T cells
| Signature | Genes |
|---|---|
| CD8_c1_Tex | CXCL13, GZMB, HAVCR2, CCL3, ENTPD1, VCAM1, LAG3, TNFRSF9, CTLA4, CCL4L1, TIGIT, TNFRSF18, PDCD1, IFNG, ACP5, LAYN, CXCR6, GNLY, PHLDA1, DUSP4, CD3D, CD3E, CD8A, CD8B |
| CD4/CD8_c4_Tstr | HSPA6, HSPA1A, HSPA1B, DNAJB1, HSPH1, HSP90AA1, HSPE1, HSPB1, BAG3, HSPD1, DNAJA1, HSP90AB1, JUN, NR4A1, HSPA8, FOSB, FOS, DUSP1, DNAJB4, DNAJA4, CD3D, CD3E, , |
| CD8_c5_Tisg | ISG15, IFI6, MX1, IFI44L, IFIT3, IFIT1, RSAD2, OAS1, IFI27, IFI44, XAF1, MX2, STAT1, OAS3, EPSTI1, SAMD9L, HERC5, EIF2AK2, IFIT2, LY6E, CD3D, CD3E, CD8A, CD8B |
| CD8_Teff | GZMK, GPR183, FGFBP2, GNLY, GZMH, CX3CR1, FCGR3A, PLEK, KLRD1, HOPX, KLRG1, NKG7, ZEB2, TBX21, PRF1, CD300A, CD244, EOMES, GZMM, SEMA4A, CD3D, CD3E, CD8A, CD8B |
| CD8_Tn | LEF1, SELL, TCF7, CCR7, FHIT, KLF2, CD3D, CD3E, CD8A, CD8B |
| CD4_c1_Treg | FOXP3, IL2RA, TNFRSF4, TIGIT, TNFRSF18, BATF, CTLA4, RTKN2, TNFRSF9, IKZF2, TNFRSF1B, LAYN, CD27, GBP5, IL2RB, IL1R2, DUSP4, GBP2, ICOS, ENTPD1, CD4, CD3D, CD3E, |
| CD4_c3_Tfh | CXCL13, BCL6, PDCD1, LAG3, CXCR5, TOX2, GNG4, TIGIT, NR3C1, SH2D1A, SMCO4, CHI3L2, TOX, TNFRSF4, BTLA, TNFRSF18, NMB, CD200, CD4, CD3D, CD3E |
| CD4_c0_Tcm | ANXA1, LMNA, KLRB1, IL7R, GPR183, CXCR4, FOS, JUND, KLF2, CD69, CD4, CD3D, CD3E |
| CD4_Tn | CCR7, FHIT, KLF2, LEF1, SELL, TCF7, ACTN1, CD3D, CD3E, CD4 |
CD8 T cell state
| Signature | Genes |
|---|---|
| Naïve | IL7R, CCR7, SELL, FOXO1, KLF2, KLF3, LEF1, TCF7, ACTN1, FOXP1 |
| Activation:Effector function | FAS, FASLG, CD44, CD69, CD38, NKG7, KLRB1, KLRD1, KLRF1, KLRG1, KLRK1, FCGR3A, CX3CR1, CD300A, FGFBP2, ID2, ID3, PRDM1, RUNX3, TBX21, ZEB2, BATF, IRF4, NR4A1, NR4A2, NR4A3, PBX3, ZNF683, HOPX, FOS, FOSB, JUN, JUNB, JUND, STAT1, STAT2, STAT5A, STAT6, STAT4, EOMES |
| Exhaustion | PDCD1, LAYN, HAVCR2, LAG3, CD244, CTLA4, LILRB1, TIGIT, TOX, VSIR, BTLA, ENTPD1, CD160, LAIR1 |
