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Shawe-Taylor M, Greenwood D, Hobbs A, Dowgier G, Penn R, Sanderson T, Stevenson-Leggett P, Bazire J, Harvey R, Libri V, Kassiotis G, Gamblin S, Lewis NS, Williams B, Swanton C, Gandhi S, Carr EJ, Wu MY, Bauer DLV, Wall EC. Divergent performance of vaccines in the UK autumn 2023 COVID-19 booster campaign. Lancet 2024; 403:1133-1136. [PMID: 38484752 DOI: 10.1016/s0140-6736(24)00316-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/25/2024]
Affiliation(s)
- Marianne Shawe-Taylor
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | | | | | | | | | | | | | | | - Ruth Harvey
- Worldwide Influenza Centre, London NW1 1AT, UK
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - George Kassiotis
- The Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | | | | | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Edward J Carr
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Mary Y Wu
- The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype 2 Consortium (G2P2-UK), UK
| | - Emma C Wall
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK.
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2
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Townsley H, Gahir J, Russell TW, Greenwood D, Carr EJ, Dyke M, Adams L, Miah M, Clayton B, Smith C, Miranda M, Mears HV, Bailey C, Black JRM, Fowler AS, Crawford M, Wilkinson K, Hutchinson M, Harvey R, O’Reilly N, Kelly G, Goldstone R, Beale R, Papineni P, Corrah T, Gilson R, Caidan S, Nicod J, Gamblin S, Kassiotis G, Libri V, Williams B, Gandhi S, Kucharski AJ, Swanton C, Bauer DLV, Wall EC. COVID-19 in non-hospitalised adults caused by either SARS-CoV-2 sub-variants Omicron BA.1, BA.2, BA.4/5 or Delta associates with similar illness duration, symptom severity and viral kinetics, irrespective of vaccination history. PLoS One 2024; 19:e0294897. [PMID: 38512960 PMCID: PMC10956747 DOI: 10.1371/journal.pone.0294897] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 11/11/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND SARS-CoV-2 variant Omicron rapidly evolved over 2022, causing three waves of infection due to sub-variants BA.1, BA.2 and BA.4/5. We sought to characterise symptoms and viral loads over the course of COVID-19 infection with these sub-variants in otherwise-healthy, vaccinated, non-hospitalised adults, and compared data to infections with the preceding Delta variant of concern (VOC). METHODS In a prospective, observational cohort study, healthy vaccinated UK adults who reported a positive polymerase chain reaction (PCR) or lateral flow test, self-swabbed on alternate weekdays until day 10. We compared participant-reported symptoms and viral load trajectories between infections caused by VOCs Delta and Omicron (sub-variants BA.1, BA.2 or BA.4/5), and tested for relationships between vaccine dose, symptoms and PCR cycle threshold (Ct) as a proxy for viral load using Chi-squared (χ2) and Wilcoxon tests. RESULTS 563 infection episodes were reported among 491 participants. Across infection episodes, there was little variation in symptom burden (4 [IQR 3-5] symptoms) and duration (8 [IQR 6-11] days). Whilst symptom profiles differed among infections caused by Delta compared to Omicron sub-variants, symptom profiles were similar between Omicron sub-variants. Anosmia was reported more frequently in Delta infections after 2 doses compared with Omicron sub-variant infections after 3 doses, for example: 42% (25/60) of participants with Delta infection compared to 9% (6/67) with Omicron BA.4/5 (χ2 P < 0.001; OR 7.3 [95% CI 2.7-19.4]). Fever was less common with Delta (20/60 participants; 33%) than Omicron BA.4/5 (39/67; 58%; χ2 P = 0.008; OR 0.4 [CI 0.2-0.7]). Amongst infections with an Omicron sub-variants, symptoms of coryza, fatigue, cough and myalgia predominated. Viral load trajectories and peaks did not differ between Delta, and Omicron, irrespective of symptom severity (including asymptomatic participants), VOC or vaccination status. PCR Ct values were negatively associated with time since vaccination in participants infected with BA.1 (β = -0.05 (CI -0.10-0.01); P = 0.031); however, this trend was not observed in BA.2 or BA.4/5 infections. CONCLUSION Our study emphasises both the changing symptom profile of COVID-19 infections in the Omicron era, and ongoing transmission risk of Omicron sub-variants in vaccinated adults. TRIAL REGISTRATION NCT04750356.
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Affiliation(s)
- Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Joshua Gahir
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | | | - Matala Dyke
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Murad Miah
- The Francis Crick Institute, London, United Kingdom
| | | | - Callie Smith
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
| | - James R. M. Black
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | | | | | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | | | - Gavin Kelly
- The Francis Crick Institute, London, United Kingdom
| | | | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, United Kingdom
| | - Richard Gilson
- Camden and North West London NHS Community Trust, London, United Kingdom
| | - Simon Caidan
- The Francis Crick Institute, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - George Kassiotis
- The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, St Mary’s Hospital, Imperial College London, London, United Kingdom
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- Worldwide Influenza Centre, The Francis Crick Institute, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
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3
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Pan X, AbdulJabbar K, Coelho-Lima J, Grapa AI, Zhang H, Cheung AHK, Baena J, Karasaki T, Wilson CR, Sereno M, Veeriah S, Aitken SJ, Hackshaw A, Nicholson AG, Jamal-Hanjani M, Swanton C, Yuan Y, Le Quesne J, Moore DA. The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma. Nat Cancer 2024; 5:347-363. [PMID: 38200244 PMCID: PMC10899116 DOI: 10.1038/s43018-023-00694-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 11/21/2023] [Indexed: 01/12/2024]
Abstract
The introduction of the International Association for the Study of Lung Cancer grading system has furthered interest in histopathological grading for risk stratification in lung adenocarcinoma. Complex morphology and high intratumoral heterogeneity present challenges to pathologists, prompting the development of artificial intelligence (AI) methods. Here we developed ANORAK (pyrAmid pooliNg crOss stReam Attention networK), encoding multiresolution inputs with an attention mechanism, to delineate growth patterns from hematoxylin and eosin-stained slides. In 1,372 lung adenocarcinomas across four independent cohorts, AI-based grading was prognostic of disease-free survival, and further assisted pathologists by consistently improving prognostication in stage I tumors. Tumors with discrepant patterns between AI and pathologists had notably higher intratumoral heterogeneity. Furthermore, ANORAK facilitates the morphological and spatial assessment of the acinar pattern, capturing acinus variations with pattern transition. Collectively, our AI method enabled the precision quantification and morphology investigation of growth patterns, reflecting intratumoral histological transitions in lung adenocarcinoma.
