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Truncated FGFR2 is a clinically actionable oncogene in multiple cancers

Daniel Zingg, Jinhyuk Bhin, Julia Yemelyanenko, Sjors M. Kas, Frank Rolfs, Catrin Lutz, Jessica K. Lee, Sjoerd Klarenbeek, Ian M. Silverman, Stefano Annunziato, Chang S. Chan, Sander R. Piersma, Timo Eijkman, Madelon Badoux, Ewa Gogola, Bjørn Siteur, Justin Sprengers, Bim Klein, Richard R. Goeij- de Haas, Gregory M. Riedlinger, Hua Ke, Russell Madison, Anne Paulien Drenth, Eline Burg, Eva Schut, Linda Henneman, Martine H. Miltenburg, Natalie Proost, Huiling Zhen, Ellen Wientjens, Roebi Bruijn, Julian R. Ruiter, Ute Boon, Renske Korte-Grimmerink, Bastiaan Gerwen, Luis Féliz, Ghassan K. Abou-Alfa, Jeffrey S. Ross, Marieke Ven, Sven Rottenberg, Edwin Cuppen, Anne Vaslin Chessex, Siraj M. Ali, Timothy C. Burn, Connie R. Jimenez, Shridar Ganesan (), Lodewyk F. A. Wessels () and Jos Jonkers ()
Additional contact information
Daniel Zingg: Netherlands Cancer Institute
Jinhyuk Bhin: Netherlands Cancer Institute
Julia Yemelyanenko: Netherlands Cancer Institute
Sjors M. Kas: Netherlands Cancer Institute
Frank Rolfs: Netherlands Cancer Institute
Catrin Lutz: Netherlands Cancer Institute
Jessica K. Lee: Foundation Medicine
Sjoerd Klarenbeek: Netherlands Cancer Institute
Ian M. Silverman: Incyte Research Institute
Stefano Annunziato: Netherlands Cancer Institute
Chang S. Chan: Division of Medical Oncology, Rutgers Cancer Institute of New Jersey
Sander R. Piersma: Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam
Timo Eijkman: Netherlands Cancer Institute
Madelon Badoux: Netherlands Cancer Institute
Ewa Gogola: Netherlands Cancer Institute
Bjørn Siteur: Netherlands Cancer Institute
Justin Sprengers: Netherlands Cancer Institute
Bim Klein: Netherlands Cancer Institute
Richard R. Goeij- de Haas: Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam
Gregory M. Riedlinger: Rutgers University
Hua Ke: Division of Medical Oncology, Rutgers Cancer Institute of New Jersey
Russell Madison: Foundation Medicine
Anne Paulien Drenth: Netherlands Cancer Institute
Eline Burg: Netherlands Cancer Institute
Eva Schut: Netherlands Cancer Institute
Linda Henneman: Netherlands Cancer Institute
Martine H. Miltenburg: Netherlands Cancer Institute
Natalie Proost: Netherlands Cancer Institute
Huiling Zhen: Incyte
Ellen Wientjens: Netherlands Cancer Institute
Roebi Bruijn: Netherlands Cancer Institute
Julian R. Ruiter: Netherlands Cancer Institute
Ute Boon: Netherlands Cancer Institute
Renske Korte-Grimmerink: Netherlands Cancer Institute
Bastiaan Gerwen: Netherlands Cancer Institute
Luis Féliz: Incyte Biosciences International
Ghassan K. Abou-Alfa: Memorial Sloan Kettering Cancer Center
Jeffrey S. Ross: Foundation Medicine
Marieke Ven: Netherlands Cancer Institute
Sven Rottenberg: Netherlands Cancer Institute
Edwin Cuppen: Oncode Institute
Anne Vaslin Chessex: Debiopharm International
Siraj M. Ali: Foundation Medicine
Timothy C. Burn: Incyte Research Institute
Connie R. Jimenez: Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam
Shridar Ganesan: Division of Medical Oncology, Rutgers Cancer Institute of New Jersey
Lodewyk F. A. Wessels: Oncode Institute
Jos Jonkers: Netherlands Cancer Institute

Nature, 2022, vol. 608, issue 7923, 609-617

Abstract: Abstract Somatic hotspot mutations and structural amplifications and fusions that affect fibroblast growth factor receptor 2 (encoded by FGFR2) occur in multiple types of cancer1. However, clinical responses to FGFR inhibitors have remained variable1–9, emphasizing the need to better understand which FGFR2 alterations are oncogenic and therapeutically targetable. Here we apply transposon-based screening10,11 and tumour modelling in mice12,13, and find that the truncation of exon 18 (E18) of Fgfr2 is a potent driver mutation. Human oncogenomic datasets revealed a diverse set of FGFR2 alterations, including rearrangements, E1–E17 partial amplifications, and E18 nonsense and frameshift mutations, each causing the transcription of E18-truncated FGFR2 (FGFR2ΔE18). Functional in vitro and in vivo examination of a compendium of FGFR2ΔE18 and full-length variants pinpointed FGFR2-E18 truncation as single-driver alteration in cancer. By contrast, the oncogenic competence of FGFR2 full-length amplifications depended on a distinct landscape of cooperating driver genes. This suggests that genomic alterations that generate stable FGFR2ΔE18 variants are actionable therapeutic targets, which we confirmed in preclinical mouse and human tumour models, and in a clinical trial. We propose that cancers containing any FGFR2 variant with a truncated E18 should be considered for FGFR-targeted therapies.

Date: 2022
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DOI: 10.1038/s41586-022-05066-5

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