| TCR Signaling | CALM1, CALM2, CALM3, CAST, CD247, CD3D, CD3E, CD3G, CSK, DOK1, DOK2, FYN, LCK, NFATC2, NFATC1, NFATC4, NFATC3, PLEK, PAG1, PTPN11, PTPN2, PTPN22, PTPN4, PTPN6, PTPN7, PTPRC, PTPRCAP, S100A10, S100A11, S100A13, S100A4, S100A6, ZAP70, DUSP1, DUSP2, DUSP4, DUSP5, DUSP10, LAT, PLCG1, PLCG2, PPP3CA, PPP3CC, FOS, FOSB, FOSL1, FOSL2, JUN, JUNB, JUND, NR4A1, NR4A2, NR4A3, BATF, IRF4, SH2D2A |
| Cytotoxicity | GZMA, GZMB, GZMH, GZMK, GZMH, GNLY, PRF1, IFNG, TNF, SERPINB1, SERPINB6, SERPINB9, CTSA, CTSB, CTSC, CTSD, CTSW, CST3, CST7, CSTB, LAMP1, LAMP3, CAPN2 |
| Cytokine/Cytokine receptor | CSF1, IL10RA, IL16, IL17RA, IL18RAP, IL21R, IL2RB, IL2RG, IL32, IL9R, ADAM10, ADAM8, METRNL, CD70 |
| Chemokine/Chemokine receptor | CCR4, CCR5, CCR7, CXCR3, CXCR4, CXCR5, CXCR6, CCL3, CCL4, CCL4L1, CCL4L2, CCL5, CXCL13, CXCL8, XCL1, XCL2 |
| Senescence | KLRK1, IFNA1, IFNAR1, TAB1, SESN2 |
| Anergy | NT5E, IZUMO1R, LAG3, NRP1, DGKA, CBLB, RNF128, ITCH, NFATC2, EGR2, EGR3, NR4A1, TOB1 |
| NFKB Signaling | NFKB1, NFKB2, NFKBIA, NFKBIB, NFKBIZ, CHUK, IKBKB, IKBKG, REL, RELA, RELB |
| Stress response | HIKESHI, P4HB, UBA52, MAPK1, RPA2, RPA3, TNRC6A, TNRC6B, TNRC6C, NUP210, RBX1, UBB, UBC, CREBBP, ETS1, LAMTOR1, EED, LAMTOR2, HSP90AA1, RBBP4, LAMTOR4, LAMTOR5, PSMB10, CDKN1A, ANAPC11, PSMA1, ATG4D, PSMA2, WIPI2, PSMA3, TFDP2, PSMA4, ATM, CYCS, PSMA5, WDR45, ANAPC16, PSMA6, EHMT1, PSMA7, EHMT2, TERF1, PSMC1, ATR, PSMC3, SOD1, PSMC4, PSMC5, PSMC6, PSME1, ATG3, NCF1, PSME2, ATG5, CHMP2A, CHMP2B, GSK3B, RPS19BP1, TPR, MDM4, ELOB, CDC26, ELOC, ST13, RPS6KA1, EEF1A1, RPS6KA3, CHMP4A, DNAJB1, CAMK2G, RPS27A, TXN2, PRDX1, PRDX2, DNAJB6, FKBP4, PRDX3, MAP2K3, MTMR14, ATG12, PRDX5, RHEB, PRDX6, GSTP1, ATG14, RELA, GPX1, VHL, HSPA1A, UBE2D1, TERF2IP, HSPA1B, UBE2D2, TXN, UBE2D3, HSPH1, CYBA, CDK4, HSF1, CDK6, MAPKAPK3, CITED2, MAP1LC3B, PSMD12, HIF1A, HMGA1, PSMD13, MINK1, PSMD14, HSP90AB1, PTGES3, CXCL8, HSBP1, NFKB1, UVRAG, CAT, PSMB1, CDKN2C, PSMB2, CDKN2D, FOS, PSMB3, CCS, JUN, GABARAPL1, GABARAPL2, PSMB6, KDM6B, PSMB8, PSMD2, TNIK, PSMB9, PSMD3, RANBP2, ATOX1, SEM1, PSMD6, GABARAP, PSMD7, PSMF1, CHMP3, STAT3, PSMD8, TINF2, PSMD9, CHMP7, CCAR2, HSPA4, YWHAE, BAG1, HSPA5, HSPA6, BAG3, DYNLL1, HSPA8, RB1CC1, BAG5, ANAPC5, DYNLL2, VCP, DNAJC2, CABIN1, CEBPB |
