Originally published as JCO Early Release 10.1200/JCO.2007.14.8924 on July 14 2008

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Role of KRAS and EGFR As Biomarkers of Response to Erlotinib in National Cancer Institute of Canada Clinical Trials Group Study BR.21

Chang-Qi Zhu, Gilda da Cunha Santos, Keyue Ding, Akira Sakurada, Jean-Claude Cutz, Ni Liu, Tong Zhang, Paula Marrano, Marlo Whitehead, Jeremy A. Squire, Suzanne Kamel-Reid, Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

From the Division of Applied Molecular Oncology and Departments of Pathology and Medical Oncology and Hematology, University Health Network, Ontario Cancer Institute, Princess Margaret Hospital; Departments of Laboratory Medicine and Pathobiology, Medical Biophysics, and Medicine, University of Toronto, Toronto; and National Cancer Institute of Canada Clinical Trials Group and Queen's University, Kingston, Ontario, Canada

Corresponding author: Ming-Sound Tsao, MD, FRCPC, Princess Margaret Hospital, 610 University Ave, Toronto, Ontario, Canada M5G 2M9; e-mail: Ming.Tsao{at}uhn.on.ca

	ABSTRACT

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Purpose To evaluate the effect of KRAS and epidermal growth factor receptor (EGFR) genotype on the response to erlotinib treatment in the BR.21, placebo-controlled trial.

Patients and Methods We analyzed 206 tumors for KRAS mutation, 204 tumors for EGFR mutation, and 159 tumors for EGFR gene copy by fluorescent in situ hybridization (FISH). We reanalyzed EGFR deletion/mutation using two highly sensitive techniques that detect abnormalities in samples with 5% to 10% tumor cellularity. KRAS mutation was analyzed by direct sequencing.

Results Thirty patients (15%) had KRAS mutations, 34 (17%) had EGFR exon 19 deletion or exon 21 L858R mutations, and 61 (38%) had high EGFR gene copy (FISH positive). Response rates were 10% for wild-type and 5% for mutant KRAS (P = .69), 7% for wild-type and 27% for mutant EGFR (P = .03), and 5% for EGFR FISH-negative and 21% for FISH-positive patients (P = .02). Significant survival benefit from erlotinib therapy was observed for patients with wild-type KRAS (hazard ratio [HR] = 0.69, P = .03) and EGFR FISH positivity (HR = 0.43, P = .004) but not for patients with mutant KRAS (HR = 1.67, P = .31), wild-type EGFR (HR = 0.74, P = .09), mutant EGFR (HR = 0.55, P = .12), and EGFR FISH negativity (HR = 0.80, P = .35). In multivariate analysis, only EGFR FISH-positive status was prognostic for poorer survival (P = .025) and predictive of differential survival benefit from erlotinib (P = .005).

Conclusion EGFR mutations and high copy number are predictive of response to erlotinib. EGFR FISH is the strongest prognostic marker and a significant predictive marker of differential survival benefit from erlotinib.

	INTRODUCTION

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More than 50% of non–small-cell lung cancers (NSCLC) express epidermal growth factor receptor (EGFR) protein, with more frequent expression in squamous carcinoma (approximately 80%) than adenocarcinoma (approximately 50%).^1,2 Phase I and II trials of EGFR tyrosine kinase inhibitors (TKIs) reported dramatic responses in approximately 10% of patients, many of whom had demonstrated resistance to chemotherapy.^3,4 In the National Cancer Institute of Canada Clinical Trials Group BR.21 trial, the overall response rate was 8.9%,⁵ and this study was the first to demonstrate a significant survival advantage for treatment with an EGFR TKI in previously treated NSCLC patients (hazard ratio [HR] = 0.70, P < .001).

