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Table 3 Putative predictive markers of the patient’s response to bevacizumab/erlotinib

From: 24h-gene variation effect of combined bevacizumab/erlotinib in advanced non-squamous non-small cell lung cancer using exon array blood profiling

Time

Endpointa

Gene symbols

KEGG pathway enrichment

Baseline

TS12

ANO2, VPS13D, EML1, C22orf31, FERMT1, SFRP4, SUPT6H, GYS2, THBS4, ATP6V1B1, TCF21, ESRRB, NEUROD4, SOX15, GATA5, PRRC2B, SLC7A10, LOXL4, DISP2, TRIM7, DRD2, GPHA2, KCTD15, PAQR4, ANKZF1, SHROOM1, FABP7, FBXL21, KCNK5, MBL2, LY6D, VASN, FSTL5, MECP2, ROR2, TPT1-AS1, DCDC1, HS6ST2, HSPB7, NWD2, OR5M3, SLC35E3, UNC119B, OR10AB1P, UMODL1, ERN1, RNF151, CALHM1, TMPRSS12, KLK12, KRT14, LINC01551, NWD1, C15orf52, IL1RAPL2, TRRAP, TPK1, MYO18A, DSCR8, B3GNT6, RNA5SP430, C1orf132, PPAPDC1A, BTBD17, LAYN, CST9LP1, ST8SIA6-AS1, AL592528.1, RP11-337C18.4, GAPDHP44, HAUS7, AC010904.1, CELA3B, RP1-288M22.1, U3, CTA-929C8.7, ARSEP1, UBE2D3P4, RP11-38C18.2, RP11-94M14.2, AC007312.3, LINC00237, RP11-66N5.2, LINC01375, C1DP4, RP11-20P5.2, RP5-888M10.2, AC105443.2, FGFR1OP2P1, RP5-855F14.2, TFAMP1, POLR3KP1, CRYGFP, TBC1D3P7, RP11-336N8.1, DCUN1D2-AS, RP11-528G1.2, ZBTB22, TSPY15P, RP11-98G13.1, AC007679.4, KCNQ1DN, RN7SL549P, SMKR1, PNMA2, PI4KA, RP11-520P18.1, RP11-572M11.3, OR10J7P, RP11-331K21.1, RP11-340A13.1, LINC00977, RP3-368B9.2, SNORA18, HNRNPCP8, MPV17L2, NAV2-AS5, CTD-2517M22.14, ENPP7P5, RP11-150C16.1, HNRNPA3P10, RP11-316E14.2, RP11-566K19.5, RP11-521O16.1, RP11-616M22.7, RP11-523L20.2, AC009120.4, RP11-106M3.3, RP11-553K8.5, RP11-189E14.4, RP11-520P18.5, SAMD11P1, RP11-286N3.2, SNRPCP4, RP11-343K8.3, AC005307.3, AC010524.4, CTB-31C7.3, WI2-80269A6.1, RP11-401N16.1, RP11-416H1.1, RP11-1072C15.7

Phagosome (hsa04145, \(p=0.052\)) Protein digestion and absorption (hsa04974, \(p=0.058\))

 

DS12

 

OS

CASC1, HIST1H1A, FAM86C2P, Y_RNA, IGHV5-51, RP11-174G6.1, HNRNPA1P63, EEF1B2P1, RP3-403L10.3, RPL7P53, IGKV1-5, MRPS36P2, RP11-415I12.3, RNU6-412P, RNU6-1224P, RP11-61G23.2, CTD-2547H18.1, RP11-295G12.1, ZNF23

 

TTPBE

BDKRB1, NRN1, LAMC1, ZNF462, LRRC43, SGSM1, FSCN2, C9orf92, RNU6-83P, RPL7AP14, RP11-793K1.1, RP3-433F14.1, RP1-292B18.4, AC098592.7, AC114812.8, TOMM20P1, LL22NC03-88E1.17, C12orf77, RP1-213J1P__B.1, LINC01038, MARK2P12, XRCC6P3, SHC1P1, RP3-463P15.1, LL0XNC01-116E7.2, COL4A2-AS1, CYCSP44, RAC1P8, SLMO2-ATP5E, AF127577.12, STARD13-AS, RN7SL797P, RN7SL598P, RP11-544A12.8, RP11-415I12.3, RP11-61G23.2, RP11-6B19.3, RP11-136F16.2, CASC18, AC002306.1, RP11-552E10.1, RP11-361M10.3, RP11-203B7.2, RP11-475B2.1, RP11-763E3.1, RP13-516M14.2, RP11-820I16.1