| MAPK Signaling | MAP2K1, MAP2K2, MAP2K3, MAP3K4, MAP3K5, MAP3K8, MAP4K1, MAP4K5, MAPK1, MAPK3, MAPK11, MAPK13, MAPK14, MAPK1IP1L, MAPKAPK3, MAPK8, MAPK9, MAP2K7, MAPK10, MAP3K7 |
| Adhesion | ITGA1, ITGA4, ITGAE, ITGAL, ITGAM, ITGB1, ITGB2, ITGB7, SELL, SELPLG, S1PR1, VCAM1, ICAM2, ICAM3 |
| IFN Response | IFIT1, IFIT2, IFIT3, IFIT5, STAT1, STAT2, MX1, IRF1, IRF4, IRF7, IRF8, IRF9, ISG15, ISG20, IFITM1, IFITM2, IFITM3, OAS1, OAS2, OAS3, JAK1, JAK2, SOCS1, SOCS3, TRIM14, TRIM21, TRIM22, APOL1, APOL2, APOL6, IFNGR1, GBP1, GBP2, GBP4, GBP5, GBP3, BST2, CMPK2, DDX58, DDX60, DDX60L, IFI30, IFI35, IFI44, IFI44L, IFI6, IFIH1, PARP10, PARP12, PARP14 |
| Oxidative phosphorylation | ATP1B3, ATP2A3, ATP2B1, ATP2B4, ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5E, ATP5EP2, ATP5F1, ATP5F1A, ATP5F1B, ATP5F1C, ATP5F1D, ATP5F1E, ATP5G2, ATP5G3, ATP5H, ATP5I, ATP5IF1, ATP5J, ATP5J2, ATP5L, ATP5MC1, ATP5MC2, ATP5MC3, ATP5MD, ATP5ME, ATP5MF, ATP5MG, ATP5MPL, ATP5O, ATP5PB, ATP5PD, ATP5PF, ATP6AP1, ATP6AP2, ATP6V0B, ATP6V0C, ATP6V0D1, ATP6V0E1, ATP6V0E2, ATP6V1D, ATP6V1F, ATP6V1G1, ATP8B2, ATP8B4, COX16, COX17, COX4I1, COX5A, COX5B, COX6A1, COX6B1, COX6C, COX7A2, COX7B, COX7C, COX8A, CYC1, MT.ATP6, MT.ATP8, MT.CO1, MT.CO2, MT.CO3, MT.CYB, MT.ND1, MT.ND2, MT.ND3, MT.ND4, MT.ND4L, MT.ND5, MT.ND6, NDUFA1, NDUFA10, NDUFA11, NDUFA12, NDUFA13, NDUFA2, NDUFA3, NDUFA4, NDUFA5, NDUFA6, NDUFAB1, NDUFAF3, NDUFAF4, NDUFAF8, NDUFB10, NDUFB11, NDUFB2, NDUFB3, NDUFB4, NDUFB6, NDUFB7, NDUFB8, NDUFB9, NDUFC1, NDUFC2, NDUFS2, NDUFS3, NDUFS5, NDUFS6, NDUFS7, NDUFS8, NDUFV1, NDUFV2, SDHA, SDHB, TCIRG1, UQCRB, UQCRC1, UQCRC2, UQCRFS1, UQCRH, UQCRQ, SURF1, SURF4 |
| Glycolysis | SLC2A3, SLC2A8, PFKFB3, ALDOA, ENO1, GAPDH, GPI, PGAM1, PGK1, PKM, TPI1, GYG1, MDH1, MDH2, LDHA, LDHB, ADH5, IDH2 |
| Fatty acid metabolism | ACAA1, ACADM, ACADVL, ACSL5, ALDH16A1, ALDH9A1, ECH1, ECHS1, HADHA, HSD17B10, SLC27A2, DECR1, PEX16, SCP2 |
| Pro-apoptosis | BCL2L11, BID, BIN1, BIN2, BAX, BAK1, CASP8, CASP3 |
| Anti-apoptosis | BCL11B, BCL2L1, BAG3, BAG4, BIRC3, GADD45B |