The discovery that EGFR tyrosine kinase domain mutations were strongly associated with greater sensitivity of NSCLC to EGFR TKIs in vitro and higher response rates in clinical studies suggested that molecular markers could be used to identify patients most likely to benefit from EGFR TKI therapy.^6,7 Subsequent studies suggested that high EGFR gene copy number was an even stronger predictive marker for survival benefit than mutation status.⁸ Analysis of subsets of BR.21 patients indicated that the survival benefit from erlotinib therapy was greater in patients whose tumors expressed EGFR protein and in patients whose tumors demonstrated high (amplification and high polysomy) EGFR gene copy number.⁹ However, P values for interaction that compared the differential survival impact of erlotinib defined by these markers were statistically insignificant. Similar results were reported for EGFR protein and EGFR gene copy number in the Iressa Evaluation in Lung Cancer trial, but with the larger sample size, interaction P values were significant for both protein (P = .05) and copy number (P = .045).¹⁰ In BR.21, patients with both wild-type and mutated EGFR genes derived survival benefit from treatment, but the differences were not significant.

RAS genes are members of the guanidine triphosphatase (GTPase) gene superfamily. KRAS, HRAS, and NRAS encode for 21-kd proteins that share considerable sequence homology and have common intrinsic GTPase activity to hydrolyze guanidine triphosphate to guanidine diphosphate.¹¹ Importantly, Ras transduces the EGFR activation signal to multiple downstream pathways, and activated Ras-guanidine triphosphate is switched off by the intrinsic GTPase activity of Ras protein. RAS mutations on codons 12, 13, and 61 result in inhibition of GTPase activity, thus leading to the constitutive activation of Ras protein, which may render tumor cells independent of EGFR signaling and thereby resistant to EGFR TKI therapy. Pao et al¹² reported that lung adenocarcinoma patients with KRAS mutations are not responsive to gefitinib or erlotinib. In the Tarceva Response in Conjunction with Paclitaxel and Carboplatin (TRIBUTE) trial, patients with KRAS mutations had poorer survival when treated with erlotinib and chemotherapy compared with chemotherapy alone.¹³

We report here the impact of KRAS mutations in a subset of BR.21 patients. We also provide the results of reanalysis of EGFR mutation using more sensitive assays and the final results of EGFR copy number studies by fluorescent in situ hybridization (FISH) on samples that became available after our original publication.⁹

	PATIENTS AND METHODS

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Patients and Tissues
BR.21 was a phase III trial of erlotinib 150 mg daily (OSI Pharmaceuticals, Melville, NY) versus placebo in advanced NSCLC patients who experienced treatment failure with standard chemotherapy. The primary study end point was overall survival. Response¹⁴ was a secondary end point. Archival pathology samples for biomarker analyses were collected from 328 patients who provided separate written consent for optional tissue banking and correlative studies. The Research Ethics Board at the University Health Network approved this molecular study protocol. After histologic evaluation, tumor samples from 230 and 233 patients were felt to be adequate for KRAS and EGFR mutation analyses, respectively, whereas FISH analysis for EGFR copy number was attempted on 240 samples.

KRAS Mutation Analysis
After DNA isolation,⁹ exon 2 of the KRAS gene was amplified by polymerase chain reaction (PCR) using AmpliTaq Gold (Applied Biosystems, Foster City, CA) with forward primer 5'-GTGGAGTATTTGATAGTGTATTAAC-3' and reverse primer 5'-TGTATCAAAGAATGGTCCTGCA-3'. The expected products of 252 base pairs were sequenced bidirectionally using the BigDye Terminator Cycle Sequencing Kit (version 3.1; Applied Biosystems) and an ABI Genetic Analyzer (model 3100; Applied Biosystems). The sequencing primers were 5'-ACCTTATGTGTGACATGTTCTAATATAG-3' (forward) and 5'-ATGGTCCTGCACCAGTAATATGC-3' (reverse). Sequence data were analyzed using SeqScape software (Applied Biosystems) followed by manual review. Positive cases were validated by second independent PCR and sequencing.

