GBM meta-programs

SignatureGenes
NeuronSNAP25, SYT1, VSNL1, SLC17A7, RTN1, NRGN, TAGLN3, CCK, CHN1, ENC1, STMN2, DNM1, UCHL1, NEFL, OLFM1, SYN1, SYN2, CHGA, STXBP1, BASP1, GNG3, NAPB, YWHAH, SERPINI1, BEX1, SNCA, LY6H, PHYHIP, ATP1A3, ATP6V1G2, NSF, THY1, ATP1B1, SYP, TSPAN7, TUBB2A, PRKAR1B, TMEM59L, CALM3, NPTXR, TMEM130, MEG3, NELL2, HPCA, IDS, AK5, ENO2, NCDN, SNCB, CRYM
VascVWF, COL4A1, COL4A2, PDGFRB, COL1A2, ENG, FN1, RGS5, COL18A1, COL3A1, BGN, ITM2A, CLDN5, HSPG2, ESAM, MGP, MYL9, NDUFA4L2, DCN, IGFBP4, EGFL7, ITGA1, ANGPT2, GNG11, NOTCH3, COL1A1, CTGF, NID1, TAGLN, ACTA2, IGFBP7, PECAM1, PLVAP, AGRN, A2M, SERPINH1, CD93, ITGB1, MYH9, MCAM, APOLD1, HIGD1B, MIR4435-2HG, SPARC, EPAS1, LAMA4, IFI27, FSTL1, CYTOR, CD248
MES.Hyp (malig.)VEGFA, NDRG1, ADM, IGFBP5, MT1X, SLC2A1, BNIP3, PGK1, ANGPTL4, HILPDA, ERO1A, NRN1, AKAP12, LGALS3, SLC2A3, LDHA, ENO2, GAPDH, FAM162A, CA12, DDIT4, LOX, IGFBP3, S100A10, SERPINE1, IGFBP2, NUPR1, ENO1, CAV1, HSPA1B, MT2A, PLOD2, BNIP3L, CA9, CXCL8, DNAJB1, BHLHE40, PLIN2, CHPF, HMOX1, HSPA1A, ARRDC3, HSPA5, SPP1, UPP1, ZNF395, ARL4C, HK2, GLUL
MacC1QB, C1QA, FCER1G, C1QC, LAPTM5, CD14, CD74, SRGN, AIF1, FCGR3A, TYROBP, HLA-DRB1, CSF1R, HLA-DRA, TREM2, APOC1, C3, HAMP, ITGB2, VSIG4, ALOX5AP, FCGBP, SPP1, CD163, HLA-DPA1, CD68, S100A8, HLA-DRB5, MS4A6A, RGS1, RNASET2, S100A9, HLA-DPB1, CTSS, SLCO2B1, CD53, CTSC, HLA-DMB, CHI3L1, HLA-DQB1, S100A11, SLC2A5, A2M, EFEMP1, GPNMB, HLA-DQA1, LILRB4, STAB1, VAMP8, IBSP
OligoPLP1, MAG, CLDND1, TF, CLDN11, ENPP2, CNP, ERMN, PPP1R14A, TMEM144, MOG, RNASE1, SELENOP, CNTN2, MAL, MBP, PTGDS, MOBP, CARNS1, EVI2A, CNDP1, ANLN, EDIL3, LHPP, PIP4K2A, SEPT4, UGT8, APLP1, HSPA2, MYRF, GSN, QDPR, SLAIN1, KLK6, SCD, ABCA2, PLA2G16, APOD, PLLP, AMER2, ELOVL1, NKX6-2, PLEKHH1, OPALIN, SLC44A1, SPP1, BCAS1, CSRP1, HHIP, LINC00844
