A combined oncogenic pathway signature of BRAF, KRAS and PI3KCA mutation improves colorectal cancer classification and cetuximab treatment prediction
- Tian Sun1,
- Iris Simon1,
- Victor Moreno2,3,
- Paul Roepman1,
- Josep Tabernero4,
- Mireille Snel1,
- Laura van't Veer1,
- Ramon Salazar2,
- Rene Bernards1,5,
- Gabriel Capella2
- 1Research and Development, Agendia BV, Amsterdam, The Netherlands
- 2IDIBELL, Institut Català d'Oncologia, L'Hospitalet de Llobregat, Spain
- 3Medical Oncology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona, Barcelona, Spain
- 4Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
- 5Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Correspondence to Gabriel Capella, Translational Research Laboratory, Catalan Institute of Oncology-IDIBELL, Barcelona 08908, Spain;
Contributors TS, IS, VM, PR, JT, MS, LvV, RS, RB and GC have read and reviewed the final paper. TS, IS, JT, RB and GC have been involved in conception and planning of the project and analysis. TS, VM, PR, MS, LvV and RS have been involved in acquiring data and performing experiments. TS, IS, PR, RB and GC have written the manuscript.
- Revised 21 May 2012
- Accepted 13 June 2012
- Published Online First 14 July 2012
Objective To develop gene expression profiles that characterise KRAS-, BRAF- or PIK3CA-activated- tumours, and to explore whether these profiles might be helpful in predicting the response to the epidermal growth factor receptor (EGFR) pathway inhibitors better than mutation status alone.
Design Fresh frozen tumour samples from 381 colorectal cancer (CRC) patients were collected and mutations in KRAS, BRAF and PIK3CA were assessed. Using microarray data, three individual oncogenic and a combined model were developed and validated in an independent set of 80 CRC patients, and in a dataset from metastatic CRC patients treated with cetuximab.
Results 175 tumours (45.9%) harboured oncogenic mutations in KRAS (30.2%), BRAF (11.0%) and PIK3CA (11.5%). Activating mutation signatures for KRAS (75 genes), for BRAF (58 genes,) and for PIK3CA (49 genes) were developed. The development of a combined oncogenic pathway signature-classified tumours as ‘activated oncogenic’, or as ‘wildtype-like’ with a sensitivity of 90.3% and a specificity of 61.7%. The identified signature revealed other mechanisms that can activate ERK/MAPK pathway in KRAS, BRAF and PIK3CA wildtype patients. The combined signature is associated with response to cetuximab treatment in patients with metastatic CRC (HR 2.51, p<0.0009).
Conclusion A combined oncogenic pathway signature allows the identification of patients with an active EGFR-signalling pathway that could benefit from downstream pathway inhibition.
- Colorectal cancer
- EGFR-inhibitor resistance
- colorectal metastases
- drug resistance
- gene expression
- molecular oncology
- colorectal neoplasia
- cancer genetics
- cancer syndromes
- colorectal adenomas
- pancreatic cancer
TS and IS contributed equally to this work.
Correction notice This article has been corrected since it was published Online First. The author name Sun Tian has been amended to Tian Sun.
Acknowledgements We would like to thank Leiden University Medical Center, The Netherlands Cancer Institute, the Slotervaart General Hospital in The Netherlands, Institut Català d'Oncologia and Hospital Vall d'Hebron in Spain for their patient samples. We also thank Miguel Angel Pujana for deep insight and help in the early stages of this work.
Funding This study was partially supported by grants SAF 09-07319 SAF 06-6084 from the Spanish Ministry of Education and Science, from Fondo de Investigación Sanitaria (FIS 07/0475), F05-01 from the Fundació Gastroenterologia Dr. Francisco Vilardell, RCESP C03/09 and RTICCC C03/10, RTICCRD06/0020/050, Acción Transversal contra el Cáncer, the Instituto de Salud Carlos III (FIS PI08/1635, FIS PI08/1359, PS09/01037, CB07/02/2005 CIBERESP) and European Commission grant FP7-COOP-Health-2007-B ‘HiperDart’. We are especially grateful to the Asociación Española contra el Cáncer.
Competing interests Employment or Leadership Position at Agendia: TS, IS, PR, MS, LvV and RB. Stock Ownership Agendia: LvV and RB. Honoraria: none. Research funding: none. Expert testimony: none. Other remuneration: TS, IS and PR are inventors on a patent relevant to the presented work.
Patient consent Obtained.
Ethics approval Ethics approval was provided by the Medical Ethical Board of the participating medical centres and hospitals.
Provenance and peer review Not commissioned; externally peer reviewed.
Data sharing statement All signature-related gene expression data are available on the Agendia Research web site (https://research.agendia.com).