CD4 T cell state
| Signature | Genes |
|---|---|
| Naïve | IL7R, CCR7, SELL, FOXP1, KLF2, KLF3, LEF1, TCF7, ACTN1, BTG1, BTG2, TOB1 |
| Activation/Effector function | FAS, CD44, CD69, CD38, NKG7, KLRB1, KLRD1, KLRG1, CX3CR1, CD300A, FGFBP2, ID2, ID3, PRDM1, RUNX3, TBX21, ZEB2, BATF, NR4A1, NR4A2, HOPX, FOS, FOSB, FOSL2, JUN, JUNB, JUND, STAT1, STAT3, EOMES, AHR |
| Exhaustion | PDCD1, LAYN, HAVCR2, LAG3, CTLA4, TIGIT, TOX, VSIR, BTLA, ENTPD1 |
| TCR signaling | CALM1, CALM2, CALM3, CD4, CAST, CD247, CD3D, CD3E, CD3G, CSK, DOK2, FYN, LCK, NFATC1, NFATC2, PLEK, PTPN11, PTPN13, PTPN2, PTPN22, PTPN4, PTPN6, PTPN7, PTPRC, PTPRCAP, S100A10, S100A11, S100A4, S100A6, ZAP70, DUSP1, DUSP2, DUSP4, DUSP16, LAT, FOS, FOSB, FOSL2, JUN, JUNB, JUND, NR4A1, NR4A2, BATF, IRF1, SH2D1A, SH2D2A, MAP2K3, MAP3K4, MAP3K8, MAP4K1, NFKB2, NFKBIA, NFKBIZ, REL, RELB |
| Cytotoxicity | GZMA, GZMB, GZMH, GZMK, GZMM, GNLY, PRF1, IFNG, TNF, SERPINB9, CTSA, CTSB, CTSC, CTSD, CTSH, CTSW, CST7, CAPN2, PLEK |
| Cytokine/Cytokine receptor | CSF1, CSF2, ADAM19, ADAM8, ADAM12, CD70, IL12RB2, IL17A, IL17F, IL10RA, IL1R1, IL1R2, IL21R, IL21, IL26, IL2RA, IL2RB, IL2RG, IL32, IL6R, TGFB1, TGFBR2, TGFBR3 |
| Chemokine/Chemokine receptor | CCR4, CCR5, CCR6, CCR7, CCR8, CXCR3, CXCR4, CXCR5, CXCR6, CCL3, CCL4, CCL5, CCL20, CXCL13, CXCL8, XCL1 |
| Stress response | CDK4, CDK6, CDKN2A, CDKN2B, CDKN2C, CDKN2D, FOS, JUN, MAPK1, MAPK3, RPS27A, UBA52, UBB, UBC, MIR4738, BMI1, CCNA2, CDC27, CDK2, CDKN1A, CDKN1B, CEBPB, MAPK14, E2F1, E2F2, E2F3, PHC1, PHC2, EZH2, IFNB1, IGFBP7, IL1A, IL6, CXCL8, MDM2, MDM4, MAP3K5, MOV10, NFKB1, MAPK7, MAPK8, MAPK11, MAPK9, MAPK10, MAP2K3, MAP2K6, MAP2K7, RBBP4, RBBP7, RELA, RING1, RNF2, RPS6KA1, RPS6KA2, RPS6KA3, MAP2K4, STAT3, TFDP1, TFDP2, TP53, TXN, UBE2D1, UBE2E1, MAPKAPK3, CBX4, MAPKAPK5, CDC23, EED, CDC16, CCNA1, MAPKAPK2, MAP4K4, ANAPC10, EHMT2, UBE2C, SCMH1, TNIK, TNRC6B, KDM6B, CBX6, SUZ12, ANAPC15, AGO1, TNRC6A, ANAPC2, ANAPC4, MINK1, FZR1, ANAPC5, ANAPC7, ANAPC11, CBX8, TNRC6C, ANAPC1, EHMT1, PHC3, CBX2, ANAPC16, AGO3, AGO4, CDC