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Supplementary Table Section

Table legends

Table 1: Anti-EGFR drugs that are approved for cancer treatment.

Table 2: Cells used for recombinant expression of EGFR variants. Summary of cellular models transiently (t) or stably (s) transfected with EGFR variants.

Table 3: NSCLC cells with endogenous EGFR mutations and wildtype EGFR. Summary of lung cancer cell lines with endogenous EGFR kinase domain mutations and wildtype EGFR. 1 Cell lines available at ATCC. 2 Cell lines that have been successfully transfected according to published literature.

Table 4: Summary on clinical examination conducted in the context of EGFR kinase domain mutations in NSCLC patients. Adapted from Sequist et al. (Sequist et al., 2005) and updated; “---“ indicates that data were not explicitly reported in the cited articles. Some of the numbers were calculated from published primary data. 1 Response as defined in the cited articles. 2 Only Japanese patients (n=10) included in calculation of median survival. 3 Includes silent mutations. 4 All stable disease. 5 These data comprise only a part of the total data from IDEAL and INTACT trials. 6 not reached (NR) at time of publication.

Table 5: Prevalence of EGFR kinase domain mutations in NSCLC patients and their correlation with other molecular events. The right column (*) depicts selected factors that may be deregulated or mutated in lung cancer, but have not yet been extensively analyzed in context with EGFR kinase domain mutations. Tables

Table 1: Anti-EGFR drugs that are approved for cancer treatment.

Drug Company Compound Class Indications Gefitinib Astra Zeneca TKI NSCLC after failure (ZD1839/ Iressa) of standard treatments (de Bono and Rowinsky, 2002; Laskin and Sandler, 2004) Erlotinib OSI TKI NSCLC after failure (CP-358,774/ Pharmaceuticals/ of standard Genentech/ Roche treatments Tarceva/ OSI-774) (de Bono and Rowinsky, 2002; Laskin and Sandler, 2004) Cetuximab ImClone Systems/ Chimeric anti-EGFR Advanced colon (C225/ Erbitux) Bristol-Myers monoclonal antibody rectal cancer (CRC) Squibb/ Merck and squamous cell (Janmaat and Giaccone, KGaA carcinoma of the 2003; Harding and Burtness, 2005) head and neck (SCCHN) Nimotuzumab YM BioSciences/ Humanized anti- SCCHN (in India, (TheraCim/ hR-3) Oncoscience/ EGFR monoclonal Argentina, Columbia CIMAB SA/ Biocon antibody and Cuba), (Spicer et al., 2005) Biopharmaceuticals nasopharyngeal cancer (in China) Panitumumab Abgenix/ Amgen Fully human anti- Chemotherapy- (ABX-EGF/ Vectibix) EGFR monoclonal resistant CRC antibody (Davis et al., 1999; Cohenuram and Saif, 2007) Table 2: Cells used for recombinant expression of EGFR variants.

Cell line Tissue Transient (t)/ Stable (s) transfection Cos-7 African green monkey, kidney t (Lynch et al., 2004a), t (Sordella et al., 2004), t (Choong et al., 2006) NIH-3T3 Murine fibroblasts s (Greulich et al., 2005), t (Greulich et al., 2005), s (Mukohara et al., 2005), s (Shimamura et al., 2005), s (Alvarez et al., 2006), HEK293T Human kidney s (Arao et al., 2004), t (Pao et al., 2004), t (Amann et al., 2005), s (Sakai et al., 2006), NMuMg Murine mammary epithelium s (Sordella et al., 2004) CHO Chinese hamster ovary s (Amann et al., 2005), t (Engelman et al., 2005) H1299 Human NSCLC s (Chen et al., 2006) 32D Murine IL-3 dependent myeloid s (Chen et al., 2006) cells Hela Human cervix tumor t (Greulich et al., 2005) hTBE Human tracheobronchial s (Greulich et al., 2005) epithelium Baf/F3 Murine IL-3 dependent proB s (Jiang et al., 2005) lymphoid cells NR6 Murine fibroblasts s (Carey et al., 2006) PC-13 Human lung large cell carcinoma t (Akca et al., 2006) Table 3: NSCLC cells with endogenous EGFR mutations and wildtype EGFR.