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Affiliation(s)
- Xiaoxi Pan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Jose Coelho-Lima
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Anca-Ioana Grapa
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Hanyun Zhang
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Alvin Ho Kwan Cheung
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Juvenal Baena
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- AstraZeneca Computational Pathology, Munich, Germany
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Claire Rachel Wilson
- Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- Hope Against Cancer and Leicester Experimental Cancer Medicine Centre, Leicester, UK
| | - Marco Sereno
- Institute for Lung Health, NIHR Leicester Biomedical Research Centre, Leicester, UK
| | - Selvaraju Veeriah
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sarah J Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - John Le Quesne
- Molecular Pathology, School of Cancer Sciences, University of Glasgow, Glasgow, UK.
- Cancer Research UK Beatson Institute of Cancer Research, Glasgow, UK.
- NHS Greater Glasgow and Clyde, Glasgow, UK.
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Cellular Pathology, University College London Hospitals, London, UK.
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4
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Sweeney CJ, Hainsworth JD, Bose R, Burris HA, Kurzrock R, Swanton C, Friedman CF, Spigel DR, Szado T, Schulze K, Price R, Malato J, Lo AA, Levy J, Wang Y, Yu W, Meric-Bernstam F. MyPathway Human Epidermal Growth Factor Receptor 2 Basket Study: Pertuzumab + Trastuzumab Treatment of a Tissue-Agnostic Cohort of Patients With Human Epidermal Growth Factor Receptor 2-Altered Advanced Solid Tumors. J Clin Oncol 2024; 42:258-265. [PMID: 37793085 PMCID: PMC10824375 DOI: 10.1200/jco.22.02636] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 05/31/2023] [Accepted: 08/01/2023] [Indexed: 10/06/2023] Open
Abstract
Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.The MyPathway multiple-basket study (ClinicalTrials.gov identifier: NCT02091141) is evaluating targeted therapies in nonindicated tumors with relevant molecular alterations. We assessed pertuzumab + trastuzumab in a tissue-agnostic cohort of adult patients with human epidermal growth factor receptor 2 (HER2)-amplified and/or -overexpressed and/or -mutated solid tumors. The primary end point was objective response rate (ORR); secondary end points included survival and safety. At data cutoff (March 2022), 346 patients with HER2 amplification and/or overexpression with/without HER2 mutations (n = 263), or HER2 mutations alone (n = 83) had been treated. Patients with HER2 amplification and/or overexpression had an ORR of 25.9% (68/263, 95% CI, 20.7 to 31.6), including five complete responses (urothelial [n = 2], salivary gland [n = 2], and colon [n = 1] cancers). Activity was higher in those with wild-type (ORR, 28.1%) versus mutated KRAS (ORR, 7.1%). Among patients with HER2 amplification, ORR was numerically higher in patients with immunohistochemistry (IHC) 3+ (41.0%; 32/78) or 2+ (21.9%; 7/32), versus 1+ (8.3%; 1/12) or no expression (0%; 0/20). In patients with HER2 mutations alone, ORR was 6.0% (5/83, 95% CI, 2.0 to 13.5). Pertuzumab + trastuzumab showed activity in various HER2-amplified and/or -overexpressed tumors with wild-type KRAS, with the range of activity dependent on tumor type, but had limited activity in the context of KRAS mutations, HER2 mutations alone, or 0-1+ HER2 expression.
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Affiliation(s)
- Christopher J. Sweeney
- South Australian Immunogenomics Cancer Institute, University of Adelaide, Adelaide, Australia
| | - John D. Hainsworth
- Sarah Cannon Research Institute, Nashville, TN
- Tennessee Oncology, PLLC, Nashville, TN
| | - Ron Bose
- Washington University School of Medicine, St Louis, MO
| | - Howard A. Burris
- Sarah Cannon Research Institute, Nashville, TN
- Tennessee Oncology, PLLC, Nashville, TN
| | | | - Charles Swanton
- Francis Crick Institute, London, United Kingdom
- UCL Hospitals, London, United Kingdom
| | - Claire F. Friedman
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Medical College at Cornell University, New York, NY
| | - David R. Spigel
- Sarah Cannon Research Institute, Nashville, TN
- Tennessee Oncology, PLLC, Nashville, TN
| | | | | | | | | | - Amy A. Lo
- Genentech, Inc, South San Francisco, CA
| | | | - Yong Wang
- Genentech, Inc, South San Francisco, CA
| | - Wei Yu
- Genentech, Inc, South San Francisco, CA
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5
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Grigoriadis K, Huebner A, Bunkum A, Colliver E, Frankell AM, Hill MS, Thol K, Birkbak NJ, Swanton C, Zaccaria S, McGranahan N. CONIPHER: a computational framework for scalable phylogenetic reconstruction with error correction. Nat Protoc 2024; 19:159-183. [PMID: 38017136 DOI: 10.1038/s41596-023-00913-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 08/24/2023] [Indexed: 11/30/2023]
Abstract
Intratumor heterogeneity provides the fuel for the evolution and selection of subclonal tumor cell populations. However, accurate inference of tumor subclonal architecture and reconstruction of tumor evolutionary histories from bulk DNA sequencing data remains challenging. Frequently, sequencing and alignment artifacts are not fully filtered out from cancer somatic mutations, and errors in the identification of copy number alterations or complex evolutionary events (e.g., mutation losses) affect the estimated cellular prevalence of mutations. Together, such errors propagate into the analysis of mutation clustering and phylogenetic reconstruction. In this Protocol, we present a new computational framework, CONIPHER (COrrecting Noise In PHylogenetic Evaluation and Reconstruction), that accurately infers subclonal structure and phylogenetic relationships from multisample tumor sequencing, accounting for both copy number alterations and mutation errors. CONIPHER has been used to reconstruct subclonal architecture and tumor phylogeny from multisample tumors with high-depth whole-exome sequencing from the TRACERx421 dataset, as well as matched primary-metastatic cases. CONIPHER outperforms similar methods on simulated datasets, and in particular scales to a large number of tumor samples and clones, while completing in under 1.5 h on average. CONIPHER enables automated phylogenetic analysis that can be effectively applied to large sequencing datasets generated with different technologies. CONIPHER can be run with a basic knowledge of bioinformatics and R and bash scripting languages.
