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Aftimos P, Oliveira M, Irrthum A, Fumagalli D, Sotiriou C, Gal-Yam EN, Robson ME, Ndozeng J, Di Leo A, Ciruelos EM, de Azambuja E, Viale G, Scheepers ED, Curigliano G, Bliss JM, Reis-Filho JS, Colleoni M, Balic M, Cardoso F, Albanell J, Duhem C, Marreaud S, Romagnoli D, Rojas B, Gombos A, Wildiers H, Guerrero-Zotano A, Hall P, Bonetti A, Larsson KF, Degiorgis M, Khodaverdi S, Greil R, Sverrisdóttir Á, Paoli M, Seyll E, Loibl S, Linderholm B, Zoppoli G, Davidson NE, Johannsson OT, Bedard PL, Loi S, Knox S, Cameron DA, Harbeck N, Montoya ML, Brandão M, Vingiani A, Caballero C, Hilbers FS, Yates LR, Benelli M, Venet D, Piccart MJ. Genomic and Transcriptomic Analyses of Breast Cancer Primaries and Matched Metastases in AURORA, the Breast International Group (BIG) Molecular Screening Initiative. Cancer Discov 2021; 11:2796-2811. [PMID: 34183353 PMCID: PMC9414283 DOI: 10.1158/2159-8290.cd-20-1647] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [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] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 04/05/2021] [Accepted: 06/11/2021] [Indexed: 02/01/2023]
Abstract
AURORA aims to study the processes of relapse in metastatic breast cancer (MBC) by performing multi-omics profiling on paired primary tumors and early-course metastases. Among 381 patients (primary tumor and metastasis pairs: 252 targeted gene sequencing, 152 RNA sequencing, 67 single nucleotide polymorphism arrays), we found a driver role for GATA1 and MEN1 somatic mutations. Metastases were enriched in ESR1, PTEN, CDH1, PIK3CA, and RB1 mutations; MDM4 and MYC amplifications; and ARID1A deletions. An increase in clonality was observed in driver genes such as ERBB2 and RB1. Intrinsic subtype switching occurred in 36% of cases. Luminal A/B to HER2-enriched switching was associated with TP53 and/or PIK3CA mutations. Metastases had lower immune score and increased immune-permissive cells. High tumor mutational burden correlated to shorter time to relapse in HR+/HER2- cancers. ESCAT tier I/II alterations were detected in 51% of patients and matched therapy was used in 7%. Integration of multi-omics analyses in clinical practice could affect treatment strategies in MBC. SIGNIFICANCE: The AURORA program, through the genomic and transcriptomic analyses of matched primary and metastatic samples from 381 patients with breast cancer, coupled with prospectively collected clinical data, identified genomic alterations enriched in metastases and prognostic biomarkers. ESCAT tier I/II alterations were detected in more than half of the patients.This article is highlighted in the In This Issue feature, p. 2659.
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Affiliation(s)
- Philippe Aftimos
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Mafalda Oliveira
- Medical Oncology Department, Vall d'Hebron University Hospital, Barcelona, Spain
| | | | | | - Christos Sotiriou
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | | | - Mark E Robson
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin Ndozeng
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | | | | | | | - Giuseppe Viale
- IEO, Istituto Europeo di Oncologia, IRCCS, and University of Milan, Milan, Italy
| | | | - Giuseppe Curigliano
- IEO, Istituto Europeo di Oncologia, IRCCS, and University of Milan, Milan, Italy
| | - Judith M Bliss
- The Institute of Cancer Research, London, United Kingdom
| | | | - Marco Colleoni
- IEO, Istituto Europeo di Oncologia, IRCCS, and University of Milan, Milan, Italy
| | | | - Fatima Cardoso
- Breast Unit, Champalimaud Clinical Center/Champalimaud Foundation, Lisbon, Portugal
| | - Joan Albanell
- Hospital del Mar - CIBERONC; IMIM, Barcelona; Pompeu Fabra University, Barcelona, Spain
| | - Caroline Duhem
- Centre Hospitalier Luxembourg, Luxembourg City, Luxembourg
| | | | | | - Beatriz Rojas
- CIOCC (Centro Integral Oncologico "Clara Campal"), Madrid, Spain
| | - Andrea Gombos
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | | | | | - Peter Hall
- University of Edinburgh Cancer Research Centre, Edinburgh, United Kingdom
| | - Andrea Bonetti
- Department of Oncology AZIENDA ULSS 9 Verona, Verona, Italy
| | | | | | - Silvia Khodaverdi
- Sana Klinikum Offenbach, Klinik für Gynaekologie und Geburtshilfe, Offenbach, Germany
| | - Richard Greil
- Paracelsus Medical University Salzburg, Salzburg Cancer Research Institute-CCCIT and Cancer Cluster Salzburg, Salzburg, Austria
| | | | | | - Ethel Seyll
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | | | | | - Gabriele Zoppoli
- Università degli Studi di Genova and IRCCS Ospedale Policlinico San Martino, San Martino, Italy
| | - Nancy E Davidson
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, Washington
| | | | | | - Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Susan Knox
- Europa Donna- The European Breast Cancer Coalition, Milan, Italy
| | - David A Cameron
- University of Edinburgh Cancer Research Centre, Edinburgh, United Kingdom
| | - Nadia Harbeck
- Breast Center, LMU University Hospital, Munich, Germany, and West German Study Group, Moenchengladbach, Germany
| | | | - Mariana Brandão
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Andrea Vingiani
- Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | | | - Lucy R Yates
- Wellcome Trust Sanger Institute, London, United Kingdom
| | | | - David Venet
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium
| | - Martine J Piccart
- Institut Jules Bordet - Université Libre de Bruxelles, Brussels, Belgium.
- Breast International Group, Brussels, Belgium
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