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Supplementary Table 1. the Clinical Characteristics of SCC Patients Analyzed by RNA 2 Sequencing

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Supplementary Table 1. the Clinical Characteristics of SCC Patients Analyzed by RNA 2 Sequencing 1 Supplementary Table 1. The clinical characteristics of SCC patients analyzed by RNA 2 sequencing. 3 Value or number of patients (n = 23) Factor Non-smoker or Heavy smoker** light smoker* (n = 8) (n = 15) Median age (years) Median 70 72 Range 63-86 55-77 Sex Female 3 0 Male 5 15 Pathological T status T1 2 4 T2 3 10 T3 2 1 T4 1 0 Pathological N status N0 5 13 N1 1 2 N2 2 0 Pathological stage I 3 10 II, III 5 5 4 5 * ≤ 30 pack years 6 ** > 30 pack years 7 SCC, squamous cell lung cancer 8 9 1 9 Supplementary Table 2. The list of 234 candidate oncogenes of non-/light smoker squamous 10 cell lung cancer patients. 11 2 FAM136A CHAF1A UBE2K NUDT19 CDCA4 SUSD4 PLD1 CDC45 DSCC1 NDUFB4 SLC38A7 RFC4 TIMELESS CCNB2 MCM2 VANGL2 XPO5 DPP3 FAM192A MRPL30 CLCN2 FBXO45 EPHB3 CLN6 MESDC2 TRMU CDCA3 WDYHV1 MARVELD3 ISY1 DNAH14 EZH2 WDHD1 ALG3 NUP43 CHEK2 NUDT1 PAFAH1B3 TIAL1 SF3B3 KCNMB3 UMPS NUP205 BIRC5 SRRD GGCT MAGEF1 PRC1 NIPSNAP1 RFC2 FAM162A WDR62 CEP250 AK2 GOT2 BCL11A APOBEC3C CKAP4 OLA1 MCM5 EME1 PIGF MTA3 TPI1 NAA50 ACOT11 RNF7 MCM7 ESRP1 NUP37 TP63 TMEM177 LRPPRC PARD6G PREB FAM83H DNAJB11 LIG1 PCYT1A TTC39C VRK1 KIF18B SEC61A1 MOCS3 UGGT1 ABCC5 AVL9 FXYD3 TIMM8A ZNRF1 IQGAP3 TK1 C5orf34 AAGAB UCK2 C1orf112 YIPF4 SH3BP1 DTYMK DLEU1 POLQ RECQL4 LSM5 DCAF4 TBRG4 BLM SPAG5 E2F7 SAE1 MFSD9 PSME4 FEN1 PSMD11 NKRF PLEKHA8 RNASEH2A EFNA4 ABCF3 KIAA1522 SHMT2 DLX5 ASPM EIF4EBP1 XRCC3 GPN1 C8orf44 CPSF3 NUP155 FOXM1 MRPS22 TOP2A C17orf53 RAD51 DSN1 TPX2 AP2M1 LRFN1 C19orf48 SEMA4B DNAJA3 MTIF2 COX16 CDC6 POLE2 CKAP2 ATP6V1C2 PPIL2 STAP2 TMEM189 VOPP1 POLR2H POLA2 CCNE1 ANKRD52 POLR1D FKBP3 FANCI FBXO27 CSE1L MELK 3 GAPDH TRIP13 PARP16 SLC12A8 SDHAP1 SLC5A6 LMNB2 DCAF13 NCBP2 