Figure S1. Comparison of published epithelial cell senescence gene expression profiles with the gene expression changes >2 fold between normal mucosa and mortal and immortal SCCs identified by SAM analysis (FDR<1%) Normal mucosa Senescence changes >3 fold versus immortal SCC 3324* 165 in normal oral mucosa (Data from Fig. 3 (Kang et al. 3** Exp Cell Res, 287: 272-281, 2003.) 33 17*** 263 Normal mucosa versus mortal SCC *4 genes: Down regulated in immortal SCCs but up-regulated in senescent epithelial cells: CEACAM6, DSG3, MMP1 Up-regulated in immortal SCCs but down-regulated in senescent epithelial cells: SMARCA3 **3 genes: Up-regulated both in mortal SCCs and senescent epithelial cells: MMP10 Down-regulated both in mortal SCCs and senescent epithelial cells: BUB1, CDKN3 ***17 genes: Up-regulated both in mortal SCCs and senescent epithelial cells: BMPR2, CDKN2B, COL1A1, COL1A2, COL6A1, CXCL3, CYPB1, FN1, IGFBP3, Down-regulated both in mortal SCCs and senescent epithelial cells: BIRC5, CCNA2, CCNB1, CCNB2, CENPF, NRG1, PCNA, SKP2 Table S1 Clinical characteristics of tumours Biopsy Patient Culture NameSite lesion stage smoking age sex Lifespan (PDs) Normal mucosa FNB3 (N3)BM none N/A n 45 M 25.5 FNB5 (N5)BM none N/A n 40 F 20 FNB6 (N6)BM none N/A n 35 F >24 NB9 (N9)BM normal adjacent N/Ay 53 M >17 Dysplasias D6PT Leukoplakia mod/severe y 55 M 25 D8FOM Leukoplakia mild/mod y 71 M 9 D25FOM Leukoplakia severe y 58 M 28 D30FOM Leukoplakia mild y 52 M 30 D41RM Leukoplakia mild n 55 F 3.5 D47FOM Leukoplakia mod y 82 F 20 D48FOM/VT Leukoplakia mod/severe y 62 F 25.5 D17 (EL)BM Leukoplakia mild/mod y 61 M 61 E1TUU Erythroplakia CIS M 24 E2ALV Erythroplakia CIS U U M 17 E4LT Erythroplakia CIS U 65 F 41 E5LT Erythroplakia severe U 61 M 31 D4 FOM/VTLeukoplakia CIS y 51 M >100 D9VT Leukoplakia mild/mod n 84 M >100 D34LT Leukoplakia mod n 54 F >100 D38LT Leukoplakia mild n 55 F >100 D19LT erythroleukoplakia Severe/CIS y 53 M >100 D20LT Leukoplakia moderate n 50 M >100 D35FOM/VT erythroleukoplakia Severe/CIS y 68 M >100 SCCs BICR 30 (P30)LNX Carcinoma T4N1M0 y U M 17 BICR 66 (P66)RM/T Carcinoma T2N0M0 y 56 M 37 BICR 80 (P80)LNX Carcinoma T4N2CM0 y 71 M 62 BICR 1 (P1)TU68 Carcinoma T2N0M0 M 15 BICR 73 (P73)Ty49 Carcinoma T2N0M0 M 10 BICR 25 (P25)FOM Carcinoma T2N0M0 y 72 M 15 BICR 3 (P3)ALV Carcinoma T2N0M0 y 56 F >130 BICR 31 (P31)TUU Carcinoma T4N2BM0 M >130 BICR 56 (P56)Ty59 Carcinoma T4N1M0 F >130 BICR 68 (P56)BT Carcinoma T4N0M0 n 75 F >130 T4 (P4)FOM Carcinoma T4N0 U U F >130 T5 (P5)BM Carcinoma T2N2 Y 59 F >130 BICR 78 (P78)ALV Carcinoma T4N1M0 U 68 M >130 BICR 63 (P63)T Carcinoma T2N2BM0 y 70 M >130 BICR 6 (P6)HP Carcinoma T4N1M0 U U M >130 BICR10 (R10)BM Recurrence T4N0M0 n 84 F >130 BICR16 (R16)Ty49 Recurrence T2N0M0 M >130 BICR82 (R82)MX Recurrence N.D. y 48 M >130 BICR 7 (CR7)TY43 Carcinoma T4N2BM0 M 43 (crisis) LN Metastases BICR 37 (M37)Primary:T Metastasis T4N2CM0* U U F 32 BICR 22 (M22)Primary:T Metastasis T4N3M0* U 88 M >130 BICR 18 (M18)Primary:LN Metastasis T4N1M0*UU U >130 The tumor names given in brackets are the abbreviations used in the text Key: ALV, alveolus; BM, buccal mucosa; BT, base of tongue; CIS, carcinoma in situ; FOM, floor of