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Abbosh C, Birkbak NJ, Wilson GA, Jamal-Hanjani M, Constantin T, Salari R, Le Quesne J, Moore DA, Veeriah S, Rosenthal R, Marafioti T, Kirkizlar E, Watkins TBK, McGranahan N, Ward S, Martinson L, Riley J, Fraioli F, Al Bakir M, Grönroos E, Zambrana F, Endozo R, Bi WL, Fennessy FM, Sponer N, Johnson D, Laycock J, Shafi S, Czyzewska-Khan J, Rowan A, Chambers T, Matthews N, Turajlic S, Hiley C, Lee SM, Forster MD, Ahmad T, Falzon M, Borg E, Lawrence D, Hayward M, Kolvekar S, Panagiotopoulos N, Janes SM, Thakrar R, Ahmed A, Blackhall F, Summers Y, Hafez D, Naik A, Ganguly A, Kareht S, Shah R, Joseph L, Marie Quinn A, Crosbie PA, Naidu B, Middleton G, Langman G, Trotter S, Nicolson M, Remmen H, Kerr K, Chetty M, Gomersall L, Fennell DA, Nakas A, Rathinam S, Anand G, Khan S, Russell P, Ezhil V, Ismail B, Irvin-Sellers M, Prakash V, Lester JF, Kornaszewska M, Attanoos R, Adams H, Davies H, Oukrif D, Akarca AU, Hartley JA, Lowe HL, Lock S, Iles N, Bell H, Ngai Y, Elgar G, Szallasi Z, Schwarz RF, Herrero J, Stewart A, Quezada SA, Peggs KS, Van Loo P, Dive C, Lin CJ, Rabinowitz M, Aerts HJWL, Hackshaw A, Shaw JA, Zimmermann BG, Swanton C. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 2017; 545:446-451. [PMID: 28445469 PMCID: PMC5812436 DOI: 10.1038/nature22364] [Citation(s) in RCA: 1089] [Impact Index Per Article: 155.6] [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: 01/27/2017] [Accepted: 04/13/2017] [Indexed: 12/13/2022]
Abstract
The early detection of relapse following primary surgery for non-small-cell lung cancer and the characterization of emerging subclones, which seed metastatic sites, might offer new therapeutic approaches for limiting tumour recurrence. The ability to track the evolutionary dynamics of early-stage lung cancer non-invasively in circulating tumour DNA (ctDNA) has not yet been demonstrated. Here we use a tumour-specific phylogenetic approach to profile the ctDNA of the first 100 TRACERx (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy (Rx)) study participants, including one patient who was also recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and analyse the tumour-volume detection limit. Through blinded profiling of postoperative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients who are very likely to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastasis, providing a new approach for ctDNA-driven therapeutic studies.
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MESH Headings
- Biopsy/methods
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/surgery
- Cell Lineage/genetics
- Cell Tracking
- Clone Cells/metabolism
- Clone Cells/pathology
- DNA Mutational Analysis
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Disease Progression
- Drug Resistance, Neoplasm/genetics
- Early Detection of Cancer/methods
- Evolution, Molecular
- Humans
- Limit of Detection
- Lung Neoplasms/blood
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/surgery
- Multiplex Polymerase Chain Reaction
- Neoplasm Metastasis/diagnosis
- Neoplasm Metastasis/genetics
- Neoplasm Metastasis/pathology
- Neoplasm Recurrence, Local/diagnosis
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/pathology
- Postoperative Care/methods
- Reproducibility of Results
- Tumor Burden
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Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Gareth A Wilson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Tudor Constantin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Raheleh Salari
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - John Le Quesne
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - David A Moore
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Rachel Rosenthal
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Teresa Marafioti
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Eser Kirkizlar
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Thomas B K Watkins
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Luke Martinson
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Joan Riley
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Francesco Fraioli
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Maise Al Bakir
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eva Grönroos
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Francisco Zambrana
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Raymondo Endozo
- Department of Nuclear Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London, NW1 2BU, UK
| | - Wenya Linda Bi
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Fiona M Fennessy
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nicole Sponer
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Seema Shafi
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Justyna Czyzewska-Khan
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nik Matthews
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Tumour Profiling Unit Genomics Facility, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
| | - Samra Turajlic
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, 250 Euston Road, London NW1 2BU, UK
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - Elaine Borg
- Department of Pathology, University College London Hospitals, 21 University Street, London WC1 6JJ, UK
| | - David Lawrence
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Martin Hayward
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Shyam Kolvekar
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Nikolaos Panagiotopoulos
- Department of Cardiothoracic Surgery, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Sam M Janes
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, Rayne Building, University College London, 5 University Street, London WC1E 6JF, UK
| | - Ricky Thakrar
