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1 doi: /nature13898 Supplementary Information Table 1 Kras mutation status of carcinogen-induced mouse lung adenomas Tumour Treatment Strain Grade Genotype Kras status (WES)* Kras status (Sanger) 32T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 32T2 Urethane FVB Adenoma Kras+/- Q61R Q61R 32T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 33T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 33T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 33T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 33T4 Urethane FVB Adenoma Kras+/- Q61L Q61L 33T5 Urethane FVB Adenoma Kras+/- Q61L Q61L 47T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 48T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 48T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 48T5 Urethane FVB Adenoma Kras+/- Q61L Q61L 1793T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 1793T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 1793T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 1800T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 1800T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 1800T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 309T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 309T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 66T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 66T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 66T3 Urethane FVB Adenoma Kras+/- Q61H Q61H 75T1 Urethane FVB Adenoma Kras+/- Q61L Q61L 75T2 Urethane FVB Adenoma Kras+/- Q61L Q61L 75T3 Urethane FVB Adenoma Kras+/- Q61L Q61L 45T3 Urethane FVB Adenoma WT Q61R NA 45T4 Urethane FVB Adenoma WT Q61R No mut 45T5 Urethane FVB Adenoma WT Q61R Q61R 45T6 Urethane FVB Adenoma WT Q61R Q61R 44T2 Urethane FVB Adenoma WT Q61R Q61R 44T3 Urethane FVB Adenoma WT Q61R Q61R 35T1 Urethane FVB Adenoma WT Q61R Q61R 35T2 Urethane FVB Adenoma WT Q61R Q61R 35T3 Urethane FVB Adenoma WT Q61R Q61R 63T1 Urethane FVB Adenoma WT Q61R NA 1T1 Urethane FVB Adenoma WT Q61L Q61L 1T2 Urethane FVB Adenoma WT Q61R NA 1T3 Urethane FVB Adenoma WT Q61R No mut 2T1 Urethane FVB Adenoma WT Q61R Q61R 2T2 Urethane FVB Adenoma WT Q61R Q61R 2T3 Urethane FVB Adenoma WT Q61R Q61R 1790T1 Urethane FVB Adenoma WT Q61R Q61R 1790T3 Urethane FVB Adenoma WT Q61R Q61R 1039T2 MNU FVB Adenoma Kras+/- G12D NA 1039T3 MNU FVB Adenoma Kras+/- G12D G12D 1039T4 MNU FVB Adenoma Kras+/- G12D G12D 1039T5 MNU FVB Adenoma Kras+/- G12D NA 1024T1 MNU FVB Adenoma Kras+/- G12D G12D 1024T2 MNU FVB Adenoma Kras+/- G12D G12D 1024T3 MNU FVB Adenoma Kras+/- G12D G12D 1024T4 MNU FVB Adenoma Kras+/- G12D G12D 1024T5 MNU FVB Adenoma Kras+/- G12D NA 1024T6 MNU FVB Adenoma Kras+/- G12D NA 1024T7 MNU FVB Adenoma Kras+/- G12D G12D 1024T8 MNU FVB Adenoma Kras+/- G12D G12D 1024T9 MNU FVB Adenoma Kras+/- G12D G12D 1024T10 MNU FVB Adenoma Kras+/- G12D G12D 1024T11 MNU FVB Adenoma Kras+/- G12D G12D 1045T1 MNU FVB Adenoma Kras+/- G12D No mut 1045T2 MNU FVB Adenoma Kras+/- G12D G12D 1045T3 MNU FVB Adenoma Kras+/- G12D NA 1045T4 MNU FVB Adenoma Kras+/- G12D G12D 1045T5 MNU FVB Adenoma Kras+/- G12D G12D 1045T7 MNU FVB Adenoma Kras+/- G12D G12D 1012T3 MNU FVB Adenoma WT No mut NA 1026T1 MNU FVB Adenoma WT G12D G12D 1026T2 MNU FVB Adenoma WT G12D NA 1011T1 MNU FVB Adenoma WT G12D NA 1029T1 MNU FVB Adenoma WT G12D NA NA = data not available due to assay failure * Kras status (WES): Kras mutation determined by whole-exome sequencing 1