26, MIR3605, MIR6755, ATM, CCNE1, ERF, ETS1, ETS2, HMGA1, ID1, LMNB1, MRE11, NBN, RB1, SP1, TERF1, TERF2, HIRA, HMGA2, CCNE2, RAD50, KAT5, CABIN1, ASF1A, POT1, TINF2, UBN1, TERF2IP, EP400, ACD, NUDT2, AQP8, ARNT, ATOX1, ATP7A, ATR, BAG1, CA9, CAMK2A, CAMK2B, CAMK2D, CAMK2G, CAT, CREBBP, CYBA, CYBB, EEF1A1, EP300, EPAS1, EPO, FKBP4, MTOR, GPX1, GPX2, GPX3, GPX5, GPX7, GSK3B, GSR, GSTP1, HIF1A, HSBP1, HSF1, HSPA1A, HSPA1B, HSPA1L, HSPA2, HSPA4, HSPA5, HSPA6, HSPA7, HSPA8, HSPA9, HSP90AA1, HSP90AB1, DNAJB1, NCF2, NCF4, NUP88, NUP98, P4HB, PRDX1, PIK3C3, PRKAA1, PRKAA2, PRKAB1, PRKAB2, PRKAG1, PSMA1, PSMA2, PSMA3, PSMA4, PSMA5, PSMA6, PSMA7, PSMB1, PSMB2, PSMB3, PSMB4, PSMB5, PSMB6, PSMB7, PSMB8, PSMB9, PSMB10, PSMC1, PSMC2, PSMC3, PSMC4, PSMC5, PSMC6, PSMD1, PSMD2, PSMD3, PSMD4, PSMD5, PSMD7, PSMD8, PSMD9, PSMD10, PSMD11, PSMD12, PSMD13, PSME1, PSME2, RANBP2, RHEB, RPA1, RPA2, RPA3, SOD1, SOD2, SOD3, ST13, HSPA13, ELOC, ELOB, PRDX2, TPR, TSC1, TSC2, DNAJC7, TXNRD1, UBE2D2, UBE2D3, UVRAG, VCP, VEGFA, VHL, YWHAE, SEM1, NUP214, AAAS, ULK1, CUL2, RAE1, LAMTOR3, DYNLL1, BECN1, MTMR3, LIMD1, ATG12, ATG5, PSMF1, BAG5, BAG4, BAG3, BAG2, PRDX6, NUP155, NUP93, ATG13, NUP58, RB1CC1, PSMD6, POM121, NUP153, CCS, RBX1, HDAC6, DNAJB6, PSME3, PSMD14, RRAGB, CITED2, ATG7, LAMTOR5, TXNRD2, RRAGA, PTGES3, NUP50, HSPH1, PRDX3, WDR45, GABARAP, GABARAPL2, HSPA4L, ATG14, NUP205, ATG4B, PSME4, NUP210, NUP160, SIRT1, NUP188, NUP62, GABARAPL1, GABARAPL3, PRDX5, TXN2, CHMP2B, HIGD1A, WIPI2, DNAJC2, CHMP2A, LAMTOR2, CHMP4A, ERO1A, PIK3R4, NOX4, HSPA14, PRKAG2, HIKESHI, CHMP3, NUP54, PRKAG3, CYCS, EGLN1, LAMTOR1, ATG16L1, WIPI1, AMBRA1, HIF1AN, NDC1, NUP133, WDR45B, NUP107, RPTOR, CCAR2, RRAGD, ATG101, RRAGC, MLST8, HIF3A, MTMR14, ATG3, NUP37, ATG9A, NOX5, CHMP6, NUP85, MAP1LC3B, SEH1L, ATG10, AKT1S1, MAP1LC3A, ATG4C, AJUBA, ATG4D, RPS19BP1, CHMP7, CHMP4C, EGLN2, EGLN3, ATG4A, HSPA12B, PSMB11, WTIP, CHMP4B, NUP35, DYNLL2, PSMA8, GPX6, HSPA12A, ATG9B, NUP43, LAMTOR4, MAP1LC3C, GPX8, NCF1, POM121C, SOD2-OT1, MIR1281, MIR7703 |