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Affiliation(s)
- Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Lab, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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6
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Carr EJ, Dowgier G, Greenwood D, Herman LS, Hobbs A, Ragno M, Stevenson-Leggett P, Gahir J, Townsley H, Harvey R, Bailey C, Fowler AS, Miah M, Smith C, Miranda M, Bawumia P, Mears HV, Adams L, Hatipoglu E, O'Reilly N, Warchal S, Sawyer C, Ambrose K, Strange A, Kelly G, Beale R, Papineni P, Corrah T, Gilson R, Gamblin S, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Bauer DLV, Wall E, Wu MY. SARS-CoV-2 mucosal neutralising immunity after vaccination. Lancet Infect Dis 2024; 24:e4-e5. [PMID: 38070528 DOI: 10.1016/s1473-3099(23)00705-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/30/2023] [Accepted: 11/08/2023] [Indexed: 12/24/2023]
Affiliation(s)
- Edward J Carr
- UCL Department of Renal Medicine, Royal Free Hospital, Rowland Hill Street, London, UK; The Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | | | | | - Joshua Gahir
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | | | - Ruth Harvey
- Worldwide Influenza Centre, London NW1 1AT, UK
| | | | | | - Murad Miah
- The Francis Crick Institute, London NW1 1AT, UK
| | | | | | | | | | - Lorin Adams
- Worldwide Influenza Centre, London NW1 1AT, UK
| | - Emine Hatipoglu
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | | | | | | | | | - Amy Strange
- The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- The Francis Crick Institute, London NW1 1AT, UK
| | - Rupert Beale
- The Francis Crick Institute, London NW1 1AT, UK; The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype UK National Virology Consortium, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and North West London NHS Foundation Trust, London, UK; University College London, London, UK
| | | | - George Kassiotis
- The Francis Crick Institute, London NW1 1AT, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | - Vincenzo Libri
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK; University College London, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - David L V Bauer
- The Francis Crick Institute, London NW1 1AT, UK; Genotype-to-Phenotype UK National Virology Consortium, London, UK
| | - Emma Wall
- The Francis Crick Institute, London NW1 1AT, UK; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - Mary Y Wu
- COVID Surveillance Unit, London NW1 1AT, UK; The Francis Crick Institute, London NW1 1AT, UK.
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7
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Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman LAC, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DLV, Wall EC, Kucharski AJ. Combined analyses of within-host SARS-CoV-2 viral kinetics and information on past exposures to the virus in a human cohort identifies intrinsic differences of Omicron and Delta variants. PLoS Biol 2024; 22:e3002463. [PMID: 38289907 PMCID: PMC10826969 DOI: 10.1371/journal.pbio.3002463] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 12/07/2023] [Indexed: 02/01/2024] Open
Abstract
The emergence of successive Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) during 2020 to 2022, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics-such as varying levels of immunity-can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform Coronavirus Disease 2019 (COVID-19) planning and response and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both interindividual variation in Ct values and complex host characteristics-such as vaccination status, exposure history, and age-we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least 5 prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs. Trial Registration: The Legacy study is a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening for SARS-CoV-2 at University College London Hospitals or at the Francis Crick Institute (NCT04750356) (22,23). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469). The Legacy study was approved by London Camden and Kings Cross Health Research Authority Research and Ethics committee (IRAS number 286469) and is sponsored by University College London Hospitals. Written consent was given by all participants.