mouth; HP, hypopharynx; LN, lymph node; LNX, larynx; LT, lateral tongue; MX, maxilla; N/A, not applicable; N.D., not determined; normal adjacent, apparently normal mucosa from patient with SCC; PT, posterior tongue; RM, retromolar trigone; T, tongue; U, information not available; VT, ventral tongue; *, staging of primary SCC. Table S2. Gene expression changes common to mortal and immortal SCCs Average expression levels (AV) are given from the microarray data with standard deviations (SD). carcinomas normal mortal immortal recurrence Common Genbank Systematic AV SD AV SD AV SD AV SD ASS NM_000050 207076_s_at 138 53 767 424 760 708 794 274 CKB NM_001823 200884_at 99 25 327 104 243 82 347 92 CUGBP2 U69546 202157_s_at 261 34 112 34 76 11 83 5 CYP27B1 NM_000785 205676_at 657 118 306 171 196 86 163 62 FOXQ1 AI676059 227475_at 134 39 280 89 384 199 622 394 ITM2A; E25A; AL021786 202746_at 43 17 16 8 17 19 11 1 MO25 NM_016289 217873_at 1240 191 620 195 696 268 344 114 MTR3 AF131796 231916_at 123 30 54 45 38 15 56 22 PLCD4 BC006355 224505_s_at 187 23 91 32 77 4 82 3 SIX1 N79004 228347_at 58 5 168 73 144 84 147 35 THBS2 NM_003247 203083_at 233 104 92 14 117 69 63 8 Table S3. Genes consistently 5-fold different in expression between mortal and immortal SCCs by SAM (FDR<1%) AF1Q 211071_s_at NM_006818 ALDH1A3 203180_at NM_000693 ANLN 222608_s_at NM_018685 ASNS 205047_s_at NM_133436 ASPM 219918_s_at NM_018123 AURKB 209464_at NM_004217 BF 202357_s_at NM_001710 BIRC5 202095_s_at NM_001168 BPGM 203502_at NM_001724 BUB1B 203755_at NM_001211 C10orf3 218542_at NM_018131 C1orf10 220090_at NM_016190 C3 217767_at NM_000064 CCL20 205476_at NM_004591 CCNA2 203418_at NM_001237 CCNB1 214710_s_at NM_031966 CCNB2 202705_at NM_004701 CD24 209772_s_at NM_013230 CDC2 203214_x_at NM_001786 CDC20 202870_s_at NM_001255 CDC6 203968_s_at NM_001254 CDCA7 224428_s_at NM_031942 CDKN2B 236313_at NM_078487 CDKN3 209714_s_at NM_005192 CDSN 206193_s_at NM_001264 CEACAM1 209498_at NM_001712 CEACAM5 201884_at NM_004363 CEACAM6 203757_s_at NM_002483 CENPF 207828_s_at NM_005196 CKS1B 201897_s_at NM_001826 CKS2 204170_s_at NM_001827 COL1A1 202310_s_at NM_000088 COL1A2 202403_s_at NM_000089 COL6A3 201438_at NM_004369 CSPG2 221731_x_at NM_004385 CXCL1 204470_at NM_001511 CXCL5 214974_x_at NM_002994 CXCL6 206336_at NM_002993 DEFB1 210397_at NM_005218 DHRS9 224009_x_at NM_005771 DLG7 203764_at NM_014750 DSC2 204751_x_at NM_004949 ECG2 223720_at NM_032566 ECM1 209365_s_at NM_004425 EHF 225645_at NM_012153 EPS8L1 221665_s_at NM_133180 FAP 209955_s_at NM_004460 FEN1 204768_s_at NM_004111 FKBP1B 206857_s_at NM_054033 FLJ32029 229256_at NM_173582 FN1 216442_x_at NM_002026 FOXM1 202580_x_at NM_021953 FYB 227266_s_at NM_001465 G0S2 213524_s_at NM_015714 GABRP 205044_at NM_014211 HEC 204162_at NM_006101 HES2 231928_at AK091122 HIST2H2AA 214290_s_at NM_003516 HMGB2 208808_s_at NM_002129 HOP 211597_s_at NM_032495 HOXD10 229400_at NM_002148 HSD11B1 205404_at NM_181755 IL1RN 212657_s_at NM_173843 IL8 202859_x_at NM_000584 INSR 227432_s_at NM_000208 IVL 214599_at NM_005547 KIAA0101 202503_s_at NM_014736 KIAA0186 206102_at NM_021067 KIAA1359 231941_s_at AB037780 KLK5 222242_s_at AF243527 KLK6 204733_at NM_002774 