MES (malig.)EFEMP1, CHI3L1, CD44, C1R, MGST1, LTF, ANXA1, C1S, CHI3L2, SOD2, AQP1, TNC, ID3, MAOB, CCL2, CP, F3, MAN1C1, NAMPT, S100A10, AL049839.2, ATP1B2, C3, CLU, GAP43, SERPING1, RCAN1, ZFP36, ACTN1, GJA1, IGFBP7, LRIG1, S100A6, NTRK2, SOCS3, WLS, FOS, EMP1, KCNN3, MAPK4, SCARA3, VIM, PDPN, NNMT, TRIM47, EFEMP1, CHI3L1, CD44, C1R, MGST1
Prolif.Metab (malig.)GGCX, LRRC75A, IQCK, TRA2A, CTNNB1, HNRNPH1, SYNC, ATP1B1, C1orf56, GOLIM4, PHKG1, AC018557.1, ARGLU1, ACOT13, GATC, LIG3, CCDC152, NME7, STARD7, EIF2S3, EIF5A, KIF21A, MAP3K12, SLC16A1, SOX9, YWHAG, AC009133.1, CDC42SE1, F3, HEPN1, MMACHC, PPP1CB, SUMF2, TP53, AC011603.2, ARPC4, BEST1, CNTD1, CTBP1, FGD5-AS1, MARCKS, MSH6, PAQR3, PDGFA, RAB6A, RPL23, SPTBN1, ZBTB18, AC092069.1
MES.Ast (malig.)METTL7B, GPC1, CXCL14, LPL, MOXD1, POSTN, RCAN1, TNFRSF12A, FABP5, FABP7, HOPX, MT2A, PDLIM4, PTN, F3, GAP43, KCNF1, KLHDC8A, LGALS3, PDPN, SERPINE1, FJX1, SCG2, SPOCD1, AGT, CHI3L1, CHPF, DNAJB1, ELOVL2, GADD45A, GDF15, IGFBP2, IGFBP3, LMO2, LZTS1, MT3, NAMPT, PLA2G5, RAMP1, S100A16, SLC6A11, SLN, TMEM158, TTYH3, EMP1, JAG1, HMGA1, CCL2, COL9A3, ZYX
Reactive.AstMGST1, S100A13, FXYD1, MT1M, MT1E, S100A1, SLC1A2, ADIRF, AGT, CLU, DTNA, HLA-DRA, LINC00844, PTGDS, AHCYL1, AQP4, CSRP1, FAM107A, GJA1, GSN, HLA-DPB1, HLA-DRB1, IFITM3, METTL7A, MYBPC1, S100A10, AL078639.1, ATP1A2, ATP1B2, CD44, CD74, CPE, GFAP, IFITM2, LGALS3, MBP, MT1F, MT1G, NTRK2, PLPP3, S100A6, SEC62, SLC1A3, SPARC, ECEL1, CHI3L1, AQP1
NPC (malig.)INA, NELL2, NEUROD2, NSG2, SYT4, ZBTB18, CDK5R1, DCX, NSG1, RUNX1T1, STMN2, BASP1, BHLHE22, CAMK2B, CXADR, LY6H, NREP, RAB3A, REEP1, SNAP25, SYT1, TUBB4A, UCHL1, ATP1A3, PCP4, KIF21B, EPHA5, CAMKV, RPRM, CDKN2D, MARCH4, STX1A, TUBB3, MPPED1, SCN3B, TMEM35A, BCL11A, OLFM1, EPHA4, STMN4, CD24, GNAO1, SEPT3, TUBB2A, MLLT11, JPT1, ENC1, STMN1, DPYSL3
InflammatoryMacCCL2, CCL3, CCL4, CCL4L2, DNAJB1, EGR1, IL1B, NR4A1, CD83, FOS, BTG2, CCL3L1, CH25H, CXCL10, CYR61, DUSP1, GBP1, HSPA1A, HSPA1B, HSPA6, HSPH1, IER2, IER5, IRF1, JUN, JUNB, RGS1, ZFP36, AHRR, EGR3, CLPTM1L, TAP1, STAT1, SERPINE1, EXOC3-AS1, GADD45B, SEZ6L, IGFBP3, ATF3, SLPI, ROPN1L, GPX3, AZGP1, WARS, CCDC127, G0S2, PLAUR, VGF, CD14, APLNR