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Affiliation(s)
- Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Hermaleigh Townsley
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joel Hellewell
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, United Kingdom
| | - Edward J. Carr
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Lloyd A. C. Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Lancaster University, Bailrigg, Lancaster, United Kingdom
| | - Rachael Pung
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | | | - Lorin Adams
- The Francis Crick Institute, London, United Kingdom
| | - Chris Bailey
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | | | - Ruth Harvey
- The Francis Crick Institute, London, United Kingdom
| | | | | | - Yenting Ngai
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Jerome Nicod
- The Francis Crick Institute, London, United Kingdom
| | | | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- University College London, London, United Kingdom
| | - Sonia Gandhi
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Charles Swanton
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
| | - Rupert Beale
- The Francis Crick Institute, London, United Kingdom
- University College London, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
| | - David L. V. Bauer
- The Francis Crick Institute, London, United Kingdom
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK), London, United Kingdom
| | - Emma C. Wall
- The Francis Crick Institute, London, United Kingdom
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, United Kingdom
- University College London, London, United Kingdom
| | - Adam J. Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
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8
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Caswell DR, Gui P, Mayekar MK, Law EK, Pich O, Bailey C, Boumelha J, Kerr DL, Blakely CM, Manabe T, Martinez-Ruiz C, Bakker B, De Dios Palomino Villcas J, I Vokes N, Dietzen M, Angelova M, Gini B, Tamaki W, Allegakoen P, Wu W, Humpton TJ, Hill W, Tomaschko M, Lu WT, Haderk F, Al Bakir M, Nagano A, Gimeno-Valiente F, de Carné Trécesson S, Vendramin R, Barbè V, Mugabo M, Weeden CE, Rowan A, McCoach CE, Almeida B, Green M, Gomez C, Nanjo S, Barbosa D, Moore C, Przewrocka J, Black JRM, Grönroos E, Suarez-Bonnet A, Priestnall SL, Zverev C, Lighterness S, Cormack J, Olivas V, Cech L, Andrews T, Rule B, Jiao Y, Zhang X, Ashford P, Durfee C, Venkatesan S, Temiz NA, Tan L, Larson LK, Argyris PP, Brown WL, Yu EA, Rotow JK, Guha U, Roper N, Yu J, Vogel RI, Thomas NJ, Marra A, Selenica P, Yu H, Bakhoum SF, Chew SK, Reis-Filho JS, Jamal-Hanjani M, Vousden KH, McGranahan N, Van Allen EM, Kanu N, Harris RS, Downward J, Bivona TG, Swanton C. The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance. Nat Genet 2024; 56:60-73. [PMID: 38049664 PMCID: PMC10786726 DOI: 10.1038/s41588-023-01592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/25/2023] [Indexed: 12/06/2023]
Abstract
In this study, the impact of the apolipoprotein B mRNA-editing catalytic subunit-like (APOBEC) enzyme APOBEC3B (A3B) on epidermal growth factor receptor (EGFR)-driven lung cancer was assessed. A3B expression in EGFR mutant (EGFRmut) non-small-cell lung cancer (NSCLC) mouse models constrained tumorigenesis, while A3B expression in tumors treated with EGFR-targeted cancer therapy was associated with treatment resistance. Analyses of human NSCLC models treated with EGFR-targeted therapy showed upregulation of A3B and revealed therapy-induced activation of nuclear factor kappa B (NF-κB) as an inducer of A3B expression. Significantly reduced viability was observed with A3B deficiency, and A3B was required for the enrichment of APOBEC mutation signatures, in targeted therapy-treated human NSCLC preclinical models. Upregulation of A3B was confirmed in patients with NSCLC treated with EGFR-targeted therapy. This study uncovers the multifaceted roles of A3B in NSCLC and identifies A3B as a potential target for more durable responses to targeted cancer therapy.
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Affiliation(s)
- Deborah R Caswell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
| | - Philippe Gui
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Manasi K Mayekar
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Emily K Law
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - D Lucas Kerr
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tadashi Manabe
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Carlos Martinez-Ruiz
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Bjorn Bakker
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Natalie I Vokes
- Department of Thoracic and Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michelle Dietzen
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Beatrice Gini
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Whitney Tamaki
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Paul Allegakoen
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Timothy J Humpton
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
- CRUK Beatson Institute, Glasgow, UK
- Glasgow Caledonian University, Glasgow, UK
| | - William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mona Tomaschko
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Wei-Ting Lu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Franziska Haderk
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ai Nagano
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | | | - Roberto Vendramin
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Vittorio Barbè
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Miriam Mugabo
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Clare E Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Bruna Almeida
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College London, London, UK
| | - Mary Green
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Carlos Gomez
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Shigeki Nanjo
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Dora Barbosa
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chris Moore
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Joanna Przewrocka
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - James R M Black
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alejandro Suarez-Bonnet
- Experimental Histopathology, The Francis Crick Institute, London, UK
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Simon L Priestnall
- Experimental Histopathology, The Francis Crick Institute, London, UK
- Department of Pathobiology & Population Sciences, The Royal Veterinary College, London, UK
| | - Caroline Zverev
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - Scott Lighterness
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - James Cormack
- Biological Research Facility, The Francis Crick Institute, London, UK
| | - Victor Olivas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lauren Cech
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Trisha Andrews
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Paul Ashford
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Cameron Durfee
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Subramanian Venkatesan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nuri Alpay Temiz
- Institute for Health Informatics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Lisa Tan
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lindsay K Larson
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Prokopios P Argyris
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
- School of Dentistry, University of Minnesota, Minneapolis, MN, USA
- College of Dentistry, Ohio State University, Columbus, OH, USA
| | - William L Brown
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Elizabeth A Yu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Sutter Health Palo Alto Medical Foundation, Department of Pulmonary and Critical Care, Mountain View, CA, USA
| | - Julia K Rotow
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Udayan Guha
- Thoracic and GI Malignancies Branch, NCI, NIH, Bethesda, MD, USA
- NextCure Inc., Beltsville, MD, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Johnny Yu
- Biomedical Sciences Program, University of California, San Francisco, San Francisco, CA, USA
| | - Rachel I Vogel
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN, USA
| | - Nicholas J Thomas
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Antonio Marra
- Division of Early Drug Development for Innovative Therapy, European Institute of Oncology IRCCS, Milan, Italy
| | - Pier Selenica
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Helena Yu
- Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Medicine, Weill Cornell College of Medicine, New York City, NY, USA
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
| | - Su Kit Chew
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Karen H Vousden
- p53 and Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London, Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Eliezer M Van Allen
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Reuben S Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Trever G Bivona
- Departments of Medicine and Cellular and Molecular Pharmacology, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
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9
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Greenwood HE, Edwards RS, Tyrrell WE, Barber AR, Baark F, Tanc M, Khalil E, Falzone A, Ward NP, DeBlasi JM, Torrente L, Pearce DR, Firth G, Smith LM, Timmermand OV, Huebner A, George ME, Swanton C, Hynds RE, DeNicola GM, Witney TH. Imaging the master regulator of the antioxidant response in non-small cell lung cancer with positron emission tomography. bioRxiv 2023:2023.12.16.572007. [PMID: 38168428 PMCID: PMC10760199 DOI: 10.1101/2023.12.16.572007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Mutations in the NRF2-KEAP1 pathway are common in non-small cell lung cancer (NSCLC) and confer broad-spectrum therapeutic resistance, leading to poor outcomes. The cystine/glutamate antiporter, system xc-, is one of the >200 cytoprotective proteins controlled by NRF2, which can be non-invasively imaged by (S)-4-(3-18F-fluoropropyl)-l-glutamate ([18F]FSPG) positron emission tomography (PET). Through genetic and pharmacologic manipulation, we show that [18F]FSPG provides a sensitive and specific marker of NRF2 activation in advanced preclinical models of NSCLC. We validate imaging readouts with metabolomic measurements of system xc- activity and their coupling to intracellular glutathione concentration. A redox gene signature was measured in patients from the TRACERx 421 cohort, suggesting an opportunity for patient stratification prior to imaging. Furthermore, we reveal that system xc- is a metabolic vulnerability that can be therapeutically targeted for sustained tumour growth suppression in aggressive NSCLC. Our results establish [18F]FSPG as predictive marker of therapy resistance in NSCLC and provide the basis for the clinical evaluation of both imaging and therapeutic agents that target this important antioxidant pathway.