Reanalyses of EGFR Mutations
Two assays capable of detecting EGFR mutations in DNA samples containing 5% to 10% tumor were used to reanalyze remaining DNA samples. The Amplified Refractory Mutation System was conducted using the EGFR ScorpionsIM Kits (DxS, Manchester, United Kingdom) for detection of exon 19 (E746_A750del) deletions and exon 21 (L858R) mutation.¹⁵ Assays were performed according to the manufacturer's protocol and using the Mx3000P real-time PCR system (Stratagene, La Jolla, CA). The PCR condition included denaturation at 95°C for 10 minutes, followed by 50 cycles of 95°C for 30 seconds 62°C for 60 seconds, with fluorescence reading set for FAM to allow optical excitation at 480 nm and measurement at 520 nm at the end of each cycle. Data analysis used Mx3000P Software version 2.0 (Stratagene). Fragment analysis, as described by Pan et al,¹⁶ was also conducted looking for different length PCR products resulting from deletion or new Sau96I restriction site created by L858R (2573T_G) mutation using the ABI 3130XL genetic analyzer (Applied Biosystems).

EGFR Gene Copy Number by FISH
EGFR copy number was evaluated by FISH⁹ using the Vysis LSI EGFR probe (Abbott Molecular, Des Plaines, IL) labeled with Spectrum Orange and the CEP7 chromosome 7 centromere (7p11.1 through q11.1) probe labeled with Spectrum Green. The six FISH categories of Cappuzzo et al⁸ were used to define EGFR copy number, and high degrees of polysomy or amplification were considered to be FISH positive.

Statistical Analysis
Exploratory analyses were performed to characterize relationships between KRAS and EGFR status with baseline patient characteristics and outcomes. Analysis populations include all 731 randomly assigned BR.21 patients in survival analyses and all 427 erlotinib-treated patients who were assessable for response.¹⁴ Subgroup analyses included patients with data for each biomarker. A ² or Fisher's exact test was used to assess association between variables. Survival distributions were estimated by the product-limit method and compared using the log-rank test. Cox regression models were used to correlate molecular biomarkers and other baseline factors with survival. Statistical analyses were carried out using SAS version 8.1 (SAS Institute, Cary, NC). All reported P values are two-sided.

	RESULTS

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Patient Populations
Table 1 lists the baseline characteristics of patients with analysis results for KRAS mutation, EGFR FISH, and EGFR mutation. P values are given when the distribution of patient demographics or tumor characteristics differs significantly from the distribution in the remaining patients without marker results (Appendix Table A1, online only). Overall survival for patients with marker results is shown in Figure 1; erlotinib had similar effects in each subgroup of patients compared with patients with marker unknown.

View larger version (34K): [in this window] [in a new window] [PowerPoint Slide for Teaching]   Fig 1. Kaplan-Meier survival curves of subgroup studied for various markers as well as impact of erlotinib according to marker status. HR, hazard ratio.

KRAS mutations were found in 30 patients (15%; Table 2). These included 26 codon 12 mutations (TGT/cys, n = 17; GTT/val, n = 6; GAT/asp, n = 2; and AGT/ser, n = 1) and four codon 13 mutations (TGC/cys, n = 2; AGC/ser, n = 1; and GAC/asp, n = 1). Mutations were more common among adenocarcinoma than other histologies (22% v 5%, respectively; P < .001; Table 3). There were no significant differences between ever and never smokers (16% v 11%, respectively; P = .33) or men and women (15% v 14%, respectively; P = 1.0). No mutations were identified in 15 Asian patients tested. Three patients with KRAS mutations also harbored EGFR mutations.

Among 91 patients assessable for response to erlotinib, the response rate was significantly higher (P = .02) in FISH-positive patients compared with FISH-negative patients (21% v 5%, respectively). The survival benefit for erlotinib compared with placebo was significant (P = .004) in FISH-positive patients (HR = 0.43; 95% CI, 0.23 to 0.78) but not in FISH-negative patients (HR = 0.80; 95% CI, 0.49 to 1.29; P = .35; Table 4, Figs 1E and 1H). FISH-positive and EGFR immunohistochemistry-positive patients had a higher response rate than FISH-negative/IHC-negative patients (Table 4), but the erlotinib effect on overall survival was not significantly different (interaction P = .33, Table 4).