MTBP C2orf68 BCL2L12 GSS KDELR2 DEPDC5 CEP72 MAP7 SNRPD1 SIAH2 EIF2B5 YDJC ESPL1 GTSE1 TDP1 CHAF1B PRIM2 UNC119 ASF1B PLEKHG3 SRD5A1 CENPA FARSB ECE2 DCTN5 SKP2 ALG1L PSMD2 CSNK1G1 OIP5 MRPL47 CDCA7 TRAF3 WDR53 POP5 ACAD9 UBE2T TUBG1 CRIPT TMEM41A SNRPA1 STX6 NIT2 PSMD7 GINS1 PLEKHG6 KPTN MRPL42 EIF2S3 TCF3 ZNF74 NIF3L1 METTL2A CNP CIAO1 HPS4 IRF6 CCDC137 EXO1 RANBP1 PAWR NUF2 CENPO YKT6 GTF2E1 11 12 13 4 13 Supplementary Table 3. The list of 968 candidate oncogenes of heavy smoker squamous cell 14 lung cancer patients 15 16 5 GPATCH1 FKBP3 CDCA3 SNRPD3 SMG5 KIAA0907 RNF187 EZH2 RBM34 WDYHV1 DTNB RPS7 CLPB POLA2 CCNB1IP1 FAM136A GAPDH UBA5 FANCI WDHD1 TNRC6B SLC5A6 TMEM138 TRIP13 PAFAH1B3 FAM118A FUNDC1 ATIC LMNB2 MRPS14 SLC38A7 WDR92 NUDT1 TCF19 SPRYD4 XYLT2 XRCC2 DVL3 GEN1 PA2G4 MLF2 C2orf68 C1orf131 POFUT1 TMEM206 CBX1 AFMID CADM4 FXR1 MPP6 TCF20 FBL COX10 CDK2AP1 RAD51C TCTEX1D2 SMARCD1 UMPS PHF13 FBXL20 HAUS5 RNASEH1 TUBB TOMM34 C17orf75 KLRG2 TMEM17 TRIM28 TTC9C NUP205 CLCN2 GMNN MAGEF1 GNGT1 PDIA4 ABCA5 SIAH2 EDC3 PACSIN3 LIMK2 MOGS GTSE1 NUP85 DNAJC19 LTBR ATP11B ATMIN THUMPD3 GRK7 PRC1 TRMU ZNF3 FETUB TTF2 TMEM106C DNAH14 CLK2 ACBD6 KIF14 UBE2E3 CHEK2 MSI2 CDK4 EIF3B PDXP YEATS2 UNC119 PRPS2 LRRC42 CEP250 PPM1G ARHGAP8 RAD9A BCL2L12 MTA3 SGPL1 CENPA HDGF CEP72 MCM7 TARBP1 STAR STAMBP GNB5 RCC2 KCNMB3 CHD6 WDR62 AARS2 MARS CBFA2T2 ACTL6A FRMD6 MRPL12 NFRKB USP21 NUP50 BCL7A FARSA SNAP47 GGCT B4GALT4 ZNF174 EIF2B5 PDIA3 KAT2A ZNF786 ZNF623 DNMT3A ANKRD13B GCAT SOX4 C12orf73 ACTR3B TOP1MT SMG7 ZCRB1 RNF7 PSPH NOP56 6 PATZ1 DDX11 TMEM177 PIGX CDK16 ZNF18 WNT3 SMOX TDP1 EBPL ZNF785 BOP1 CEP78 BLCAP PPME1 STON2 DHRS13 STIP1 ASF1B LRPPRC TNK2 PRPSAP1 TRAPPC2 CSNK2A1 MRPL9 FAM162A HOMEZ FAM117B FARSB INTS8 ANKRD16 CCDC77 BRCA1 RPL39L TMEM60 BCL11A MRM1 NIT1 PYCR2 ANAPC1 SOX2 TOR3A DNAJB11 MCM8 PIK3R2 FOXRED2 SKP2 ZNF138 POMT2 HRG EME1 FZR1 FAM83G ALG1L STOML2 MYPOP PARP1 ZNF572 DNMT1 BRIX1 OTX1 PSMG3 PRCC SNRPG FANCF GEMIN6 SNRPF SIGMAR1 BDH1 ZSWIM1 TP63 RUSC1 