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Affiliation(s)
- Hannah E. Greenwood
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Richard S. Edwards
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Will E. Tyrrell
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Abigail R. Barber
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Friedrich Baark
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Muhammet Tanc
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Eman Khalil
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Aimee Falzone
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Nathan P. Ward
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Janine M. DeBlasi
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Laura Torrente
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - David R. Pearce
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, WC1E 6DD, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - George Firth
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Lydia M. Smith
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Oskar Vilhelmsson Timmermand
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Ariana Huebner
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, WC1E 6DD, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Madeleine E. George
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
| | - Charles Swanton
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, WC1E 6DD, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Robert E. Hynds
- CRUK Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, WC1E 6DD, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, UK
| | - Gina M. DeNicola
- Department of Metabolism and Physiology, H. Lee Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Timothy H. Witney
- School of Biomedical Engineering & Imaging Sciences, King’s College London, St Thomas’ Hospital, London, SE1 7EH, UK
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10
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O'Brien H, Salm M, Morton L, Szukszto M, O'Farrell F, Boulton C, Becker PD, Samuels Y, Swanton C, Mansour MR, Reker Hadrup S, Quezada SA. Breaking the performance ceiling for neoantigen immunogenicity prediction. Nat Cancer 2023; 4:1618-1621. [PMID: 38102360 DOI: 10.1038/s43018-023-00675-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Affiliation(s)
| | - Max Salm
- Achilles Therapeutics Ltd, London, UK.
| | | | - Maciej Szukszto
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Charlotte Boulton
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | | | | | - Marc R Mansour
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | | | - Sergio A Quezada
- Achilles Therapeutics Ltd, London, UK.
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK.
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11
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Usaite I, Biswas D, Dijkstra K, Watkins TB, Pich O, Puttick C, Angelova M, Thakkar K, Hiley C, Birkbak N, Kok M, Zaccaria S, Wu Y, Litchfield K, Swanton C, Kanu N. Quantifying the impact of immunotherapy on RNA dynamics in cancer. J Immunother Cancer 2023; 11:e007870. [PMID: 37914385 PMCID: PMC10626770 DOI: 10.1136/jitc-2023-007870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/03/2023] Open
Abstract
BACKGROUND Checkpoint inhibitor (CPI) immunotherapies have provided durable clinical responses across a range of solid tumor types for some patients with cancer. Nonetheless, response rates to CPI vary greatly between cancer types. Resolving intratumor transcriptomic changes induced by CPI may improve our understanding of the mechanisms of sensitivity and resistance. METHODS We assembled a cohort of longitudinal pre-therapy and on-therapy samples from 174 patients treated with CPI across six cancer types by leveraging transcriptomic sequencing data from five studies. RESULTS Meta-analyses of published RNA markers revealed an on-therapy pattern of immune reinvigoration in patients with breast cancer, which was not discernible pre-therapy, providing biological insight into the impact of CPI on the breast cancer immune microenvironment. We identified 98 breast cancer-specific correlates of CPI response, including 13 genes which are known IO targets, such as toll-like receptors TLR1, TLR4, and TLR8, that could hold potential as combination targets for patients with breast cancer receiving CPI treatment. Furthermore, we demonstrate that a subset of response genes identified in breast cancer are already highly expressed pre-therapy in melanoma, and additionally we establish divergent RNA dynamics between breast cancer and melanoma following CPI treatment, which may suggest distinct immune microenvironments between the two cancer types. CONCLUSIONS Overall, delineating longitudinal RNA dynamics following CPI therapy sheds light on the mechanisms underlying diverging response trajectories, and identifies putative targets for combination therapy.
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Affiliation(s)
- Ieva Usaite
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Krijn Dijkstra
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Oncology and Immunology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Thomas Bk Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Krupa Thakkar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Crispin Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Nicolai Birkbak
- Department of Molecular Medicine, Aarhus Universitet, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus Universitet, Aarhus, Denmark
| | - Marleen Kok
- Division of Tumor Biology & Immunology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Yin Wu
- Department of Medical Oncology, Guy's and St. Thomas' NHS Foundation Trust, London, UK
- Peter Gorer Department of Immunobiology and Centre for Inflammation Biology and Cancer Immunology, King's College London, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
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12
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Aldea M, Bernard E, Swanton C, Andre F. Placing the patient at the heart of discovery science. Eur J Cancer 2023; 193:113306. [PMID: 37742469 DOI: 10.1016/j.ejca.2023.113306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 08/18/2023] [Indexed: 09/26/2023]
Affiliation(s)
- Mihaela Aldea
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Paris Saclay University, Kremlin-Bicetre, France
| | - Elsa Bernard
- Department of Computational Biology, Gustave Roussy, Villejuif, France; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK
| | - Fabrice Andre
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Paris Saclay University, Kremlin-Bicetre, France.