Chromatin.reg (malig.)ATRX, BPTF, ZBTB20, ANKRD12, CCDC88A, EIF5B, HBA2, MAN1A2, NFIX, DST, HBA1, HBB, NEAT1, NFIC, TTC3, ZC3H13, AKAP9, CCNI, GOLGA4, HIST1H4C, KMT2E, MTRNR2L12, MTRNR2L8, PPIG, PRRC2C, ELAVL3, MAP4K4, NFIB, PLCG2, PLEKHA4, RSF1, SPECC1, TCAF1, APC, ARHGAP5, BRD4, EEA1, GOLGB1, KTN1, NCOR1, NFIA, PCDH9, SLPI, SOX4, TCF4, VCAN, ZNF91
OPC (malig.)SIRT2, SOX10, BCAN, BCAS1, GPR17, PLP1, MBP, OLIG1, OLIG2, SCRG1, SOX8, CNP, TUBB4A, DLL3, HES6, MARCKSL1, SLC44A1, VCAN, AC009041.2, CLDN11, DBI, ERBB3, FIBIN, GNB4, S100B, SNX22, TCF12, TSC22D4, TTYH1, MYRF, PLPPR1, PTPRZ1, SMOC1, CADM2, CNTN1, CSPG5, ETV1, FXYD6, HMGB2, MAG, PTN, SCD5, TNR, TNS3, TSPAN7, UGT8, AC008080.4, ANP32B
AC (malig.)BCAN, MYBPC1, S100B, ALDOC, AQP1, TTYH1, ATP1A2, AQP4, TSC22D4, GPR37L1, MLC1, C1orf61, CST3, NDRG2, LINC00844, PLP1, FADS2, HEPACAM, SLC1A2, FAM107A, GFAP, GJA1, HES6, ID3, METTL7A, DDR1, ADCYAP1R1, ADGRG1, AGT, FAM181B, HOPX, MBP, RGMA, CSPG5, ENHO, CKB, CRISPLD1, EDNRB, GATM, ITM2C, PTN, SLC1A3

IDH-mutant meta-programs

SignatureGenes
PLIN2, ADM, ADORA2B, AK4, ALDOC, ANG, ATF3, BNIP3, BNIP3L, CA9, CA12, CAV1, CCNG2, KLF6, DUSP1, EFNA1, ENO2, F3, FOS
macrophageLAPTM5, SPP1, TYROBP, APOC1, C1QB, C1QC, CD68, CD74, FCER1G, S100A11, C1QA, C3, FTL, HLA-DRA, HLA-DRB1, NPC2, TREM2, A2M, CTSB, CYBA, HLA-DPA1, CTSS, GPNMB, HLA-DPB1, LGALS1, APOE, CD14, CD53, CSF1R, CTSD, HLA-B, ITGB2, KCTD12, LGMN, NUPR1, PSAP, SCIN, SRGN, TMSB10, TMSB4X, VIM, ZFP36L2, GFAP, LYZ, GRN, CXCR4, SLCO2B1, RGS1, VSIG4, GPR34
oligoCLDN11, CLDND1, CNP, APOD, ENPP2, ERMN, MAG, MAL, MOG, RNASE1, SELENOP, TF, TMEM144, TUBB4A, ABCA2, APLP1, CARNS1, CNDP1, CNTN2, PLP1, PPP1R14A, ANLN, EDIL3, HSPA2, RAPGEF5, SPOCK3, MOBP, MYRF, PIP4K2A, SLAIN1, STMN4, GPR37, QDPR, TTYH2, UGT8, CHADL, ELOVL1, EVI2A, KLK6, MBP, PMP22, SLC12A2, SORT1, ATP1B1, PLEKHH1, MTURN, NKX6-2, CDKN1C, SLC44A1