2 Supplementary Information Table 2 Mouse lung adenoma cancer driver gene SNVs compared against COSMIC database of human cancers This table is provided as a separate excel 2
3 Supplementary Information Table 3 MTUS1 expression and overall survival in lung cancer patients Study Platform Class Stages Patients (n) Covariates χ2 p-value TCGA_LUAD exp_hiseqv2 Shedden K, et al. (2008) TCGA_LUSC exp_hiseqv2 Raponi M, et al. (2006) Illumina HiSeq 2000 RNA Seq Affymetrix U133A Expression Illumina HiSeq 2000 RNA Seq Affymetrix U133A Expression ADCA I-IV 354 Sex, Age, Pack Years, Stage ADCA I-III 440 Sex, Age, Stage SCC I-IV 308 Sex, Age, Pack Years, Stage SCC I-III 130 Sex, Age, Pack Years, Stage
4 Supplementary Information Table 4 Kras mutation status of urethane-induced mouse lung adenocarcinomas Tumour Treatment Strain Grade* Genotype Kras status (WES) Kras status (Sanger) 006B2 AC1 Urethane A/J Adenocarcinoma WT NA Q61R 006B3 AC Urethane A/J Adenocarcinoma WT G12V G12V 006C8 AC1 Urethane A/J Adenocarcinoma WT NA Q61L 006C8 AC2 Urethane A/J Adenocarcinoma WT Q61R Q61R 004E3 AC1 Urethane A/J Adenocarcinoma WT Q61R Q61R 004E3 AC2 Urethane A/J Adenocarcinoma WT Q61L Q61L 004E4 AC1 Urethane A/J Adenocarcinoma WT Q61R Q61R 004E4 AC2 Urethane A/J Adenocarcinoma WT Q61R Q61R 004E4 AC3 Urethane A/J Adenocarcinoma WT NA Q61R 011A5 AC Urethane A/J Adenocarcinoma WT NA Q61R 010E7 AC1 Urethane A/J NA WT Q61R Q61R 010E7 AC4 Urethane A/J NA WT Q61R Q61R 010E7 AC6 Urethane A/J NA WT NA Q61R 51 AC1 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L 66 AC1 Urethane FVB Adenocarcinoma WT Q61R Q61R 2913 AC1 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L 2913 AC2 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L 2915 AC1 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L 2915 AC2 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L 2916 AC1 Urethane FVB Adenocarcinoma Kras+/- Q61H Q61H 2916 AC2 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L 2916 AC3 Urethane FVB Adenocarcinoma Kras+/- Q61L Q61L * NA = data not available due to insufficient tissue for histology Kras status (WES): Kras mutation determined by whole-exome sequencing. NA = data not available due to poor coverage at Kras in some samples 4
5 Supplementary Information Table 5 Mouse adenocarcinoma SNVs in established cancer driver genes and Fat4 Chr Position Gene Exon Substitution Consequence Observed Tumours Validated Validation Method B2m 2 CAC>G T88A 1 004E3 AC1 Yes Sanger Fbxw7 3 CAC>T T147S 1 006B3 AC Yes Sanger Ezh2 10 AGG>A G356R AC3 Yes Sanger Vhl 1 CAG>C Q62P 1 006B3 AC Yes Sanger Setd2 15 AGT>A S2254N AC1 Yes Sanger Gna11 6 AAC>G N274S 1 010E7 AC1 Yes Sanger Nf2 15 AAA>G K550R 1 004E3 AC2 Yes Sanger Dnmt3a 5 GAA>G N180D 1 66 AC1 Yes Sanger Map3k1 19 CAG>T Q1406L AC1 Yes Sanger Mll2 19 CGC>A A1524T 1 006C8 AC1 Yes Sanger Men1 2 CGC>A A74T AC1 Yes Sanger Fat4 1 CGT>A V307M 1 66 AC1 Yes Sanger Fat4 4 AAC>G T1908A AC2 Yes Sanger Fat4 9 AAT>C L3017V 1 006B3 AC Yes Sanger 5