EGFR Mutations
Because exon 19 deletions and exon 21 L858R mutations constitute 85% to 90% of known EGFR mutations and the functional significance of other rare variants may be unclear, we focused our reanalyses on exons 19 and 21. Residual DNA or tissue samples were available for reanalysis in 169 patients using the Scorpion Amplified Refractory Mutation System and fragment length EGFR mutation assays; these included 21 of 24 patients with previously detected mutations and DNA samples that failed previous assay by direct sequencing. Previous mutations were confirmed in 20 patients, but one sample with exon 19 deletion could not be confirmed despite repeated analyses. From 148 patient samples scored previously as negative or failed,⁴ we discovered 11 new samples with exon 19 deletions. All newly detected deletions were confirmed by independent repeat assays. No new L858R mutation was found. Our final results now include 26 exon 19 and eight exon 21 mutations in 204 patients (overall mutation rate, 17%; Table 2). Three samples had both exon 19 deletions and L858R mutations. Only exon 19 and 21 mutations were correlated with clinical factors and outcome.

Patients with known EGFR genotype, compared with patients with unknown EGFR mutation status (Appendix Table A1), included fewer East Asians (6% v 15%, respectively; P = .002), fewer patients with one prior regimen (40% v 54%, respectively; P = .001), and fewer patients with an interval 12 months from diagnosis to random assignment (38% v 50%, respectively; P = .006; Table 1). EGFR mutations were significantly more common among never smokers compared with ever smokers (28% v 14%, respectively; P = .04) and East Asians compared with other ethnicities (38% v 15%, respectively; P = .045). Mutations were not significantly different in females compared with males (18% v 16%, respectively; P = .84) or patients with adenocarcinoma compared with other histologies (20% v 13%, respectively; P = .26; Table 3).

Among 116 assessable patients with EGFR mutation status known (Table 4), the response rate was significantly higher in patients with mutations (27% v 7%, respectively; P = .035) compared with patients with wild-type or other indeterminate mutations. The survival benefit from erlotinib compared with placebo was slightly greater with EGFR mutations (HR = 0.55; 95% CI, 0.25 to 1.19; P = .12; Fig 1F) than EGFR wild-type or indeterminate variants (HR = 0.74; 95% CI, 0.52 to 1.05; P = .09; Fig 1I), but the interaction was not significant (P = .47).

Multivariate Analyses
Multivariate Cox regression models were used to assess the prognostic and predictive effect on overall survival of each molecular marker individually (including patients with unknown marker status) while adjusting for the prognostic factors of the trial population, with stepwise selection at a 0.1 level (Table 5). For EGFR FISH, it was found that FISH-positive status was both prognostic for worse survival in untreated patients (P = .025) and predictive of greater survival benefit from erlotinib (P = .005). The only other significant predictive factor was smoking history, with never smokers deriving greater benefit from erlotinib (P = .009). Baseline prognostic factors for better survival included good performance status (P < .001), weight loss less than 5% (P < .001), complete/partial response to chemotherapy (P = .04), stable disease in response to chemotherapy (P = .004), and Asian race (P = .04). Patients who had received platinum therapy (P = .02) and patients with time from diagnosis to random assignment of 12 months (P < .001) had shorter survival time.

	DISCUSSION

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We reported previously that, in BR.21, patients whose tumors expressed EGFR protein by immunohistochemistry and patients whose tumors had high EGFR copy number by FISH derived significant survival benefits from erlotinib compared with placebo.⁹ Patients with wild-type or EGFR mutations derived survival benefit from treatment, although the differences in survival compared with placebo were not significant. With analyses of additional samples that became available after our original report and a reanalysis of available samples for EGFR mutation by more sensitive techniques, the previous roles of EGFR mutation status and copy number were confirmed. We also report here that patients whose tumors have KRAS codon 12 and 13 mutations do not seem to derive any survival benefit from erlotinib therapy.