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13
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Ghorani E, Swanton C, Quezada SA. Cancer cell-intrinsic mechanisms driving acquired immune tolerance. Immunity 2023; 56:2270-2295. [PMID: 37820584 DOI: 10.1016/j.immuni.2023.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023]
Abstract
Immune evasion is a hallmark of cancer, enabling tumors to survive contact with the host immune system and evade the cycle of immune recognition and destruction. Here, we review the current understanding of the cancer cell-intrinsic factors driving immune evasion. We focus on T cells as key effectors of anti-cancer immunity and argue that cancer cells evade immune destruction by gaining control over pathways that usually serve to maintain physiological tolerance to self. Using this framework, we place recent mechanistic advances in the understanding of cancer immune evasion into broad categories of control over T cell localization, antigen recognition, and acquisition of optimal effector function. We discuss the redundancy in the pathways involved and identify knowledge gaps that must be overcome to better target immune evasion, including the need for better, routinely available tools that incorporate the growing understanding of evasion mechanisms to stratify patients for therapy and trials.
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Affiliation(s)
- Ehsan Ghorani
- Cancer Immunology and Immunotherapy Unit, Department of Surgery and Cancer, Imperial College London, London, UK; Department of Medical Oncology, Imperial College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Immunology Unit, Research Department of Hematology, University College London Cancer Institute, London, UK.
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14
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Swanton C. Turning a failing PhD around. Nat Cancer 2023; 4:1399-1400. [PMID: 37880414 DOI: 10.1038/s43018-023-00597-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
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15
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Affiliation(s)
- James L Reading
- Pre-Cancer Immunology Laboratory, UCL Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
| | - Deborah R Caswell
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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16
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Watkins TBK, Colliver EC, Huska MR, Kaufmann TL, Lim EL, Duncan CB, Haase K, Van Loo P, Swanton C, McGranahan N, Schwarz RF. Refphase: Multi-sample phasing reveals haplotype-specific copy number heterogeneity. PLoS Comput Biol 2023; 19:e1011379. [PMID: 37871126 PMCID: PMC10621967 DOI: 10.1371/journal.pcbi.1011379] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 11/02/2023] [Accepted: 07/22/2023] [Indexed: 10/25/2023] Open
Abstract
Most computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient's disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample phasing. We demonstrate Refphase's ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
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Affiliation(s)
- Thomas B. K. Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | | | - Matthew R. Huska
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
| | - Tom L. Kaufmann
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- Department of Electrical Engineering & Computer Science, Technische Universität Berlin, Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Emilia L. Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Cody B. Duncan
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Kerstin Haase
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Van Loo
- The Francis Crick Institute, London, United Kingdom
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, United Kingdom
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) Berlin, Germany
- BIFOLD—Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
- Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
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17
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Zalay O, Bontempi D, Bitterman DS, Birkbak N, Shyr D, Haugg F, Qian JM, Roberts H, Perni S, Prudente V, Pai S, Dekker A, Haibe-Kains B, Guthier C, Balboni T, Warren L, Krishan M, Kann BH, Swanton C, Ruysscher DD, Mak RH, Aerts HJWL. Decoding biological age from face photographs using deep learning. medRxiv 2023:2023.09.12.23295132. [PMID: 37745558 PMCID: PMC10516042 DOI: 10.1101/2023.09.12.23295132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Because humans age at different rates, a person's physical appearance may yield insights into their biological age and physiological health more reliably than their chronological age. In medicine, however, appearance is incorporated into medical judgments in a subjective and non-standardized fashion. In this study, we developed and validated FaceAge, a deep learning system to estimate biological age from easily obtainable and low-cost face photographs. FaceAge was trained on data from 58,851 healthy individuals, and clinical utility was evaluated on data from 6,196 patients with cancer diagnoses from two institutions in the United States and The Netherlands. To assess the prognostic relevance of FaceAge estimation, we performed Kaplan Meier survival analysis. To test a relevant clinical application of FaceAge, we assessed the performance of FaceAge in end-of-life patients with metastatic cancer who received palliative treatment by incorporating FaceAge into clinical prediction models. We found that, on average, cancer patients look older than their chronological age, and looking older is correlated with worse overall survival. FaceAge demonstrated significant independent prognostic performance in a range of cancer types and stages. We found that FaceAge can improve physicians' survival predictions in incurable patients receiving palliative treatments, highlighting the clinical utility of the algorithm to support end-of-life decision-making. FaceAge was also significantly associated with molecular mechanisms of senescence through gene analysis, while age was not. These findings may extend to diseases beyond cancer, motivating using deep learning algorithms to translate a patient's visual appearance into objective, quantitative, and clinically useful measures.
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Affiliation(s)
- Osbert Zalay
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
- Division of Radiation Oncology, Queen’s University, Kingston, Canada
| | - Dennis Bontempi
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
- Department of Radiation Oncology (MAASTRO), Maastricht University, Maastricht, The Netherlands
| | - Danielle S Bitterman
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Nicolai Birkbak
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Center, Aarhus University, Aarhus, Denmark
| | - Derek Shyr
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston
| | - Fridolin Haugg
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Jack M Qian
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Hannah Roberts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Subha Perni
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Vasco Prudente
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| | - Suraj Pai
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| | - Andre Dekker
- Department of Radiation Oncology (MAASTRO), Maastricht University, Maastricht, The Netherlands
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Christian Guthier
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Tracy Balboni
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Laura Warren
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Monica Krishan
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Benjamin H Kann
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Dirk De Ruysscher
- Department of Radiation Oncology (MAASTRO), Maastricht University, Maastricht, The Netherlands
| | - Raymond H Mak
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
| | - Hugo JWL Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, United States of America
- Department of Radiation Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, United States of America
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, United States of America
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18
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Hasan AMM, Cremaschi P, Wetterskog D, Jayaram A, Wong SQ, Williams S, Pasam A, Trigos A, Trujillo B, Grist E, Friedrich S, Vainauskas O, Parry M, Ismail M, Devlies W, Wingate A, Linch M, Naceur-Lombardelli C, Swanton C, Jamal-Hanjani M, Lise S, Sandhu S, Attard G. Copy number architectures define treatment-mediated selection of lethal prostate cancer clones. Nat Commun 2023; 14:4823. [PMID: 37563129 PMCID: PMC10415299 DOI: 10.1038/s41467-023-40315-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Despite initial responses to hormone treatment, metastatic prostate cancer invariably evolves to a lethal state. To characterize the intra-patient evolutionary relationships of metastases that evade treatment, we perform genome-wide copy number profiling and bespoke approaches targeting the androgen receptor (AR) on 167 metastatic regions from 11 organs harvested post-mortem from 10 men who died from prostate cancer. We identify diverse and patient-unique alterations clustering around the AR in metastases from every patient with evidence of independent acquisition of related genomic changes within an individual and, in some patients, the co-existence of AR-neutral clones. Using the genomic boundaries of pan-autosome copy number changes, we confirm a common clone of origin across metastases and diagnostic biopsies, and identified in individual patients, clusters of metastases occupied by dominant clones with diverged autosomal copy number alterations. These autosome-defined clusters are characterized by cluster-specific AR gene architectures, and in two index cases are topologically more congruent than by chance (p-values 3.07 × 10-8 and 6.4 × 10-4). Integration with anatomical sites suggests patterns of spread and points of genomic divergence. Here, we show that copy number boundaries identify treatment-selected clones with putatively distinct lethal trajectories.