vascularAPOLD1, CLDN5, FN1, IFI27, CTGF, ITM2A, EPAS1, GNG11, SLC2A1, IFITM3, MT1E, BGN, COL1A2, DCN, MFSD2A, VWF, A2M, COL4A1, COL4A2, MT2A, RGS5, SLC38A5, ENG, HYAL2, IGFBP7, MYH9, NDUFA4L2, SLC7A5, TIMP1, TMSB10, ABCG2, CAVIN2, COL3A1, HLA-B, PECAM1, SLCO2B1, SRGN, TAGLN2, ESAM, VIM, CD93, COL18A1, SERPINH1, MT1M, IGFBP3, NET1, MCAM, TIMP3, SLC39A10, ITIH5
low.qualityPLCG2, MALAT1, MTRNR2L12, MTRNR2L8, MT-ATP8, MT-ND4L, AL078639.1, MT-ND5, MTRNR2L1, AL355075.4, HBA2, HBB, TAF1D, MAP2, MT-ND1, C5orf63, DST, EIF4A2, MT-CO1, MT-CO3, MT-ND2, MT-ND4, SNHG12, ZBTB20, HBA1, MAP1B, MT-ATP6, MT-ND3, NCL, NEAT1, RPL27A, RPL39, WDR74, AD000090.1, CLOCK, MT-CYB, CSKMT, ANKRD12, CCDC88A, SLC1A2, SOX2, RBM25, BPTF, RPL23A, DYNC1H1, PEG10, NRCAM, SNHG19, COX8A, TNR
ACGJA1, LRIG1, AGT, EDNRB, MLC1, SFRP2, ATP1A2, SLC1A2, SLC1A3, ALDOC, CPE, ETNPPL, TTYH1, ADCYAP1R1, ANOS1, AQP4, BAG3, CDC42EP4, DCLK2, DDAH1, DKK 3.00, GABBR1, GPRC5B, ID4, KCNN3, NMB, NTSR2, NUDT4, SLC4A4, SPARCL1, TIMP3, WLS, AQP1, GABBR2, ADGRB1, EEPD1, EFEMP1, NCAN, EZR, MAOB, TRIL, PLPP3, ITM2C, LIFR, MGST1, BBOX1, IGFBP7, RGMA, ATP1B2, FAM213A
OC.NPC1HES6, OLIG2, DLL3, ETV1, H2AFV, PDGFRA, SMOC1, SOX8, AC009041.2, AC084033.3, AC091138.1, AMOTL2, B4GALNT1, CCND2, CD24, CDK4, CDKN2A, CDKN2C, CKS2, DCTN2, DSEL, DTX3, FERMT1, HMGB2, JPT1, MARCH9, NOVA1, OLIG1, OS9, PGRMC1, PHLDA1, SHD, SOX4, TCF12, TOP2A, TRIM28, TSFM, TSPAN31, MBD6, GRIA2, ELMO1, FAM110B, SALL3, TNR, ASCL1, SQLE, MMP16, SCN3A, SOX10, APCDD1
neuronDNM1, ENC1, NAPB, NEFL, NRGN, SLC17A7, SNCA, STMN2, SYT1, VSNL1, ATP1B1, RAB3A, RTN1, SNAP25, SYN1, SYP, TAGLN3, UCHL1, BASP1, CHN1, MAP1LC3A, NNAT, OLFM1, PLD3, PTPRN, STXBP1, SYN2, SYNGR1, TAC1, TUBA4A, TUBB2A, YWHAG, VGF, SCG2, CCK, NPTX2, GNG3, NPTXR, PHYHIP, PNOC, HPCA, BEX1, NRN1, VAMP2, SNCB, PRKAR1B, TMEM130, SNCG, GABARAPL1, CHGB

Ref1

  1. Greenwald A C, Darnell N G, Hoefflin R, et al. Integrative spatial analysis reveals a multi-layered organization of glioblastoma. Cell, 2024, 187(10): 2485-2501. e26. ↩︎