KLK7 239381_at NM_005046 KRT13 207935_s_at NM_153490 KRT19 201650_at NM_002276 KRT23 218963_s_at NM_015515 KRT4 213240_s_at NM_002272 KRT7 209016_s_at NM_005556 LCN2; NGAL 212531_at NM_005564 LIPG 219181_at NM_006033 MAC30 212279_at NM_014573 MAD2L1 203362_s_at NM_002358 MAL 204777_s_at NM_002371 MAP17 219630_at NM_005764 MCM2 202107_s_at NM_004526 MCM4 222037_at NM_005914 MCM5 216237_s_at NM_006739 MCM7 208795_s_at NM_182776 MKI67 212022_s_at NM_002417 MMP1 204475_at NM_002421 MMP10 205680_at NM_002425 MMP7 204259_at NM_002423 MYL9 201058_s_at NM_006097 NICE-1 220620_at NM_019060 NMES1 223484_at NM_032413 NTN4 223315_at NM_021229 NUSAP1 218039_at NM_016359 OSF-2 210809_s_at NM_006475 PCNA 201202_at NM_002592 Pfs2 221521_s_at NM_016095 PI3 203691_at NM_002638 PIGR 226147_s_at AA838075 PLAB 221577_x_at NM_004864 PLAT 201860_s_at NM_000930 PMSCL1 213226_at NM_005033 PPBP 214146_s_at NM_002704 PRC1 218009_s_at NM_003981 PTGS1 215813_s_at NM_000962 PTGS2 204748_at NM_000963 RAMP 218585_s_at NM_016448 RARRES1 206391_at NM_002888 RBPMS 209488_s_at NM_006867 RCP 225177_at NM_025151 RFC3 204127_at NM_002915 RFC4 204023_at NM_002916 RHCG 219554_at NM_016321 RPS4Y 201909_at NM_001008 RRM2 209773_s_at NM_001034 S100A7 205916_at NM_002963 S100A8 202917_s_at NM_002964 S100A9 203535_at NM_002965 S100P 204351_at NM_005980 SAA2 208607_s_at NM_030754 SAT 213988_s_at NM_002970 SCEL 206884_s_at NM_144777 SCGB1A1 205725_at NM_003357 SDP35 222958_s_at NM_017779 SERPINA3 202376_at NM_000624 SERPINB1 212268_at NM_030666 SERPINB3 209719_x_at NM_006919 SIAT7A 227725_at NM_018414 SLC6A14 219795_at NM_007231 SLPI 203021_at NM_003064 SMC2L1 204240_s_at NM_006444 SMC4L1 201664_at NM_005496 SNRPN 201522_x_at NM_022807 SPINK5 205185_at NM_006846 SPRR1A 213796_at NM_005987 SPRR1B 205064_at NM_003125 SPRR2B 208539_x_at NM_006945 SPRR3 232082_x_at NM_005416 STK6 208079_s_at NM_003158 TAGLN 205547_s_at NM_015996 TCN1 205513_at NM_001062 TGFB2 228121_at NM_003238 TOP2A 201292_at NM_001067 TOPK 219148_at NM_018492 TP53I3 210609_s_at NM_004881 TPX2 210052_s_at NM_012112 TRIM22 213293_s_at NM_006074 TRIP13 204033_at NM_004237 TTK 204822_at NM_003318 TUBA3 209118_s_at NM_006009 TYMS 202589_at NM_001071 UBE1C 229831_at NM_003968 UBE2C 202954_at NM_181802 UHRF1 225655_at NM_013282 UPK1B 210064_s_at NM_006952 VRK1 203856_at NM_003384 ZNF367 229551_x_at NM_153695 ZWINT 204026_s_at NM_032997 Table S4. Gene expression changes associated with dysplasia and SCC immortality Mean SD CV AFFY ID Gene Symbol N (n=4) MD (n=11) MC (n=4) ID (n=7) IC (n=11) N (n=4) MD (n=11) MC (n=4) ID (n=7) IC (n=11) N (n=4) MD (n=11) MC (n=4) ID (n=7) IC (n=11) 222162_s_at ADAMTS1 388 409 638 159 165 68 97 195 46 104 18 24 31 29 63 211071_s_at AF1Q 307 419 1186 101 152 85 132 980 48 96 28 32 83 48 63 203180_at ALDH1A3 1542 4102 4537 538 518 852 1337 2724 376 836 55 33 60 70 162 203722_at ALDH4A1 306 404 243 136 154 43 159 99 34 53 14 39 41 25 34 203404_at ALEX2 151 124 181 50 59 8 28 46 23 52 6 23 26 46 89 206385_s_at ANK3 88 106 92 45 53 24 37 24 16 22 27 35 26 37 41 204244_s_at ASK 36 32 19 77 90 4 8 3 24 47 12 27 18 30 52 202095_s_at BIRC5 290 235 90 540 540 65 95 29 160 152 22 40 32 30 28 219555_s_at BM039