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Affiliation(s)
| | | | | | - Anuradha Jayaram
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Stephen Q Wong
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Scott Williams
- The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | - Anupama Pasam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna Trigos
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Blanca Trujillo
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | - Emily Grist
- University College London Cancer Institute, London, UK
| | | | | | - Marina Parry
- University College London Cancer Institute, London, UK
| | | | - Wout Devlies
- University College London Cancer Institute, London, UK
| | - Anna Wingate
- University College London Cancer Institute, London, UK
| | - Mark Linch
- University College London Cancer Institute, London, UK
- University College London Hospitals, London, UK
| | | | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Stefano Lise
- University College London Cancer Institute, London, UK
| | | | - Gerhardt Attard
- University College London Cancer Institute, London, UK.
- University College London Hospitals, London, UK.
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19
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Attig J, Pape J, Doglio L, Kazachenka A, Ottina E, Young GR, Enfield KS, Aramburu IV, Ng KW, Faulkner N, Bolland W, Papayannopoulos V, Swanton C, Kassiotis G. Human endogenous retrovirus onco-exaptation counters cancer cell senescence through calbindin. J Clin Invest 2023; 133:e164397. [PMID: 37192000 PMCID: PMC10348765 DOI: 10.1172/jci164397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 05/11/2023] [Indexed: 05/17/2023] Open
Abstract
Increased levels and diversity of human endogenous retrovirus (HERV) transcription characterize most cancer types and are linked with disease outcomes. However, the underlying processes are incompletely understood. Here, we show that elevated transcription of HERVH proviruses predicted survival of lung squamous cell carcinoma (LUSC) and identified an isoform of CALB1, encoding calbindin, ectopically driven by an upstream HERVH provirus under the control of KLF5, as the mediator of this effect. HERVH-CALB1 expression was initiated in preinvasive lesions and associated with their progression. Calbindin loss in LUSC cell lines impaired in vitro and in vivo growth and triggered senescence, consistent with a protumor effect. However, calbindin also directly controlled the senescence-associated secretory phenotype (SASP), marked by secretion of CXCL8 and other neutrophil chemoattractants. In established carcinomas, CALB1-negative cancer cells became the dominant source of CXCL8, correlating with neutrophil infiltration and worse prognosis. Thus, HERVH-CALB1 expression in LUSC may display antagonistic pleiotropy, whereby the benefits of escaping senescence early during cancer initiation and clonal competition were offset by the prevention of SASP and protumor inflammation at later stages.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - George Kassiotis
- Retroviral Immunology
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
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20
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Rane JK, Frankell AM, Weeden CE, Swanton C. Clonal Evolution in Healthy and Premalignant Tissues: Implications for Early Cancer Interception Strategies. Cancer Prev Res (Phila) 2023; 16:369-378. [PMID: 36930945 PMCID: PMC7614725 DOI: 10.1158/1940-6207.capr-22-0469] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023]
Abstract
Histologically normal human tissues accumulate significant mutational burden with age. The extent and spectra of mutagenesis are comparable both in rapidly proliferating and post-mitotic tissues and in stem cells compared with their differentiated progeny. Some of these mutations provide increased fitness, giving rise to clones which, at times, can replace the entire surface area of tissues. Compared with cancer, somatic mutations in histologically normal tissues are primarily single-nucleotide variations. Interestingly though, the presence of these mutations and positive clonal selection in isolation remains a poor indicator of potential future cancer transformation in solid tissues. Common clonally expanded mutations in histologically normal tissues also do not always represent the most frequent early mutations in cancers of corresponding tissues, indicating differences in selection pressures. Preliminary evidence implies that stroma and immune system co-evolve with age, which may impact selection dynamics. In this review, we will explore the mutational landscape of histologically normal and premalignant human somatic tissues in detail and discuss cell-intrinsic and environmental factors that can determine the fate of positively selected mutations within them. Precisely pinpointing these determinants of cancer transformation would aid development of early cancer interventional and prevention strategies.