NUCKS1 P4HB LIG1 KCTD1 ATP5G1 KIF18B MRPL47 SEC61A1 CAD CCDC142 ZWILCH ALG8 UBXN2A SSR3 SLC25A39 SHOX2 EFTUD2 CEBPG LYSMD1 WDR53 SUPT16H LIN9 ANLN NUP133 CENPF CCT3 CRIPT KRBA1 FAM83H TUBG1 AVL9 KDM1A C5orf34 VRK1 PRPSAP2 RPAP1 TFDP2 HDAC1 NCS1 XPNPEP3 ERAL1 NIT2 SH3BP1 CD3EAP SEMA4F MRPL35 GLRX5 LSM5 ZC3H8 TRIB3 RRM2 KPTN FBXO48 ABCC5 CDK5 TK1 ASCC2 MRPL51 IQGAP3 TPRKB RFC5 CHD1L BRIP1 HRASLS STX6 UBE2O COPS7A NRBP1 C1orf112 CASP2 SNRNP200 ZNF74 MED10 CAPN1 PLEKHG6 DBF4B CBX8 LSM2 POLQ OCIAD2 INPP5F PPP2R3A PSMD11 CCDC58 KIF3C ALDOC BICD2 PSMD3 7 LSM14B DERL1 RECQL4 CIAO1 RSRC1 MKKS DDOST CCT7 EXO1 GYS1 ALDH18A1 TLCD1 NAT9 CENPO HNRNPA3 NOL10 HDAC2 SHROOM2 KLHL12 ABCF3 DDX10 RNF43 RBM8A UBE2K ODF2 NCAPD2 CCT4 PGAM1 CDC45 TOMM40 DLG1 TCF3 NPLOC4 GMPS NMNAT3 PDCD5 CNP IDH2 SUMO2 CENPL WDR12 CCDC137 HTATIP2 GTF3C2 CPSF4 BLM NUF2 SPAG5 TIMELESS EIF4EBP1 SUPT7L MRPS16 CUL7 TIMM8B CSNK1E PSME4 CHAF1A YARS DPP3 C1orf74 GTF2F2 DHX35 PARL VPS72 MRPS23 DCAKD PDAP1 FEN1 CAMK2N2 COX5A RARS2 CS USP5 MDH2 RPA1 NUPL2 ZNF251 LANCL2 EPHB3 NUP155 CCHCR1 MORC2 USP39 BLMH MAPK13 KLHL24 QSOX2 ASPM TFR2 LIPT2 TP53BP1 NDC80 METTL8 PRDX4 HSPE1 RNASEH2A RAB40B FBXO46 RANGAP1 LLGL1 PAK1 ATAD5 CBX3 CSTF1 C19orf48 RNF215 PLD1 NACC1 PSMA1 CDC6 TOP2A ZNF133 VPS37D GPR19 DUT DVL2 RFC4 CPSF3 CDC25B ADM2 PHB2 XPO5 FAM189B TUBGCP4 KIF20B ACP1 CDAN1 C17orf53 GINS4 SNRPE AP2M1 FLAD1 LRFN1 TSPAN33 UCHL3 MTIF2 CCT6A COPZ1 TBL2 STAP2 EXOSC3 FKBP4 ECT2 TSSC1 EXOSC2 PVT1 ABHD10 NKIRAS2 RAD51AP1 LIMK1 TMEM99 RCCD1 SMARCD2 SALL4 IGF2BP2 LSM4 TTPAL MSH6 SEC61G ILF2 8 TRAF7 PSMC3IP ZNF367 PNPT1 TBX1 MAP6D1 FBXO45 UBAP2 STRADA DHCR7 POLR2H TMEM81 NAA20 RPF2 SPATA5L1 DTL UBAP2L C12orf65 RNF216 CCNE1 MRPS7 PDCD11 RNPS1 SPATS2 RRM1 ATXN10 CKS2 PRMT3 TRIM37 PRPF19 PDHA1 CDK6 RABIF CENPN ANAPC7 PARP16 USP35 DSG2 DBF4 PREB PPIL1 TMEM5 PARD3 DAP3 DPY30 NAT10 ETFA AAGAB HMBS UGGT1 ZNF212 HCCS DTYMK CDCA7L SLC25A12 MRPS10 DCUN1D5 C12orf66 GPR89A MYBL2 DCAF13 RAE1 NOL8 ABCB9 C1QBP LDHB GRTP1 IPPK PHF5A LRRC28 