- Department of Respiratory Medicine, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, 235 Euston Road, Fitzrovia, London NW1 2BU, UK
| | - Fiona Blackhall
- Institute of Cancer Studies, University of Manchester, Oxford Road, Manchester M13 9PL, UK
- The Christie Hospital, Manchester M20 4BX, UK
| | | | - Dina Hafez
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Ashwini Naik
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Apratim Ganguly
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Stephanie Kareht
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | - Rajesh Shah
- Department of Cardiothoracic Surgery, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Leena Joseph
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Anne Marie Quinn
- Department of Pathology, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Phil A Crosbie
- North West Lung Centre, University Hospital South Manchester, Manchester M23 9LT, UK
| | - Babu Naidu
- Department of Thoracic Surgery, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham B15 2TT, UK. University College London Hospitals NHS Foundation Trust, London, UK
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham B15 2TT, UK
| | - Gerald Langman
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Simon Trotter
- Department of Cellular Pathology, Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Marianne Nicolson
- Department of Medical Oncology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Hardy Remmen
- Department of Cardiothoracic Surgery, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Keith Kerr
- Department of Pathology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZD, UK
| | - Mahendran Chetty
- Department of Respiratory Medicine, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Lesley Gomersall
- Department of Radiology, Aberdeen University Medical School and Aberdeen Royal Infirmary, Aberdeen AB25 2ZN, UK
| | - Dean A Fennell
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | - Apostolos Nakas
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Sridhar Rathinam
- Department of Thoracic Surgery, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Girija Anand
- Department of Radiotherapy, North Middlesex University Hospital, London N18 1QX, UK
| | - Sajid Khan
- Department of Respiratory Medicine, Royal Free Hospital, Pond Street, London NW3 2QG, UK
- Department of Respiratory Medicine, Barnet and Chase Farm Hospitals, Wellhouse Lane, Barnet EN5 3DJ, UK
| | - Peter Russell
- Department of Respiratory Medicine, The Princess Alexandra Hospital, Hamstel Road, Harlow CM20 1QX, UK
| | - Veni Ezhil
- Department of Clinical Oncology, St.Luke's Cancer Centre, Royal Surrey County Hospital, Guildford GU2 7XX, UK
| | - Babikir Ismail
- Department of Pathology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Melanie Irvin-Sellers
- Department of Respiratory Medicine, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Vineet Prakash
- Department of Radiology, Ashford and St. Peter's Hospital, Guildford Road, Chertsey, Surrey KT16 0PZ, UK
| | - Jason F Lester
- Department of Clinical Oncology, Velindre Hospital, Cardiff CF14 2TL, UK
| | | | - Richard Attanoos
- Department of Cellular Pathology, University Hospital of Wales and Cardiff University, Heath Park, Cardiff, UK
| | - Haydn Adams
- Department of Radiology, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Helen Davies
- Department of Respiratory Medicine, University Hospital Llandough, Cardiff CF64 2XX, UK
| | - Dahmane Oukrif
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Ayse U Akarca
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - John A Hartley
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Helen L Lowe
- University College London Experimental Cancer Medicine Centre GCLP Facility, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Sara Lock
- Department of Respiratory Medicine, The Whittington Hospital NHS Trust, London, N19 5NF, UK
| | - Natasha Iles
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Harriet Bell
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Yenting Ngai
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Greg Elgar
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Advanced Sequencing Facility, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Zoltan Szallasi
- Centre for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Lyngby, Denmark
- Computational Health Informatics Program (CHIP), Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, 1091 Budapest, Hungary
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Aengus Stewart
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Sergio A Quezada
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
| | - Karl S Peggs
- Cancer Immunology Unit, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Research Department of Haematology, University College Cancer Institute, London WC1E 6DD, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Human Genetics, University of Leuven, B-3000 Leuven, Belgium
| | - Caroline Dive
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Cancer Research UK Manchester Institute, University of Manchester, Wilmslow Road, Manchester M20 4BX, UK
| | - C Jimmy Lin
- Natera Inc., 201 Industrial Road, San Carlos, California 94070, USA
| | | | - Hugo J W L Aerts
- Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Medical School, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215-5450, USA
| | - Allan Hackshaw
- University College London, Cancer Research UK and UCL Cancer Trials Centre, London W1T 4TJ, UK
| | - Jacqui A Shaw
- Cancer Studies, University of Leicester, Leicester LE2 7LX, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence London and Manchester, University College London Cancer Institute, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD, UK
- Translational Cancer Therapeutics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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