Pao et al¹² first suggested that occurrences of KRAS and EGFR mutations are mutually exclusive and that patients with KRAS mutations are nonresponsive to treatment with EGFR TKIs. The mutual exclusivity of EGFR and KRAS mutations was reported in three other studies,^17-19 but occasional tumors with coexisting EGFR and KRAS mutations have also been reported.^13,20,21 We identified coexisting EGFR and KRAS mutations in three patients (all treated with placebo).

Pao et al¹² reported that none of 21 patients sensitive to gefitinib or erlotinib had KRAS mutations, whereas nine (24%) of 38 patients who were refractory to these drugs had mutations. Han et al²² also reported that none of nine NSCLC patients with KRAS mutations responded to gefitinib. In the Southwest Oncology Group S0126 trial, 19 (30%) of 63 patients with lung adenocarcinoma with bronchioloalveolar features had KRAS mutations; one patient responded to gefitinib therapy.²⁰ None of four patients with both EGFR and KRAS mutations responded. More recently, Miller et al²³ reported that, among 79 patients with lung adenocarcinoma with bronchioloalveolar carcinoma features, 18 (23%) had KRAS mutations and none responded to erlotinib. In our series, 10 (10%) of 98 KRAS wild-type patients assessable for response had confirmed response to erlotinib, whereas only one (5%) of 20 KRAS mutant patients responded. Interestingly, this responding patient also had EGFR amplification but not EGFR mutation. Taken together, there is good evidence that NSCLC patients with KRAS mutations are unlikely to respond to EGFR TKI therapy, unless possibly when they have EGFR amplification.

In the phase III TRIBUTE study that evaluated the efficacy of erlotinib plus carboplatin/paclitaxel versus chemotherapy alone, KRAS mutations were found in 55 (20%) of 274 patients. Patients with KRAS mutations who received erlotinib plus chemotherapy demonstrated worse overall survival (HR = 2.1; 95% CI, 1.1 to 3.8; P = .02) than patients who received chemotherapy alone. Although the HR for death for the erlotinib-treated KRAS patients compared with placebo patients was 1.67 (95% CI, 0.62 to 4.50) in our study, there were only eight patients on placebo compared with 22 patients on erlotinib. This resulted in an insignificant P value (P = .31) and also an insignificant P value for interaction.

After our original report, we obtained and evaluated 106 additional samples for molecular analysis. In our original publication, we reported all EGFR mutations identified, including indeterminate variants that had not been or were not confirmed by independent PCR assay, which could potentially represent sequencing artifact. In this report, we have focused on the most relevant mutations, exon 19 deletions and exon 21 L858R mutations. We have shown, as have others, that these mutations are associated with a higher response rate. Patients with these mutations also derive considerable survival benefit, although a differentially greater survival benefit for patients with mutations could not be demonstrated. Our separate analysis of samples with exon 19 deletion gave the same results. Although we originally reported⁹ an approximately 3:2 ratio of exon 19 deletion to L858R mutation, consistent with most other reports, this ratio is now 3:1 (Table 2) because all new mutations found were exon 19 deletions. The higher ratio most likely represents normal variation between studies because a similar ratio was reported recently in other studies.^24,25

With our updated FISH results, the difference in response rates for patients with high versus low EGFR gene copy remained significant (21% v 5%, respectively; P = .02), and patients with high copy number derived significant survival benefit from erlotinib (HR = 0.43; 95% CI, 0.23 to 0.78; P = .004), whereas those with low copy number had less survival benefit (HR = 0.80; 95% CI, 0.49 to 1.29; P = .35). Moreover, in the multivariate Cox model, high EGFR copy number was both a significant prognostic factor of poorer survival (P = .025) and a significant predictive factor of erlotinib effect (P = .005) on survival, even when smoking history was included in the model where significant interaction was also seen for lifetime nonsmokers (P = .009).

