUROD1, BEX1 | ||
| Myoid | EPCAM, MYOD1, DES | ||
| Myelin+ | EPCAM, SOX10, MPZ | ||
| Mesenchyme | PDGFRA, LUM, LAMA2 | ||
| Pericytes | PDGFRB, MCAM, CPSG4, FST | ||
| Endothelial | Endo-1 | PECAM1, ACKR1, SELE, APLNR, LGALS3 | |
| Endo-2 | PECAM1, VEGFC, GJA4 | ||
| Endo-3 | PECAM1, ACKR1, APLNR, FN1 | ||
| Endo-4 | LYVE1, PROX1, CCL21 | ||
| Mesothelium | MSLN, UPK3B, PRG4 | ||
| Heimli et al., 2023 | TEC | cTEC | EPCAM, PSMB11, PRSS16, CCL25 |
| NEURL2+ TEC | EPCAM, PRSS16, NEURL2, DLL4 | ||
| mcTEC | EPCAM, DLK2, CCL2, KRT15 | ||
| mTECI | EPCAM, DLK2, CCL2, KRT15, CCL19, CXCL14 | ||
| mTECII | EPCAM, AIRE, HLA-DRA, NTHL1 | ||
| mTECIII | EPCAM, IVL, ANXA1, ANXA9 | ||
| mTEC(myo) | EPCAM, MYOG, MYOD1, DES | ||
| mTEC(neuro) | EPCAM, NEUROD1, BEX1 | ||
| Ciliated | EPCAM, ATOH1, GFI1, LHX3, FOXJ1 | ||
| Ionocyte-like | EPCAM, FOXI1,ASCL3, CFTR, CLCNKB | ||
| Fibroblast | Fibro_1 | COL15A1, SFRP2 | |
| Fibro_2 | IL33, CCL19 | ||
| Fibro_3 | CCL19, CXCL9, CXCL10, CD40, HLA-DRA | ||
| Fibro_4 | DPP4, PI16, SEMA3C, MFAP5,FBN1 | ||
| Endothelial | Endo_1 | PECAM1, ACKR1, ICAM1, SELE | |
| Endo_2 | PECAM1, ACKR1 | ||
| Endo_3 | PECAM1, CXCL12, SEMA3G, HEY1, NOTCH4, IL32 | ||
| Endo_4 | LYVE1, PROX1, FLT4 | ||
| Mural | Mural_1 | ATF3, NR4A1, CDKN1A, MYH11, TAGLN | |
| Mural_2 | MYH11 | ||
| Mural_3 | CCL21, CCL19, CXCL12 | ||
| Ragazzini et al., 2023 | TEC | cTEC immediate-early genes | CD274, TBATA, PRSS16, FOXN1, AP-1 |
| cTEC conventional I–III | TBATA, PRSS16, CTSV, KCNIP3 | ||
| cTEC differentiating | TBATA, PRSS16, ATF3, CCL5 | ||
| PolyKRT | KRT5, KRT8, KRT13, KRT14, KRT15, KRT17 | ||
| PolyKRT proliferating | KRT5, KRT8, KRT13, KRT14, KRT15, KRT17, HMGB2 | ||
| mTEC Hassall’s body region | KRT1, KRT6A,KRT10, AIRE, FEZF2 | ||
| mTEC Ionocytes | CFTR, TFCP2L1, ASCL3, FOXI1, KRT7 | ||
| mTEC differentiating | ASCL1, CLDN3-4 | ||
| mTEC Myoid | MYOD, MYOG, TTN, MEFC2 | ||
| mTEC Neuro early | NEUROD1, GNG8, SOX11, NKX6-2, MGP, AVP | ||
| mTEC Neuro intermediate | NEUROD1, GNG8, POUF4F1, HIGD1B, GKAP1 | ||
| mTEC Mechano high | S100A1, POUF4F3, IRX2, SOX2 | ||
| mTEC Mechano low | S100A1, POUF4F3, IRX2, ATOH1 | ||
| Stankiewicz et al., 2023, Preprint | TEC | cTEC | PSMB11, KRT5, KRT8 |
| mTEC | EPCAM, KRT5, KRT8 | ||
| Activated mTEC | EPCAM, CLASS I, CLASS II | ||
| Specialty TEC | EPCAM, NEUROD1, MYOG, POU4F1 | ||
| Fibroblast | DPP4+ capsular (cap) Fibs | PDGFRA, PI16, DPP4 | |
| capFibs | PDGFRA, PI16 | ||
| Medullary Fibs | PDGFRA, CCL19, CLASS I | ||