 

TTPCT

KRTAP2-3, AC090957.2, KALP, RP11-157I4.4, TSIX

24h after initiation of BE

TS12

PDZD4, SH3BP1, CALD1, SPX, MAPKBP1, MMRN1, EGF, PLOD2, ANKRD61, FZD5, CLEC1B, SLC39A13, SMCO4, BCRP2, TSNARE1, TDRP, TOP1MT, TPTE2P3, RNU105C, Y_RNA, RN7SKP257, AC006988.1, ATP5HP3, RNU6-887P, RP11-361F15.2, BANF1P2, AC099344.2, LINC00884, DDX39BP2, RP11-486M23.1, RP11-167N24.3, RP11-693J15.3, RP11-433P17.3

Pathways in cancer (hsa05200, \(p=0.031\))

 

DS12

 

OS

MYO1C, Y_RNA, DEFB134, Y_RNA, IGLV3-21, IGLC7, IGHA2, IGHA1, IGHV3-15, IGHV3-23, IGHV5-51, SOD1P1, AC016768.1, LINC01032, ZSCAN31, RP11-169N13.4, IGKV1-5, IGHV3-65, IGLC4, RP11-280K24.1

 

TTPBE

TNMD, TSPAN9, PRICKLE3, RAD51, MCM10, TCF3, ATP2A3, OPHN1, FBXL19, PCK2, PLTP, E2F1, PCYT1B, CKM, APBA1, CNTNAP1, FOXM1, KIF20A, CIT, HJURP, E2F8, KLF16, APOC1, ATP8B3, EPHB2, CTIF, TICRR, CTU1, CPXCR1, GRIK4, C16orf78, CKB, VKORC1, TK1, METTL7B, MZB1, ZNF296, RRM2, JUP, PCP2, CADM2, SLC25A22, KLHL28, GJC1, MARCH11, GAS2L1, MITF, HIST1H2BM, SLC25A29, SRC, MYO1C, RNU12-2P, Y_RNA, D86998.1, IGLV6-57, IGLV3-21, IGHG1, IGHJ1, IGHV6-1, IGHV4-28, AP005482.3, RP3-407E4.4, RP11-535M15.1, IPPKP1, FAM195B, RP11-69C17.2, HDGFP1, SCAMP4, RD3L, TUBB4AP1, SDAD1P2, RP11-321L2.1, SPATA31B1P, AC005772.2, RP11-22C8.1, VN1R38P, ITGA9-AS1, NIFK-AS1, B3GNT9, RP11-252M21.6, RN7SL60P, RP11-266N13.2, RP11-517I3.1, RP11-364C11.2, RACGAP1P, RP11-545N8.3, RP11-81A1.3, RP11-2C24.5, AF213884.2, PRKCA-AS1, CTD-2319I12.2

Melanoma (hsa05218, \(p=0.029\)) Pancreatic cancer (hsa05212, \(p=0.029\)) PPAR signaling cancer (hsa03320, \(p=0.029\)) arginine and proline metabolism (hsa00330, \(p=0.029\)) Pathways in cancer (hsa05200, \(p=0.029\)) Pyrimidine metabolism (hsa00240, \(p=0.041\))

 

TTPCT

TTTY14, MTND1P4, RP11-875H7.2, LINC01021, AC008565.1, LINC01486

  1. Gene significantly predictive of the patient’s response (\(p<0.001\)) are reported together with the associated enriched KEGG pathways. Genes that belonged to the KEGG pathway “Pathways in cancer” are highlighted in italic
  2. aTS12: tumor shrinkage at 12 weeks; DS12: disease stabilization at 12 weeks; OS: overall survival; TTPBE: time-to-progression under bevacizumab/erlotinib; TTPCT: time-to-progression under chemotherapy