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Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024:OF1-OF24. [PMID: 38527495 DOI: 10.1158/2159-8290.cd-23-1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs.
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Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
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Ferrando L, Vingiani A, Garuti A, Vernieri C, Belfiore A, Agnelli L, Dagrada G, Ivanoiu D, Bonizzi G, Munzone E, Lippolis L, Dameri M, Ravera F, Colleoni M, Viale G, Magnani L, Ballestrero A, Zoppoli G, Pruneri G. ESR1 gene amplification and MAP3K mutations are selected during adjuvant endocrine therapies in relapsing Hormone Receptor-positive, HER2-negative breast cancer (HR+ HER2- BC). PLoS Genet 2023; 19:e1010563. [PMID: 36595552 PMCID: PMC9839248 DOI: 10.1371/journal.pgen.1010563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/13/2023] [Accepted: 12/08/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Previous studies have provided a comprehensive picture of genomic alterations in primary and metastatic Hormone Receptor (HR)-positive, Human Epidermal growth factor Receptor 2 (HER2)-negative breast cancer (HR+ HER2- BC). However, the evolution of the genomic landscape of HR+ HER2- BC during adjuvant endocrine therapies (ETs) remains poorly investigated. METHODS AND FINDINGS We performed a genomic characterization of surgically resected HR+ HER2- BC patients relapsing during or at the completion of adjuvant ET. Using a customized panel, we comprehensively evaluated gene mutations and copy number variation (CNV) in paired primary and metastatic specimens. After retrieval and quality/quantity check of tumor specimens from an original cohort of 204 cases, 74 matched tumor samples were successfully evaluated for DNA mutations and CNV analysis. Along with previously reported genomic alterations, including PIK3CA, TP53, CDH1, GATA3 and ESR1 mutations/deletions, we found that ESR1 gene amplification (confirmed by FISH) and MAP3K mutations were enriched in metastatic lesions as compared to matched primary tumors. These alterations were exclusively found in patients treated with adjuvant aromatase inhibitors or LHRH analogs plus tamoxifen, but not in patients treated with tamoxifen alone. Patients with tumors bearing MAP3K mutations in metastatic lesions had significantly worse distant relapse-free survival (hazard ratio [HR] 3.4, 95% CI 1.52-7.70, p value 0.003) and worse overall survival (HR 5.2, 95% CI 2.10-12.8, p-value < 0.001) independently of other clinically relevant patient- and tumor-related variables. CONCLUSIONS ESR1 amplification and activating MAP3K mutations are potential drivers of acquired resistance to adjuvant ETs employing estrogen deprivation in HR+ HER2- BC. MAP3K mutations are associated with worse prognosis in patients with metastatic disease.
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Affiliation(s)
| | - Andrea Vingiani
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Anna Garuti
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Claudio Vernieri
- Department of Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- IFOM, The FIRC Institute of Molecular Oncology, Milan, Italy
| | - Antonino Belfiore
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luca Agnelli
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Gianpaolo Dagrada
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Giuseppina Bonizzi
- Department of Pathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Elisabetta Munzone
- Division of Medical Senology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Luana Lippolis
- Division of Pathology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Dameri
- Department of Internal Medicine (DiMI), University of Genoa, Genova, Italy
| | - Francesco Ravera
- Department of Internal Medicine (DiMI), University of Genoa, Genova, Italy
| | - Marco Colleoni
- Division of Medical Senology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Giuseppe Viale
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Pathology, IEO European Institute of Oncology IRCCS, Milan, Italy
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Alberto Ballestrero
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Internal Medicine (DiMI), University of Genoa, Genova, Italy
| | - Gabriele Zoppoli
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
- Department of Internal Medicine (DiMI), University of Genoa, Genova, Italy
| | - Giancarlo Pruneri
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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Smith SL, Lones MA, Bedder M, Alty JE, Cosgrove J, Maguire RJ, Pownall ME, Ivanoiu D, Lyle C, Cording A, Elliott CJH. Computational approaches for understanding the diagnosis and treatment of Parkinson's disease. IET Syst Biol 2016; 9:226-33. [PMID: 26577157 DOI: 10.1049/iet-syb.2015.0030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This study describes how the application of evolutionary algorithms (EAs) can be used to study motor function in humans with Parkinson's disease (PD) and in animal models of PD. Human data is obtained using commercially available sensors via a range of non-invasive procedures that follow conventional clinical practice. EAs can then be used to classify human data for a range of uses, including diagnosis and disease monitoring. New results are presented that demonstrate how EAs can also be used to classify fruit flies with and without genetic mutations that cause Parkinson's by using measurements of the proboscis extension reflex. The case is made for a computational approach that can be applied across human and animal studies of PD and lays the way for evaluation of existing and new drug therapies in a truly objective way.
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Affiliation(s)
- Stephen L Smith
- Department of Electronics, University of York, Heslington, York Y010 5DD.
| | - Michael A Lones
- School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh EH14 4AS
| | - Matthew Bedder
- Department of Computer Science, University of York, Heslington, York Y010 5GW
| | - Jane E Alty
- Neurology Department, Leeds Teaching Hospitals NHS Trust, Leeds LS1 3EX
| | - Jeremy Cosgrove
- Neurology Department, Leeds Teaching Hospitals NHS Trust, Leeds LS1 3EX
| | - Richard J Maguire
- Department of Biomedical Science, University of Sheffield, Sheffield S10 2TN
| | | | - Diana Ivanoiu
- Department of Biology, University of York, Heslington, York Y010 5DD
| | - Camille Lyle
- Department of Biology, University of York, Heslington, York Y010 5DD
| | - Amy Cording
- Department of Biology, University of York, Heslington, York Y010 5DD
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