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Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis

Celine Lefebvre 1 Thomas Bachelot 2 Thomas Filleron 3 Marion Pedrero 1 Mario Campone 4 Jean-Charles Soria 1, 5, 6 Christophe Massard 5 Christelle Levy 7 Monica Arnedos 6 Magali Lacroix-Triki 1 Julie Garrabey 8 Yannick Boursin 9 Marc Deloger 9 Yu Fu 1 Frederic Commo 1 Véronique Scott 1 Ludovic Lacroix 1, 10 Maria Dieci 11, 12 Maud Kamal 13 Véronique Dieras 13 Anthony Gonçalves 14 Jean-Marc Ferrerro 15 Gilles Romieu 16 Laurence Vanlemmens 17 Marie-Ange Reynier 18 Jean-Christophe Théry 19 Fanny Le Du 20 Séverine Guiu 21, 22 Florence Dalenc 3, 23 Gilles Clapisson 24 Hervé Bonnefoi 25 Marta Jimenez 8 Christophe Le Tourneau 13, 26 Fabrice André 1, 6
1 U981 - Biomarqueurs prédictifs et nouvelles stratégies moléculaires en thérapeutique anticancéreuse
2 CRCL - Centre de Recherche en Cancérologie de Lyon
3 CRLCC Institut Claudius Regaud
4 ICO Nantes - Institut de cancérologie de l'Ouest - Nantes
5 DITEP - Département d’Innovation Thérapeutique et essais précoces [Gustave Roussy]
6 Département de médecine oncologique [Gustave Roussy]
7 CRLC François Baclesse - Centre Régional de Lutte contre le Cancer François Baclesse
8 R&D Unicancer [Paris]
9 Plateforme de Bioinformatique [Gustave Roussy]
AMMICa - Analyse moléculaire, modélisation et imagerie de la maladie cancéreuse
10 Département de biologie et pathologie médicales [Gustave Roussy]
11 Universita degli Studi di Padova
12 Veneto Institute of Oncology
13 Institut Curie
14 Institut Paoli-Calmettes
15 CRLCC Antoine Lacassagne
16 Département d'oncologie Médicale
17 Center Oscar Lambret
18 CRLCC Jean Perrin
19 CRLCC Henri Becquerel
20 CRLCC - CRLCC Eugène Marquis
21 Département d'oncologie médicale [Centre Georges-François Leclerc]
22 IRCM - U1194 Inserm - UM - Institut de Recherche en Cancérologie de Montpellier
23 IUCT Oncopole - UMR 1037 - Institut Universitaire du Cancer de Toulouse - Oncopole
24 Centre Léon Bérard [Lyon]
25 VINCO - Validation et identification de nouvelles cibles en oncologie
26 RISCQ - Risques cliniques et sécurité en santé des femmes et en santé périnatale
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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UNIV-MONTPELLIER | UNIV-TLSE3 | ICR | CGFL | BERGONIE | VALDAURELLE | CURIE | LAMBRET | CJP | BACLESSE | PAOLI_CALMETTES | LACASSAGNE | MARQUIS | PAPIN | ICO | GAUDUCHEAU | UVSQ | CNRS | FNCLCC | BECQUEREL | RISCQ | UNIV-LYON1 | BS | CRCL | IRCM | ISCC | PSL | UNIV-PARIS-SACLAY | SORBONNE-UNIVERSITE | SU-SCIENCES | COMUE-NORMANDIE | IGR | UDL

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Celine Lefebvre, Thomas Bachelot, Thomas Filleron, Marion Pedrero, Mario Campone, et al.. Mutational Profile of Metastatic Breast Cancers: A Retrospective Analysis. PLoS Medicine, Public Library of Science, 2016, 13 (12), pp.e1002201. ⟨10.1371/journal.pmed.1002201⟩. ⟨hal-02297451⟩

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