Research Papers:

Genetic heterogeneity and actionable mutations in HER2-positive primary breast cancers and their brain metastases

Leticia De Mattos-Arruda _, Charlotte K.Y. Ng, Salvatore Piscuoglio, Maria Gonzalez-Cao, Raymond S. Lim, Maria R. De Filippo, Nicola Fusco, Anne M. Schultheis, Carolina Ortiz, Santiago Viteri, Alexandra Arias, Gabriel S. Macedo, Mafalda Oliveira, Patricia Gomez, Cristina Teixidó, Paolo Nuciforo, Vicente Peg, Cristina Saura, Santiago Ramon y Cajal, Francesc Tresserra Casas, Britta Weigelt, Javier Cortes, Joan Seoane and Jorge S. Reis-Filho

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Oncotarget. 2018; 9:20617-20630. https://doi.org/10.18632/oncotarget.25041

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Leticia De Mattos-Arruda1,2,3,*, Charlotte K. Y. Ng1,4,5,*, Salvatore Piscuoglio1,4, Maria Gonzalez-Cao6, Raymond S. Lim1, Maria R. De Filippo1, Nicola Fusco1, Anne M. Schultheis1, Carolina Ortiz2, Santiago Viteri6, Alexandra Arias2, Gabriel S. Macedo1, Mafalda Oliveira2, Patricia Gomez2, Cristina Teixidó6, Paolo Nuciforo2, Vicente Peg7, Cristina Saura2, Santiago Ramon y Cajal7, Francesc Tresserra Casas6, Britta Weigelt1, Javier Cortes2,3,8, Joan Seoane2,3,9 and Jorge S. Reis-Filho1,10

1Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA

2Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron University Hospital, Barcelona, Spain

3Universitat Autònoma de Barcelona, Barcelona, Spain

4Institute of Pathology, University Hospital Basel, Basel, Switzerland

5Department of Biomedicine, University of Basel, Basel, Switzerland

6Quirón Dexeus University Hospital, Barcelona, Spain

7Vall d'Hebron Institute of Research, Vall d'Hebron University Hospital, Barcelona, Spain

8Ramon y Cajal University Hospital, Madrid, Spain

9Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

10Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA

*These authors contributed equally to this work

Correspondence to:

Leticia De Mattos-Arruda, email: [email protected]

Jorge S. Reis-Filho, email: [email protected]

Keywords: metastatic breast cancer; HER2-positive; brain metastasis; actionable genetic alterations; personalized medicine

Received: January 16, 2018     Accepted: March 12, 2018     Published: April 17, 2018


Brain metastases constitute a challenge in the management of patients with HER2-positive breast cancer treated with anti-HER2 systemic therapies. Here we sought to define the repertoire of mutations private to or enriched for in HER2-positive brain metastases. Massively parallel sequencing targeting all exons of 254 genes frequently mutated in breast cancers and/or related to DNA repair was used to characterize the spatial and temporal heterogeneity of HER2-positive breast cancers and their brain metastases in six patients. Data were analyzed with state-of-the-art bioinformatics algorithms and selected mutations were validated with orthogonal methods. Spatial and temporal inter-lesion genetic heterogeneity was observed in the HER2-positive brain metastases from an index patient subjected to a rapid autopsy. Genetic alterations restricted to the brain metastases included mutations in cancer genes FGFR2, PIK3CA and ATR, homozygous deletion in CDKN2A and amplification in KRAS. Shifts in clonal composition and the acquisition of additional mutations in the progression from primary HER2-positive breast cancer to brain metastases following anti-HER2 therapy were investigated in additional five patients. Likely pathogenic mutations private to or enriched in the brain lesions affected cancer and clinically actionable genes, including ATR, BRAF, FGFR2, MAP2K4, PIK3CA, RAF1 and TP53. Changes in clonal composition and the acquisition of additional mutations in brain metastases may affect potentially actionable genes in HER2-positive breast cancers. Our observations have potential clinical implications, given that treatment decisions for patients with brain metastatic disease are still mainly based on biomarkers assessed in the primary tumor.

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