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Lefebvre C, Bachelot T, Filleron T, Pedrero M, Campone M, Soria JC, Massard C, Lévy C, Arnedos M, Lacroix-Triki M, Garrabey J, Boursin Y, Deloger M, Fu Y, Commo F, Scott V, Lacroix L, Dieci MV, Kamal M, Diéras V, Gonçalves A, Ferrerro JM, Romieu G, Vanlemmens L, Mouret Reynier MA, Théry JC, Le Du F, Guiu S, Dalenc F, Clapisson G, Bonnefoi H, Jimenez M, Le Tourneau C, André F. Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis. PLoS Med 2016; 13:e1002201. [PMID: 28027327 PMCID: PMC5189935 DOI: 10.1371/journal.pmed.1002201] [Citation(s) in RCA: 270] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/11/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Major advances have been achieved in the characterization of early breast cancer (eBC) genomic profiles. Metastatic breast cancer (mBC) is associated with poor outcomes, yet limited information is available on the genomic profile of this disease. This study aims to decipher mutational profiles of mBC using next-generation sequencing. METHODS AND FINDINGS Whole-exome sequencing was performed on 216 tumor-blood pairs from mBC patients who underwent a biopsy in the context of the SAFIR01, SAFIR02, SHIVA, or Molecular Screening for Cancer Treatment Optimization (MOSCATO) prospective trials. Mutational profiles from 772 primary breast tumors from The Cancer Genome Atlas (TCGA) were used as a reference for comparing primary and mBC mutational profiles. Twelve genes (TP53, PIK3CA, GATA3, ESR1, MAP3K1, CDH1, AKT1, MAP2K4, RB1, PTEN, CBFB, and CDKN2A) were identified as significantly mutated in mBC (false discovery rate [FDR] < 0.1). Eight genes (ESR1, FSIP2, FRAS1, OSBPL3, EDC4, PALB2, IGFN1, and AGRN) were more frequently mutated in mBC as compared to eBC (FDR < 0.01). ESR1 was identified both as a driver and as a metastatic gene (n = 22, odds ratio = 29, 95% CI [9-155], p = 1.2e-12) and also presented with focal amplification (n = 9) for a total of 31 mBCs with either ESR1 mutation or amplification, including 27 hormone receptor positive (HR+) and HER2 negative (HER2-) mBCs (19%). HR+/HER2- mBC presented a high prevalence of mutations on genes located on the mechanistic target of rapamycin (mTOR) pathway (TSC1 and TSC2) as compared to HR+/HER2- eBC (respectively 6% and 0.7%, p = 0.0004). Other actionable genes were more frequently mutated in HR+ mBC, including ERBB4 (n = 8), NOTCH3 (n = 7), and ALK (n = 7). Analysis of mutational signatures revealed a significant increase in APOBEC-mediated mutagenesis in HR+/HER2- metastatic tumors as compared to primary TCGA samples (p < 2e-16). The main limitations of this study include the absence of bone metastases and the size of the cohort, which might not have allowed the identification of rare mutations and their effect on survival. CONCLUSIONS This work reports the results of the analysis of the first large-scale study on mutation profiles of mBC. This study revealed genomic alterations and mutational signatures involved in the resistance to therapies, including actionable mutations.
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Affiliation(s)
| | - Thomas Bachelot
- Department of Medical Oncology, Centre Léon Bérard, Inserm U1052, Lyon, France
| | - Thomas Filleron
- Biostatistics Department, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | | | - Mario Campone
- Department of Medical Oncology, Institut de Cancérologie de l’Ouest, Nantes, France
| | - Jean-Charles Soria
- INSERM Unit U981, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
- Faculté de Médecine, Université Paris Sud, Kremlin-Bicêtre, France
- Drug Development Department (DITEP), Gustave Roussy, Villejuif, France
| | | | - Christelle Lévy
- Department of Medical Oncology, Centre François Baclesse, Caen, France
| | - Monica Arnedos
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | | | | | - Yannick Boursin
- Bioinformatics core facility, Gustave Roussy, Villejuif, France
| | - Marc Deloger
- Bioinformatics core facility, Gustave Roussy, Villejuif, France
| | - Yu Fu
- INSERM Unit U981, Gustave Roussy, Villejuif, France
| | | | | | - Ludovic Lacroix
- INSERM Unit U981, Gustave Roussy, Villejuif, France
- Department of Medical Biology and Pathology, Translational research laboratory and biobank, Gustave Roussy, Villejuif, France
| | - Maria Vittoria Dieci
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padua, Italy
- Medical Oncology 2, Veneto Institute of Oncology IOV—IRCCS, Padua, Italy
| | - Maud Kamal
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Véronique Diéras
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
| | - Anthony Gonçalves
- Department of Medical Oncology, Institut Paoli-Calmettes, Marseille, France
| | - Jean-Marc Ferrerro
- Department of Clinical Research, Centre Antoine Lacassagne, Nice, France
| | - Gilles Romieu
- Department of Medical Oncology, Institut du Cancer de Montpellier, Montpellier, France
| | | | | | | | - Fanny Le Du
- Department of Medical Oncology, Centre Eugène Marquis, Rennes, France
| | - Séverine Guiu
- Department of Medical Oncology, Centre Georges-François Leclerc, Dijon, France
| | - Florence Dalenc
- Department of Medical Oncology, Institut Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | | | - Hervé Bonnefoi
- Department of Medical Oncology, Institut Bergonié, Université de Bordeaux, INSERM U916, Bordeaux, France
| | | | - Christophe Le Tourneau
- Department of Medical Oncology, Institut Curie, Paris & Saint-Cloud, France
- EA7285, Versailles-Saint-Quentin-en-Yvelines University, Montigny-le-Bretonneux, France
| | - Fabrice André
- INSERM Unit U981, Gustave Roussy, Villejuif, France
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
- Faculté de Médecine, Université Paris Sud, Kremlin-Bicêtre, France
- * E-mail:
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