6 Supplementary Information Table 6 Comparison of mutations involving driver genes in all carcinogeninduced mouse lung tumours and human lung adenocarcinoma Gene LUAD obs LUAD % KRAS LUAD obs KRAS LUAD % Mouse obs Mouse % AKT ALK APC ARID1A ARID1B ASXL ATM ATRX AXIN B2M BRCA BRCA CARD CBL CIC CREBBP DAXX DNMT3A EP EZH FAM123B FBXW FGFR FGFR FGFR FLT GATA GATA GNA HNF1A IDH JAK KDM5C KIT KLF MAP3K MAP3K MED MEN MET MLL MTUS NCOR NF NF NOTCH PAX PDGFRA PPP2R1A PTCH RB RET RNF SETD SF3B TNFAIP VHL Tumours = 230 Tumours = 68 Tumours = 92 Number and % of consequential mutations in TCGA LUAD WES Number and % of consequential mutations in TCGA LUAD KRAS-mutant tumours Number and % of consequential mutations in carcinogen-induced mouse tumours in this study 6
7 Supplementary Information Table 7 Mouse and human SNVs of cancer driver genes occurring in close proximity Gene Mouse mut Mouse obs Human hom aa pos LUAD mut LUAD obs Mouse SNV Consequence AKT1 E40K 1 40 E17K 1 Constitutive activation ALK G133R V132L 1 ARID1A S520F Q479* 1 ARID1B P564L G530C 1 ASXL1 P430S G434V 1 ATM S367F Q355_splice 1 Autophosphorylation site: loss of function ATM E648K Q628* 1 B2M T88A 1 88 E70* 1 CBL S401F C401F, D429_del 2 RING finger domain hotspot CIC I1432F E1405* 1 CREBBP P1353S K1367N 1 DAXX D596N L566F 1 EZH2 G356R E341K 1 FBXW7 T147S E113* 1 GATA2 Y376C S340_splice 1 MEN1 G169R A165D 1 MET K1196Q Y1235H 1 NF2 K550R E527Q 1 NOTCH2 P426S S462* 1 PDGFRA N711I E726Q 1 PDGFRA D877N A916T 1 PPP2R1A P523L A541G 1 RB1 S744F, S766F 2 751, 773 Y756C 1 Table of carcinogen-induced mouse SNVs and human TCGA LUAD SNVs in cancer driver genes occurring within + or - 40 aa of homologous position 7
8 Supplementary Information Table 8 Adenocarcinoma CGN>A (NCG>T) signature validation Chr Position Gene Exon* Substitution Consequence Obs Tumours Validated Validation Method Mll2 19 CGC>A A1524T 1 006C8 AC1 Yes Sanger Men1 2 CGC>A A74T AC1 Yes Sanger Fat4 1 CGT>A V307M 1 66 AC1 Yes Sanger Atg2a 27 CGC>A A1266T 1 006C8 AC1 Yes Sanger Hecw2 21 CGG>A R1227X 1 006C8 AC1 Yes Sanger Ipo9 13 CGA>A E448K AC1 Yes Sanger Lyn 8 CGG>A R244W 1 004E3 AC2 Yes Sanger Mtus1 9 CGG>A A982A AC2 Yes Sanger Plec 13 CGG>A R306Q 1 004E3 AC2 Yes Sanger Prkce 9 CGG>A R372X AC1 Yes Sanger Rnase6 2 CGC>A R54C 1 66 AC1 Yes Sanger Sema5b 22 CGG>A R1080W 1 004E4 AC3 Yes Sanger Sos1 20 CGG>A R1067Q AC2 Yes Sanger Gpr158 6 CGA>A R480C 1 006C8 AC2 Yes Sanger Lama4 1 CGG>A G43S AC1 Yes Both Npas3 12 CGG>A R620X 1 004E4 AC1 Yes Visual inspection Clgn 12 CGG>A R460X 1 006B2 AC1 Inconclusive Both Tmcc3 NA CGC>A NA AC2 Inconclusive Both Sfi1 NA CGT>A NA AC1 Inconclusive Both Foxa1 2 CGC>A G157G 1 51 AC1 Inconclusive Both A430088P11Rik NA CGC>A NA AC1 Inconclusive Both Smc3 5 CGA>A S85L AC1 Inconclusive Both X Srpk3 14 CGG>A R498Q AC3 Inconclusive Both * NA = non-exonic location. Variants were called inconclusive if visual inspection supported somatic origin, but variant read depth was <10. Validation Method: Both = Sanger sequencing and visual inspection. 8
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