Table 3 Gene lists for gene set signatures

IFN-y (reduced set)

CXCL10, CXCL9, HLA-DRA, IDO1, IFNG, STAT1

IFN-y (expanded set)

CCL5, CD2, CD3D, CD3E, CIITA, CXCL10, CXCL13, CXCR6, GZMB, GZMK, HLA-DRA, HLA-E, IDO1, IL2RG, LAG3, NKG7, STAT1, TAGAP

ImmunoPhenoScore (IPS)

ACAP1, ADRM1, AHSA1, AIM2, APOL3, ARHGAP10, ATM, ATP10D, B2 M, BIRC3, BRIP1, C1GALT1C1, C3AR1, CASP3, CASQ1, CCL20, CCL3L1, CCL4, CCL5, CCNB1, CCR2, CCR5, CCR7, CCT6B, CD14, CD160, CD2, CD27, CD274, CD300E, CD37, CD3D, CD3E, CD3G, CD55, CD69, CD72, CD86, CD8A, CETN3, CFLAR, CLEC5A, CMKLR1, CSE1L, CTLA4, CXCR4, DAPP1, DARS, DOCK9, DUSP2, ESCO2, ETS1, EXO1, EXOC6, EXOSC9, EZH2, FCGR2A, FCGR2B, FCGR3A, FCRL6, FERMT3, FLT3LG, FOXP3, GDE1, GEMIN6, GNLY, GPSM3, GPT2, GZMA, GZMH, GZMK, GZMM, HAPLN3, HAVCR2, HLA-A, HLA-B, HLA-C, HLA-DMB, HLA-DPA1, HLA-DPA1, HLA-DPB1, HLA-DPB1, HLA-E, HLA-F, IARS, ICOS, IDO1, IFI16, IL18BP, IL2RB, IL34, IL4R, ITGA4, ITGAL, ITGAM, KIF11, KNTC1, L1CAM, LAG3, LCK, LIME1, LIPA, LRP1, LRRC42, LTK, MARCO, MMP12, MNDA, MPZL1, MRC1, MS4A6A, NCOA4, NEFL, NFKBIA, NKG7, NUF2, PARVG, PDCD1, PDCD1LG2, PDGFRL, PELO, PIK3IP1, PLEK, PRC1, PRSS23, PSAP, PSAT1, PTGER2, PTGES2, PTGIR, PTGS1, PTRH2, REPS1, RGS1, RTKN2, S100A8, S100A9, SAMSN1, SCG2, SDPR, SELL, SETD7, SIGLEC14, SIGLEC6, SIK1, ST8SIA4, STAB 1, TAL1, TAP1, TAP2, TFEC, TIGIT, TIMM13, TIPIN, TPK1, TRAT1, TRIB2, UQCRB, USP9Y, WIPF1, ZAP70, ZCRB1

ICB resistance signature 1

ADAMTS7, AXL, COL12A1, COL8A1, FAP, FBLN1, INHBA, LOXL2, MMP1, MMP13, ROR2, TAGLN, TWIST2, WNT5A

ICB resistance signature 2

CNN1, COL3A1, MXRA7, SERPINF2

ICB resistance signature 3

CST2, LAMA3

AXL pathway

AXL, FLT1, FLT4, GAS6, KDR, MERTK, MET, RET, TEK, TYRO3