METTL1 NIF3L1 ACO2 METTL2A TXN WDR5 GTPBP3 SRPRB SMC2 TBC1D7 TSFM HPS4 TIPIN DNAJC9 EPHA1 LSG1 RANBP1 SAE1 CISD1 SLC1A5 IMPA2 TYRO3 TMX2 NANP FSCN1 NOP2 ZNF687 TIMM17A PRMT1 UCK2 SMYD5 ERGIC2 SOX12 TTK PLOD1 MRPS30 GSK3B NKRF FN3KRP EIF2AK1 TIGD2 SAAL1 MRPL45 DDB1 DHX32 PFN2 YKT6 E2F1 CRNKL1 EIF3H UNG NMT1 LAPTM4B CLNS1A PDCD2L L2HGDH NDUFA9 XRCC3 C2orf49 TBRG4 GSS DSCC1 SHCBP1 NEK2 ANP32B MRPL36 RPL22L1 SLC20A2 PDIA6 MFSD9 MRPL13 DDX31 ANAPC5 RNF26 MARCKSL1 DENND1A MAST2 EIF5A2 ENO1 PEX10 CCT5 VPS25 DCTPP1 KIAA1524 PCNA TACO1 TOPBP1 AHCY EPRS SERPINH1 9 ZDHHC13 MCM3 FOXM1 KPNA2 RUVBL1 FIGNL1 PDCL3 PYGO2 TYMS MAPKAP1 MAP7 MITD1 BET1 TPD52 PLEKHA8 GTF2IRD1 RPGRIP1L GNPAT HRAS CORO2A YDJC MRPL18 MEN1 FRMD8 PABPC1 COPB2 PRKAB2 DSN1 POLE3 FOXRED1 MYO19 IMMT KIF18A IMPDH1 OTUB2 NUDT5 POLDIP2 POLE2 UBE2C SHMT2 ZNF706 PRPF4 PFDN4 YARS2 GPN1 CHAF1B MAGOHB SMARCB1 GLI4 RIPK4 PLEKHG3 RPAP2 C12orf29 CKAP5 PNPLA4 FGF12 DTD1 TFB1M CDCA4 RPLP0 EIF4G1 IGSF11 DLGAP5 METTL5 TAF6 RHBDD3 EIF3M PIGU NCAPH MRPS28 VARS2 POLR3K CSE1L COX7A2L WDR77 RAP2B UBE2S TARBP2 FAM57A TPX2 ECE2 SARS2 SSRP1 NDUFB4 PAICS ZNF496 BAIAP2L1 COIL MCM2 DNAJA3 TRIT1 RBM28 SRD5A3 ANP32A FAM102A PPAT MARVELD3 MRPS33 IPO9 MICALL1 NFS1 TBCE SLC12A8 STEAP1 EMG1 ADCK5 PSMB5 YTHDF1 GARS MTX2 ABHD4 AMZ2 GOSR2 MRPL30 FOXK1 TIMM9 GPI TFG BID NME2 ENTPD6 METAP1 NCBP2 PSMD14 NAE1 TUFT1 RNF121 TMEM147 HARBI1 REPS1 PSMD2 SUB1 METTL13 BUB3 KDELR1 NDUFB3 SKA1 AURKA PSMC4 FBXL18 GANAB APEX1 METTL2B AVEN NUDT21 UAP1L1 NUP62 ARHGEF5 TM9SF4 SH3BP5L MAZ SDCCAG3 NME1 ELMOD2 QPCTL EARS2 HNRNPD ZMYND19 PREP TARS 10 B4GALT2 SEC22A FAM104A CCDC86 MELK TOMM22 PTPRF DNMT3B DENR GTF2E2 LTB4R ZNF606 KDELR2 UBFD1 NDUFB5 DKC1 ZNF343 SAMM50 MMACHC ADSL DARS2 TCFL5 CLDND1 POLR2G CHEK1 NRM RACGAP1 SNRPD1 ISY1 VCP VAPB ALG3 GLG1 DOLPP1 ATP6V1E2 TBL1XR1 PALB2 CDCA5 SNRPD2 MTBP GTPBP8 TSEN15 DIABLO NUP43 CDKN3 TRIM59 TIAL1 TYSND1 SF3B3 MCM5 ELAVL1 SKA2 PRIM2 SLC25A10 RPA3 HYOU1 RAI1 CD276 PCCB DDTL ACAD9 PARP2 AHSG GTPBP10 NAA50 RBL1 