Abstract

Colorectal cancer is the third most common cancer worldwide, with 1.2 million patients diagnosed annually. In late-stage colorectal cancer, the most commonly used targeted therapies are the monoclonal antibodies cetuximab and panitumumab, which prevent epidermal growth factor receptor (EGFR) activation1. Recent studies have identified alterations in KRAS2,3,4 and other genes5,6,7,8,9,10,11,12,13 as likely mechanisms of primary and secondary resistance to anti-EGFR antibody therapy. Despite these efforts, additional mechanisms of resistance to EGFR blockade are thought to be present in colorectal cancer and little is known about determinants of sensitivity to this therapy. To examine the effect of somatic genetic changes in colorectal cancer on response to anti-EGFR antibody therapy, here we perform complete exome sequence and copy number analyses of 129 patient-derived tumour grafts and targeted genomic analyses of 55 patient tumours, all of which were KRAS wild-type. We analysed the response of tumours to anti-EGFR antibody blockade in tumour graft models and in clinical settings and functionally linked therapeutic responses to mutational data. In addition to previously identified genes, we detected mutations in ERBB2, EGFR, FGFR1, PDGFRA, and MAP2K1 as potential mechanisms of primary resistance to this therapy. Novel alterations in the ectodomain of EGFR were identified in patients with acquired resistance to EGFR blockade. Amplifications and sequence changes in the tyrosine kinase receptor adaptor gene IRS2 were identified in tumours with increased sensitivity to anti-EGFR therapy. Therapeutic resistance to EGFR blockade could be overcome in tumour graft models through combinatorial therapies targeting actionable genes. These analyses provide a systematic approach to evaluating response to targeted therapies in human cancer, highlight new mechanisms of responsiveness to anti-EGFR therapies, and delineate new avenues for intervention in managing colorectal cancer.

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Accessions

Primary accessions

EMBL/GenBank/DDBJ

Data deposits

Sequence data have been deposited at the European Genome-phenome Archive, which is hosted at the European Bioinformatics Institute, under study accession EGAS00001001305.

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Acknowledgements

We thank S. Angiuoli, D. Riley, L. Kann, M. Shukla, and C. L. McCord for their assistance with next-generation sequencing analyses, and F. Galimi and S. M. Leto for their help with Sanger sequencing analyses and functional studies. This work was supported by the John G. Ballenger Trust, FasterCures Research Acceleration Award, the European Community’s Seventh Framework Programme, the AIRC Italian Association for Cancer Research (Special Program Molecular Clinical Oncology 5×1000, project 9970, and Investigator Grants projects 14205 and 15571), American Association for Cancer Research (AACR) – Fight Colorectal Cancer Career Development Award in memory of Lisa Dubow (project 12-20-16-BERT), the Commonwealth Foundation, Swim Across America, US National Institutes of Health grant CA121113, Fondazione Piemontese per la Ricerca sul Cancro-ONLUS (5×1000 Italian Ministry of Health 2011), Oncologia Ca’ Granda ONLUS, and the SU2C-DCS International Translational Cancer Research Dream Team Grant (SU2C-AACR-DT1415). We acknowledge Merck for a gift of cetuximab. Stand Up To Cancer is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research. A.B. and L.T. are members of the EurOPDX Consortium.

Author information

Author notes

    • Dario Ribero

    Present address: European Institute of Oncology (IEO), 20141 Milan, Italy

    • Andrea Bertotti
    •  & Eniko Papp

    These authors contributed equally to this work.

    • Livio Trusolino
    •  & Victor E. Velculescu

    These authors jointly supervised this work.

Affiliations

  1. Department of Oncology, University of Turin Medical School, 10060 Candiolo, Turin, Italy

    • Andrea Bertotti
    • , Barbara Lupo
    • , Giorgia Migliardi
    • , Eugenia R. Zanella
    •  & Livio Trusolino
  2. Translational Cancer Medicine, Surgical Oncology, and Clinical Trials Coordination, Candiolo Cancer Institute – Fondazione del Piemonte per l’Oncologia IRCCS, 10060 Candiolo, Turin, Italy

    • Andrea Bertotti
    • , Barbara Lupo
    • , Francesco Sassi
    • , Francesca Cottino
    • , Giorgia Migliardi
    • , Eugenia R. Zanella
    • , Alfredo Mellano
    • , Andrea Muratore
    • , Silvia Marsoni
    •  & Livio Trusolino
  3. National Institute of Biostructures and Biosystems (INBB), 00136 Rome, Italy

    • Andrea Bertotti
  4. Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA

    • Eniko Papp
    • , Vilmos Adleff
    • , Valsamo Anagnostou
    • , Jillian Phallen
    • , Carolyn A. Hruban
    • , Qing Kay Li
    • , Rachel Karchin
    • , Robert Scharpf
    • , Luis A. Diaz Jr
    •  & Victor E. Velculescu
  5. Personal Genome Diagnostics, Baltimore, Maryland 21224, USA

    • Siân Jones
    • , Mark Sausen
    • , Monica Nesselbush
    •  & Karli Lytle
  6. Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland 21204, USA

    • Collin Tokheim
    • , Noushin Niknafs
    •  & Rachel Karchin
  7. Department of Surgery, Mauriziano Umberto I Hospital, 10128 Turin, Italy

    • Dario Ribero
    •  & Nadia Russolillo
  8. Liver Transplantation Center, San Giovanni Battista Hospital, 10126 Turin, Italy

    • Gianluca Paraluppi
    •  & Mauro Salizzoni
  9. Department of Surgical Sciences, University of Turin Medical School, 10126 Turin, Italy

    • Mauro Salizzoni
  10. Symphogen A/S, 2750 Ballerup, Denmark

    • Michael Kragh
    •  & Johan Lantto
  11. Niguarda Cancer Center, Ospedale Niguarda Ca’ Granda, 20162 Milan, Italy

    • Andrea Cassingena
    • , Andrea Sartore-Bianchi
    •  & Salvatore Siena
  12. University of Milan Medical School, 20162 Milan, Italy

    • Salvatore Siena
  13. Swim Across America Laboratory, The Ludwig Center for Cancer Genetics and Therapeutics at Johns Hopkins, Baltimore, Maryland 21287, USA

    • Luis A. Diaz Jr

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Contributions

A.B. and E.P. conceived the project, designed and performed experiments, interpreted results and co-wrote the manuscript. S.J., V.A., V.A., B.L., M.S., J.P., C.A.H., M.N., K.L., F.S., F.C., G.M., E.R.Z., D.R., N.R., A.M., A.M., G.P., M.S., S.M., and A.C. performed experiments, analysed data, prepared tables, or participated in discussion of the results. M.K. and J.L. contributed reagents. Q.K.L. undertook all pathological evaluations. C.T., N.N., R.K., and R.S. performed statistical analyses. A.S.-B., S.S., and L.A.D. provided clinically annotated samples and supervised experimental designs. L.T. and V.E.V. conceived the project, supervised experimental designs, interpreted results, and co-wrote the manuscript.

Competing interests

L.A.D. and V.E.V. are co-founders of Personal Genome Diagnostics and are members of its Board of Directors. V.E.V. and L.A.D. own Personal Genome Diagnostics stock, which is subject to certain restrictions under Johns Hopkins University policy. The authors are entitled to a share of the royalties received by the University on sales of products related to genes described in this manuscript. The terms of these arrangements are managed by the Johns Hopkins University in accordance with its conflict-of-interest policies.

Corresponding authors

Correspondence to Andrea Bertotti or Livio Trusolino or Victor E. Velculescu.

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DOI

https://doi.org/10.1038/nature14969

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