| Adhesion | ITGA6, ITGA4, ITGAE, ITGAL, ITGAM, ITGB1, ITGB2, ITGB7, SELL, SELPLG, S1PR1, ICAM2 |
| IFN response | STAT1, STAT3, MX1, IRF1, ISG15, ISG20, IFITM1, IFITM2, IFITM3, OAS1, OAS2, OASL, SOCS1, SOCS3, TRIM22, APOL6, IFNAR2, IFNGR1, GBP1, GBP2, GBP4, GBP5, BST2, IFI16, IFI35, IFI44L, IFI6, PARP8, PARP9 |
| Treg signature | FOXP3, IKZF2, IKZF4, IL2RA, ENTPD1, CCR4, ICOS, IL10RA, TGFB1, TIGIT, CTLA4, LAG3, HAVCR2, PDCD1 |
| Costimulatory molecules | TNFRSF25, TNFRSF1B, TNFRSF4, TNFRSF9, TNFRSF18, CD27, CD28, CD44, CD48, ICOS, CD2, SLAMF1, CD40LG, CD84 |
| OXPHOS | ATP1B1, ATP1B3, ATP2B1, ATP2B4, ATP5A1, ATP5B, ATP5C1, ATP5D, ATP5E, ATP5F1, ATP5F1A, ATP5F1B, ATP5F1C, ATP5F1D, ATP5F1E, ATP5G1, ATP5G2, ATP5G3, ATP5H, ATP5I, ATP5IF1, ATP5J, ATP5J2, ATP5MG, ATP5MC2, ATP5MC3, ATP5MD, ATP5MF, ATP5MG, ATP5MPL, ATP5O, ATP5PB, ATP5PD, ATP5PF, ATP6V0B, ATP6V0C, ATPIF1, COX16, COX17, COX5A, COX6A1, COX6C, COX8A, MT-ATP6, MT-ATP8, MT-CO1, MT-CO3, MT-CYB, MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND4L, MT.CO1, MT.CO2, MT.CO3, MT.CYB, MT.ND1, MT.ND2, MT.ND3, MT.ND4, MT.ND5, NDUFA13, NDUFA6, NDUFB2, NDUFC1, NDUFV2, UQCR10, UQCR11, UQCR11.1, UQCRB, UQCRC2, UQCRHL, SURF4, CYCS, ISCU, MTCH1 |
| Glycolysis | SLC2A3, SLC16A1, PFKFB3, ALDOA, TPI1, GAPDH, PGK1, PGAM1, ENO1, PKM, LDHA, LDHB, GYG1, GPI, UGP2, UBB, UBC |
| Lipid metabolism | ABHD3, ACADVL, ACOT9, AHR, ALOX5AP, AP2M1, AP2S1, APOBEC3C, APOBEC3G, APOBEC3H, APOL6, ARF1, ARF5, ARNTL, B3GALT2, B4GALT1, CAV1, CDIPT, CERK, CLTA, CPNE7, ELOVL1, ELOVL5, DBI, EPHX2, FABP5, FURIN, GDE1, GK, GPX1, GPX4, HDLBP, IDH2, IDI1, HPGD, INPP4B, INPP5D, INPP5F, INSIG1, KDSR, LDLRAP1, LPCAT1, MFSD2A, NCOA3, NDUFAB1, NEU1, NPC2, NUDT7, P4HB, PLA2G16, PLIN2, PPP1CA, PPP1CB, PPP1CC, PTGES3, SAR1B, SARDH, SC5D, SGMS1, SH3KBP1, SREBF2, STARD7, TNFAIP8 |
| Pro-apoptosis | BAX, BAG3, CASP1, CASP4, CYCS, BCL2L11 |
| Anti-apoptosis | BIN1, BIN2, BIRC3, BCL2, BCL2L1, MCL1 |
Ref1
Chu, Y., Dai, E., Li, Y. et al. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance. Nat Med 29, 1550–1562 (2023). https://doi.org/10.1038/s41591-023-02371-y ↩︎