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Hobor S, Al Bakir M, Hiley CT, Skrzypski M, Frankell AM, Bakker B, Watkins TBK, Markovets A, Dry JR, Brown AP, van der Aart J, van den Bos H, Spierings D, Oukrif D, Novelli M, Chakrabarti T, Rabinowitz AH, Ait Hassou L, Litière S, Kerr DL, Tan L, Kelly G, Moore DA, Renshaw MJ, Venkatesan S, Hill W, Huebner A, Martínez-Ruiz C, Black JRM, Wu W, Angelova M, McGranahan N, Downward J, Chmielecki J, Barrett C, Litchfield K, Chew SK, Blakely CM, de Bruin EC, Foijer F, Vousden KH, Bivona TG, Hynds RE, Kanu N, Zaccaria S, Grönroos E, Swanton C. Mixed responses to targeted therapy driven by chromosomal instability through p53 dysfunction and genome doubling. Nat Commun 2024; 15:4871. [PMID: 38871738 PMCID: PMC11176322 DOI: 10.1038/s41467-024-47606-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/28/2024] [Indexed: 06/15/2024] Open
Abstract
The phenomenon of mixed/heterogenous treatment responses to cancer therapies within an individual patient presents a challenging clinical scenario. Furthermore, the molecular basis of mixed intra-patient tumor responses remains unclear. Here, we show that patients with metastatic lung adenocarcinoma harbouring co-mutations of EGFR and TP53, are more likely to have mixed intra-patient tumor responses to EGFR tyrosine kinase inhibition (TKI), compared to those with an EGFR mutation alone. The combined presence of whole genome doubling (WGD) and TP53 co-mutations leads to increased genome instability and genomic copy number aberrations in genes implicated in EGFR TKI resistance. Using mouse models and an in vitro isogenic p53-mutant model system, we provide evidence that WGD provides diverse routes to drug resistance by increasing the probability of acquiring copy-number gains or losses relative to non-WGD cells. These data provide a molecular basis for mixed tumor responses to targeted therapy, within an individual patient, with implications for therapeutic strategies.
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Affiliation(s)
- Sebastijan Hobor
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Department of Medical Oncology, University College London Hospitals, 235 Euston Rd, Fitzrovia, London, NW1 2BU, UK
| | - Marcin Skrzypski
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Department of Medical Oncology, University College London Hospitals, 235 Euston Rd, Fitzrovia, London, NW1 2BU, UK
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, ul. Mariana Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Alexander M Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Bjorn Bakker
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, the Netherlands
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | - Jonathan R Dry
- Late Development, Oncology R&D, AstraZeneca, Boston, MA, USA
| | - Andrew P Brown
- Late Development, Oncology R&D, AstraZeneca, Boston, MA, USA
| | | | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, the Netherlands
| | - Diana Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, the Netherlands
| | - Dahmane Oukrif
- Research Department of Pathology, University College London Medical School, University Street, London, WC1E 6JJ, UK
| | - Marco Novelli
- Research Department of Pathology, University College London Medical School, University Street, London, WC1E 6JJ, UK
| | - Turja Chakrabarti
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - Adam H Rabinowitz
- Furlong Laboratory, EMBL Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Laila Ait Hassou
- European Organization for Research and Treatment of Cancer, Brussels, Belgium
| | - Saskia Litière
- Bioinformatics & Biostatistics; Francis Crick Institute, London, UK
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - Lisa Tan
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - Gavin Kelly
- Bioinformatics & Biostatistics; Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Matthew J Renshaw
- Advanced Light Microscopy, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Subramanian Venkatesan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Ariana Huebner
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | | | - Carl Barrett
- Late Development, Oncology R&D, AstraZeneca, Boston, MA, USA
| | - Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
| | - Elza C de Bruin
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, Groningen, 9713, the Netherlands
| | - Karen H Vousden
- p53 and Metabolism Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, CA, 94158, USA
- Chan-Zuckerberg Biohub, San Francisco, USA
| | - Robert E Hynds
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Rd, London, NW1 1AT, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.
- Department of Medical Oncology, University College London Hospitals, 235 Euston Rd, Fitzrovia, London, NW1 2BU, UK.
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