Molecular correlative studies from BR.21 and Iressa Evaluation in Lung Cancer, the only single-agent placebo controlled phase III trials of EGFR TKIs, were retrospective and restricted to patient subsets with samples; thus, all results are considered exploratory. However, both studies suggested that high EGFR gene copy was prognostic of poorer survival in advanced NSCLC patients and a predictor for better response/survival to erlotinib/gefitinib therapy. We believe that the prognostic and predictive values of this marker require further investigation. Molecular correlative studies from the Iressa Non-Small Cell Lung Cancer Trial Evaluating Response and Survival Against Taxotere (INTEREST trial),²⁶ which compared gefitinib with docetaxel in previously treated advanced NSCLC patients, identified no marker, including EGFR protein expression, EGFR gene copy number, and both EGFR and KRAS mutation status, that was predictive of significantly superior survival with either treatment. Clarification of the role of these markers in the selection of patients for EGFR TKI therapy awaits the results of larger prospectively designed validation studies.

	AUTHORS’ DISCLOSURES OF POTENTIAL CONFLICTS OF INTEREST

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Although all authors completed the disclosure declaration, the following author(s) indicated a financial or other interest that is relevant to the subject matter under consideration in this article. Certain relationships marked with a "U" are those for which no compensation was received; those relationships marked with a "C" were compensated. For a detailed description of the disclosure categories, or for more information about ASCO's conflict of interest policy, please refer to the Author Disclosure Declaration and the Disclosures of Potential Conflicts of Interest section in Information for Contributors.

Employment or Leadership Position: None Consultant or Advisory Role: Frances A. Shepherd, Roche, OSI Pharmaceuticals (C) Stock Ownership: None Honoraria: Jeremy A. Squire, Genentech; Suzanne Kamel-Reid, Genentech; Frances A. Shepherd, Roche, OSI Pharmaceuticals; Ming-Sound Tsao, Roche, Genentech Research Funding: Lesley Seymour, OSI Pharmaceuticals Expert Testimony: None Other Remuneration: None

	AUTHOR CONTRIBUTIONS

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Conception and design: Chang-Qi Zhu, Gilda da Cunha Santos, Keyue Ding, Jeremy A. Squire, Suzanne Kamel-Reid, Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

Financial support: Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

Administrative support: Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

Provision of study materials or patients: Keyue Ding, Lesley Seymour

Collection and assembly of data: Chang-Qi Zhu, Gilda da Cunha Santos, Akira Sakurada, Jean-Claude Cutz, Ni Liu, Tong Zhang, Paula Marrano, Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

Data analysis and interpretation: Chang-Qi Zhu, Gilda da Cunha Santos, Keyue Ding, Akira Sakurada, Jean-Claude Cutz, Ni Liu, Tong Zhang, Paula Marrano, Marlo Whitehead, Jeremy A. Squire, Suzanne Kamel-Reid, Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

Manuscript writing: Chang-Qi Zhu, Gilda da Cunha Santos, Keyue Ding, Ni Liu, Marlo Whitehead, Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

Final approval of manuscript: Chang-Qi Zhu, Gilda da Cunha Santos, Keyue Ding, Akira Sakurada, Jean-Claude Cutz, Ni Liu, Tong Zhang, Paula Marrano, Marlo Whitehead, Jeremy A. Squire, Suzanne Kamel-Reid, Lesley Seymour, Frances A. Shepherd, Ming-Sound Tsao

	Appendix

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View larger version (34K): [in this window] [in a new window] [PowerPoint Slide for Teaching]   Fig A1. Distribution of results according to three molecular markers studied.

	NOTES

 
published online ahead of print at www.jco.org on July 14, 2008.

Supported by grants from the Ontario Institute of Cancer Research, the Canadian Cancer Society/National Cancer Institute of Canada, the Jacqueline Seroussi Memorial Foundation for Cancer Research, and OSI Pharmaceuticals, Inc.

C.-Q.Z., G.d.C.S., and K.D. contributed equally to this study.

Authors’ disclosures of potential conflicts of interest and author contributions are found at the end of this article.

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Submitted October 12, 2007; accepted May 16, 2008.

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