ATP5G3 SRD5A1 CYC1 TCP11L1 NAPB RABEPK CKS1B NR2C2AP ATAD2 MSTO1 JAG2 FAM173B RPP30 PWP1 PLEK2 BIRC5 BOLA3 GLE1 NUP37 EIF2A NIPSNAP1 DYRK2 SRRD MTCH2 MPHOSPH9 POLR2D GGH C20orf24 WDR75 AARS EIF2AK2 CSNK1G1 MCM4 OST4 UBE2M OLA1 TTLL12 DHX37 TAF1D ASNS MRPL48 MRPL11 RFC2 PPP1R14B RAD54B RPN1 MRPS24 GOT2 GINS1 MRPS17 TPI1 TRAF3 MIF SRP68 ZP3 AP1S1 UBE2T KLC2 TRUB2 DRG1 ESRP1 PGAM5 THOP1 FANCC SLC25A17 PARD6G SLC37A4 RAN EIF2S3 SS18L1 RCC1 PSMD4 CCDC134 TMEM41A NF2 GLRX3 11 MRPL17 TRAP1 BZW2 PSMD7 MRPL42 FANCG SNRPB CLTCL1 SERBP1 UBE2Z RPN2 MRPL3 INTS7 FBXO22 PCYT1A DUS4L PYCR1 MOCS3 HNRNPL SMYD3 PHB NCBP1 NIPA1 WNT7B MTHFD1 SNRPA1 16 17 12 17 18 19 20 21 Supplementary Table 4. The list of 188 candidate oncogenes which are common to non-/light 22 and heavy smoker SCC patients and the results of log rank test of median overall survival (OS) 23 and recurrence free survival (RFS) based on The Cancer Genome Atlas dataset. 24 25 Prognosis Effect of high- Gene expression on OS RFS prognosis (p-value) (p-value) FAM136A 0.002 0.411 SLC38A7 0.004 0.019 Poor CLCN2 0.006 0.049 Good TRMU 0.008 0.096 DNAH14 0.008 0.636 CHEK2 0.008 0.036 Good KCNMB3 0.011 0.744 GGCT 0.018 0.111 FAM162A 0.024 0.006 Good BCL11A 0.025 0.123 EME1 0.026 0.427 TP63 0.028 0.205 FAM83H 0.033 0.734 VRK1 0.033 0.028 Good ABCC5 0.035 0.090 IQGAP3 0.035 0.583 C1orf112 0.037 0.297 POLQ 0.038 0.043 Good BLM 0.044 0.189 PSME4 0.045 0.756 RNASEH2A 0.050 0.027 13 TOP2A 0.052 0.529 AP2M1 0.056 0.032 MTIF2 0.056 0.894 POLR2H 0.061 0.014 FKBP3 0.063 0.457 GAPDH 0.065 0.417 SLC5A6 0.065 0.859 C2orf68 0.067 0.174 SIAH2 0.072 0.041 GTSE1 0.076 0.907 UNC119 0.077 0.002 CENPA 0.079 0.978 SKP2 0.096 0.045 WDR53 0.103 0.297 TUBG1 0.104 0.354 STX6 0.114 0.537 PLEKHG6 0.115 0.526 TCF3 0.120 0.499 CNP 0.124 0.130 CCDC137 0.124 0.313 NUF2 0.126 0.740 CHAF1A 0.127 0.068 PLD1 0.136 0.681 RFC4 0.138 0.223 XPO5 0.139 0.278 FBXO45 0.145 0.627 CDCA3 0.146 0.705 EZH2 0.149 0.068
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