Cell line EGFR Other characteristics H3255 L858R, EGFR amplification high ErbB2, ErbB3 and epiregulin expression (Tracy, 2004; Amann et al., 2005; Engelman et al., 2005; detectable amphiregulin Haura et al., 2005; Paez et al., 2004; Mukohara et al., 2005; no secretion of TGF Shimamura et al., 2005; Alvarez, 2006; Engelman, 2006) H1650 [1] delE746-A750 lack of PTEN (Sordella et al., 2004; Kwak et al., 2005; Shimamura et al., wildtype K-RAS 2005; Janmaat et al., 2006; Haura et al., 2005) H1975 [1] L858R + T790M wildtype K-RAS (Sordella et al., 2004; Haura et al., 2005; Kwak et al., 2005; Pao et al., 2005a; Shimamura et al., 2005; Yauch et al., 2005; Engelman et al., 2006) HCC-827 [1] delE746-A750, amplification high ErbB3, epiregulin and amphiregulin expression (Amann et al., 2005; Fujimoto, et al., 2005; Mukohara et al., detectable ErbB2 2005; Alvarez et al., 2006, Engelmann et al., 2006) HCC2279 del746-750; high expression detectable epiregulin and amphiregulin (Fujimoto et al., 2005; Coldren et al., 2006) of EGFR low Akt expression no ErbB2 and ErbB3 wildtype K-RAS H4006 del746-750, S752V; detectable ErbB3, epiregulin and amphiregulin (Fujimoto et al., 2005; Coldren et al., 2006) medium EGFR expression ErbB2 expression low wildtype K-RAS PC-9 [2] delE746-A750, also express high ErbB3 expression (Kakiuchi et al., 2004; Ono et al., 2004; Tracy et al., 2004; some wildtype EGFR medium EGF and TGF expression Mukohara et al., 2005; Akca et al., 2006; Sakai et al., 2006) low ErbB2 and ErbB4 expression DFCILU-011 delL747-E749 high ErbB3 expression (Engelman et al., 2005; Mukohara et al., 2005) H820 [2] Non-specified deletion contradicting K-RAS mutation data (Coldren, 2006; (Coldren et al., 2006) mutation Okudela, 2004) H1781 [1,2] Wildtype ErbB2-G776V mutation (Paez et al., 2004; Yauch et al., 2005) wildtype K-RAS H1666 [1] Wildtype TGF secretion Paez et al., 2004; Tracy et al., 2004; Sordella et al., 2004; wildtype K-RAS Mukohara et al., 2005; Shimamura et al., 2005) H358 [1,2] Wildtype high ErbB3 expression (Kakiuchi et al., 2004; Sordella et al., 2004; Engelman et al., detectable ErbB2 and amphiregulin 2005; Haura et al., 2005; Pao et al., 2005a) no ErbB4 expression K-RAS mutation H1734 [1,2] Wildtype K-RAS mutation (Sordella, 2004; Pao et al., 2005a) H1819 [1] Wildtype, small increase in ErbB2 amplification (Amann et al., 2005; Fujimoto et al., 2005) copy number high ErbB3 expression detectable amphiregulin and epiregulin H1299 [1,2] Wildtype, small increase in medium TGF expression (Lee et al., 2003; Amann et al., 2005; Engelman et al., copy number low ErbB3 expression 2005; Haura et al., 2005; Yauch et al., 2005, Akca et al., no ErbB2 and ErbB4 expression 2006) p53 mutation, wildtype PTEN and K-RAS A549 [1,2] Wildtype high TGF expression (Tracy et al., 2004; Amann et al., 2005; Engelmann et al., low ErbB2 and ErbB3 expression 2005; Haura et al., 2005; Mukohara et al., 2005; Shimamura detectable PTEN et al., 2005; Yauch et al., 2005) no EGF expression K-RAS mutation H441 [1,2] Wildtype ErbB2 and ErbB3 constitutively active (Paez et al., 2004; Mukohara et al., 2005; Yauch et al., detectable TGF secretion 2005) K-RAS and p53 mutation lack of PTEN H23 [1,2] Wildtype no ErbB2 and ErbB3 expression (Engelman et al., 2005; Yauch et al., 2005) p53 and K-RAS mutation H292 [1,2] Wildtype, high expression medium ErbB3 and EGF expression (Janmaat et al., 2006) detectable PTEN low ErbB2, HB-EGF and TGF expression K-RAS wildtype Calu-3 [1,2] Wildtype High ErbB2 and ErbB3 expression (Engelman et al., 2005) Calu-1 [1,2] Wildtype, small increase in No ErbB2 and ErbB3 expression (Amann et al., 2005; Shimamura et al., 2005; Yauch et al., copy number wildtype K-RAS 2005) H2030 [1] Wildtype K-RAS mutation (Pao et al., 2005a) Table 4: Summary on clinical examination conducted in the context of EGFR kinase domain mutations in NSCLC patients.