| Fibs proliferating | PDGFRA, MKI67 | ||
| KRT+ Fibs | PDGFRA, KRT5, KRT8 | ||
| VSMC | MCAM, ACTA2 | ||
| Pericytes | MCAM | ||
| Endothelial | ECs (Notch) | CD31, JAG1, JAG2, DLL1, DLL4 | |
| ECs | CD31 | ||
| Lymphatic endothelial cells | CD31, LYVE1 | ||
| Yayon et al., 2023, Preprint | TEC | cTECI | PSMB11, LY75, CCL25, HLA-DRA |
| cTECII | PSMB11, LY75, CCL25, HLA-DRA, DLL4, FOXN1 | ||
| cTECIII | PSMB11, LY75, CCL25, HLA-DRA, TBATA, TP53AIP1 | ||
| mcTEC | DLK2, IGFBP5, IGFBP6, CCN2, CCL2, ITGA6, KRT15 | ||
| mcTEC-Prolif | DLK2, IGFBP5, IGFBP6, CCN2, CCL2, ITGA6, MKI67 | ||
| mTECI | EPCAM, ASCL1, CCL21 | ||
| mTECI-trans | EPCAM, ASCL1 | ||
| mTECII | EPCAM, AIRE, FEZF2, CRIP1 | ||
| mTECIII | EPCAM, SLPI, IVL, KRT10, CDKN2A | ||
| TEC-neuro | EPCAM, NEUROD1, BEX1, NEUROG1, NEUROD4 | ||
| TEC-ciliated | EPCAM, NEUROD1, BEX1, PCP4, FOXJ1 | ||
| TEC-myo | EPCAM, MYOG, TTN, CHRNA1 | ||
| TEC-tuft | EPCAM, FOXI1, CFTR, POU2F3, PLCB2 | ||
| Fibroblast | PeriloFb | PDGFRA, PDGFRB, VIM, COLEC11, ALDH1A2, GDF10 | |
| PeriloFb-Prolif | PDGFRA, PDGFRB, VIM, COLEC11, ALDH1A2, GDF10, MKI67 | ||
| InterloFb | PDGFRA, PDGFRB, VIM, FBN1, PI16, MFAP5, SEMA3C | ||
| InterloFb-COL9A3 | PDGFRA, PDGFRB, VIM, FBN1, PI16, MFAP5, SEMA3C, COL9A3, COL13A1, WIF1, DHRS3 | ||
| Medullary fibroblasts (medFb) | PDGFRA, PDGFRB, VIM, CCL19, IL33, TNSF10, CXCL9, CXCL10 | ||
| medFb-RGS5 | PDGFRA, PDGFRB, VIM, CCL19, IL33, TNSF10, CXCL9, CXCL10, RGS5 | ||
| medFB-MHCIIh | PDGFRA, PDGFRB, VIM, CCL19, IL33, TNSF10, CXCL9, CXCL10, HLA-DRA, SBSPON, HEY1, LTBP1 | ||
| fetFB-CCL21 | PDGFRA, PDGFRB, VIM, CCL21, FDCSP, CXCL13 | ||
| fetFB-NKX2-5 | PDGFRA, PDGFRB, VIM, TNNT1, NKX2-5, KRT8 | ||
| fetFB-RSPO2 | PDGFRA, PDGFRB, VIM, CES1, RSPO2 | ||
| Endothelial | EC-Art | PECAM1, CDH5, CLDN5, CXCL12, SEMA3G, HEY1 | |
| EC-Art-ELN | PECAM1, CDH5, CLDN5, SULF1, ELN, CXCL12, SEMA3G, HEY1 | ||
| EC-Cap | PECAM1, CDH5, CLDN5, RGCC, PLVAP | ||
| EC-Cap-Prolif | PECAM1, CDH5, CLDN5, RGCC, PLVAP, MKI67 | ||
| EC-Ven | PECAM1, CDH5, CLDN5, PLVAP, ACKR1, ICAM1, CCL2, SELE | ||
| EC-Ven-ELN | PECAM1, CDH5, SULF1, ELN, PLVAP, ACKR1, ICAM1, CCL2, SELE | ||
| EC-Lymphatic | CLDN5, PROX1, TFF3, CCL21 | ||
| Pericytes | SMC | ACTA2, MYH11, RERGL, CASQ2, ELN | |
| Pericyte | RGS5, PDGFRB, ABCC9, KCNJ8 | ||
| Pericyte_CCL19 | RGS5, PDGFRB, ABCC9, KCNJ8, CCL19, CCL21 | ||
| Pericyte_COL1A1 | ACTA2, COL1A1, ELN | ||
| ProlifPericyte | ACTA2, RGS5, PDGFRB, ABCC9, KCNJ8, MKI67, TOP2A |