Authors EGFR Number Response rate Median Adenocarcinoma Female Never- status of to gefitinib or survival or BAC (%) (%) Smokers/Non- subjects erlotinib (%) 1 (months) Smokers (%) Lynch et al., Mut 8 100 --- 100 63 63 2004a Wt 8 13 ------Paez et al., Mut 5 100 --- 100 60 --- 2004 Wt 4 0 --- 75 75 --- Pao et al., Mut 17 100 ------2004 Wt 43 12 ------Pao, 2005b Mut 22 77 ------Wt 38 13 ------Huang et al., Mut 8 78 --- 100 75 88 2004 Wt 8 14 --- 13 75 63 Tokumo et Mut 9 89 25 89 56 78 al., 2005 Wt 12 17 14 58 25 0 Mitsudomi et Mut 33 83 NR 6 97 58 61 al., 2005 Wt 26 10 ~17 31 31 31 Han et al., Mut 17 65 31 82 71 65 2005 Wt 73 14 7 ------Taron et al., Mut 17 94 NR 6 100 65 82 2005 Wt 51 12 10 59 24 16 Kondo et al., Mut 4 100 --- 100 50 75 2005 Wt 8 0 --- 63 50 25 Rosell et al., Mut 8 88 16 2 100 50 62 2005 Wt 24 13 2 2 77 27 20 Tomizawa et Mut 10 100 --- 100 60 60 (n) al., 2005 Wt 10 3 40 --- 80 50 50 (n) Zhang et al., Mut 12 67 NR 6 92 75 91 (n) 2005 Wt 18 6 7 56 28 39 (n) Tsao et al., Mut 19 16 ------2005 Wt 81 7 ------Takano et al., Mut 39 82 20 97 46 54 2005 Wt 27 11 7 89 39 37 Niho et al., Mut 4 100 16 100 75 25 2006 Wt 9 67 4 11 78 22 0 Kimura et al., Mut 13 54 20 85 54 --- 2006 Wt 14 14 8 86 21 --- Kim et al., Mut 6 100 16 83 50 67 2005 Wt 21 --- 5 ------Cortes- Mut 10 60 13 100 70 60 Funes et al., Wt 72 8 5 44 25 20 2005 Cappuzzo et Mut 15 53 21 80 53 40 al., 2005a Wt 74 5 8 62 31 9 Chou et al., Mut 33 52 15 88 55 76 2005 Wt 21 19 5 --- Uramoto et Mut 9 78 13 100 44 56 al., 2006 Wt 11 0 4 72 45 27 Bell et al., Mut 13 5 46 5 --- 80 50 39 2005a Wt 56 5 9 5 --- 51 29 14 Mu et al., Mut 10 100 --- 90 70 --- 2005 Wt 12 3 33 --- 64 45 --- Ishikawa et Mut 6 50 --- 83 50 67 al., 2005 Wt 7 14 --- 50 25 38 Shih et al., Mut 29 69 --- 96 79 79 2006 Wt 33 9 --- 88 45 55 Table 5: Prevalence of EGFR kinase domain mutations in NSCLC patients and their correlation with other molecular events.

Positive Negative No Unclear Correlation Correlation Correlation Correlation (*) Increased genomic Increased methylation EGFR Mutation of B-Raf (v- EGFR copy number of SPARC (secreted overexpression raf murine sarcoma (Taron et al., 2005; protein acidic and rich (Taron et al., viral oncogene Takano et al., 2005) in cysteine) promoter 2005) homolog B1) (Naoki region (Suzuki et al., et al., 2002; Brose et 2006) al., 2002); Deregulation of Ras- Raf-MAPK signaling (Adjei, 2005) Increased number of K-RAS mutation p53 mutation PI3K mutation CA repeats (Taron et (Kosaka et al., 2004; (Kondo et al., (Samuels et al., 2004; al., 2005) Pao et al., 2005b; 2005) Kawano et al., 2006) Soung et al., 2005; Shigematsu et al., 2005a; Yokoyama et al., 2006) Increased phospho- ErbB2 mutation ErbB2 c-Met (hepatocyte STAT5 levels (Haura (Stephens et al., 2004; amplification growth factor et al., 2005) Shigematsu, et al., (Endo et al., receptor) mutation 2005b; Yokoyama et 2006) (Kong-Beltran et al., al., 2006) 2006) Activation of mTOR ErbB4 mutation Deregulation of Wnt (mammalian target of (Soung et al., (wingless-type MMTV Rapamycin) 2006) integration site family) signaling (Conde et signaling (Uematsu et al., 2006) al., 2003) ErbB2 and Increased PP2a (protein concomitant EGFR phospho-Akt phosphatase 2A) gene amplification levels (Han et al., (Wang et al., 1998) (Cappuzzo et al., 2006) 2005b) EGFR Increased Neurotrophin/ overexpression phospho-MAPK neurotrophin receptor (Suzuki et al., 2005) levels (Han et al., expression (Ricci et 2006) al., 2001) Calveolin-1 EMP-1 (epithelial mRNA membrane protein 1) overexpression expression (Jain et (Taron et al., al., 2005) 2005) SOCS-3 (suppressor of cytokine signaling 3) expression (He et al., 2003) Supplementary information

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