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Affiliation(s)
- Jayant K. Rane
- University College London Cancer Institute, London, UK
- Department of Clinical Oncology, University College London Hospitals, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M. Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare E. Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
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21
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Bailey C, Sanderson T, Townsley H, Goldman J, Black JRM, Young G, Goldstone R, Fowler AS, Ward S, Jackson DJ, Cubitt L, Dearing V, O'Neil O, Crawford M, Snell D, Finadis M, Edwards A, Perez-Lloret J, Gahir J, Carr EJ, Riddell A, Aitken J, Ambrose K, Sawyer C, O'Reilly N, Caidan S, Wu MY, Walker PA, Hindmarsh S, Howell M, Jordan A, Fleming J, Houlihan C, Nastouli E, Moores R, Hsu D, Papineni P, Corrah T, Gilson R, MacRae J, Hubank M, Van As N, Turajlic S, Beale R, Levi M, Barrell S, Williams B, Gamblin S, Nicod J, Gandhi S, Bauer DLV, Wall EC, Swanton C. Independent SARS-CoV-2 staff testing protected academic and health-care institutions in northwest London. Lancet 2023; 402:21-24. [PMID: 37348521 PMCID: PMC10278995 DOI: 10.1016/s0140-6736(23)00917-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/15/2023] [Accepted: 05/02/2023] [Indexed: 06/24/2023]
Affiliation(s)
- Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK
| | - Theo Sanderson
- Malaria Biochemistry Laboratory, London NW1 1AT, UK; COVID-19 Genomics UK Consortium, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Hermaleigh Townsley
- Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK
| | | | - James R M Black
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; University College London, London, UK
| | - George Young
- Applied Biotechnology Laboratory, London NW1 1AT, UK
| | - Robert Goldstone
- Advanced Sequencing Facility, London NW1 1AT, UK; Bioinformatics and Biostatistics STP, London NW1 1AT, UK
| | | | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Advanced Sequencing Facility, London NW1 1AT, UK
| | | | - Laura Cubitt
- Advanced Sequencing Facility, London NW1 1AT, UK
| | | | - Olga O'Neil
- Advanced Sequencing Facility, London NW1 1AT, UK
| | | | - Daniel Snell
- Advanced Sequencing Facility, London NW1 1AT, UK
| | | | | | | | - Joshua Gahir
- Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK
| | - Edward J Carr
- Cell Biology of Infection Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK
| | | | - Jim Aitken
- Information Technology Office, London NW1 1AT, UK
| | | | | | | | | | - Mary Y Wu
- COVID Surveillance Unit, London NW1 1AT, UK
| | | | | | | | | | | | | | - Eleni Nastouli
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Desmond Hsu
- Royal Free London NHS Foundation Trust, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and Northwest London NHS Foundation Trust, London, UK
| | | | - Michael Hubank
- Royal Marsden Hospitals NHS Foundation Trust, London, UK
| | | | | | - Rupert Beale
- Cell Biology of Infection Laboratory, London NW1 1AT, UK; University College London, London, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK
| | - Marcel Levi
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Bryan Williams
- University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK
| | | | - Jerome Nicod
- Advanced Sequencing Facility, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK
| | - Sonia Gandhi
- Neurodegeneration Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London, London, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, London NW1 1AT, UK; Genotype to Phenotype Consortium UK, Imperial College London, London, UK
| | - Emma C Wall
- Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, London NW1 1AT, UK; Francis Crick Institute, London NW1 1AT, UK; University College London Hospitals NHS Foundation Trust, London, UK; University College London, London, UK
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22
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Sasieni P, Smittenaar R, Hubbell E, Broggio J, Neal RD, Swanton C. Modelled mortality benefits of multi-cancer early detection screening in England. Br J Cancer 2023; 129:72-80. [PMID: 37185463 PMCID: PMC10307803 DOI: 10.1038/s41416-023-02243-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Screening programmes utilising blood-based multi-cancer early detection (MCED) tests, which can detect a shared cancer signal from any site in the body with a single, low false-positive rate, could reduce cancer burden through early diagnosis. METHODS A natural history ('interception') model of cancer was previously used to characterise potential benefits of MCED screening (based on published performance of an MCED test). We built upon this using a two-population survival model to account for an increased risk of death from cfDNA-detectable cancers relative to cfDNA-non-detectable cancers. We developed another model allowing some cancers to metastasise directly from stage I, bypassing intermediate tumour stages. We used incidence and survival-by-stage data from the National Cancer Registration and Analysis Service in England to estimate longer-term benefits to a cohort screened between ages 50-79 years. RESULTS Estimated late-stage and mortality reductions were robust to a range of assumptions. With the least favourable dwell (sojourn) time and cfDNA status hazard ratio assumptions, we estimated, among 100,000 screened individuals, 67 (17%) fewer cancer deaths per year corresponding to 2029 fewer deaths in those screened between ages 50-79 years. CONCLUSION Realising the potential benefits of MCED tests could substantially reduce late-stage cancer diagnoses and mortality.
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Affiliation(s)
- Peter Sasieni
- Comprehensive Cancer Centre, King's College London, Guy's Campus, Great Maze Pond, London, SE1 1UL, UK.
| | | | | | - John Broggio
- NHS Digital, 7 and 8 Wellington Place, Leeds, West Yorkshire, LS1 4AP, UK
| | - Richard D Neal
- Department of Health and Community Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, WC1E 6DD, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, NW1 1AT, UK
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23
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Hennequart M, Pilley SE, Labuschagne CF, Coomes J, Mervant L, Driscoll PC, Legrave NM, Lee Y, Kreuzaler P, Macintyre B, Panina Y, Blagih J, Stevenson D, Strathdee D, Schneider-Luftman D, Grönroos E, Cheung EC, Yuneva M, Swanton C, Vousden KH. ALDH1L2 regulation of formate, formyl-methionine, and ROS controls cancer cell migration and metastasis. Cell Rep 2023; 42:112562. [PMID: 37245210 DOI: 10.1016/j.celrep.2023.112562] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/10/2023] [Accepted: 05/09/2023] [Indexed: 05/30/2023] Open
Abstract
Mitochondrial 10-formyltetrahydrofolate (10-formyl-THF) is utilized by three mitochondrial enzymes to produce formate for nucleotide synthesis, NADPH for antioxidant defense, and formyl-methionine (fMet) to initiate mitochondrial mRNA translation. One of these enzymes-aldehyde dehydrogenase 1 family member 2 (ALDH1L2)-produces NADPH by catabolizing 10-formyl-THF into CO2 and THF. Using breast cancer cell lines, we show that reduction of ALDH1L2 expression increases ROS levels and the production of both formate and fMet. Both depletion of ALDH1L2 and direct exposure to formate result in enhanced cancer cell migration that is dependent on the expression of the formyl-peptide receptor (FPR). In various tumor models, increased ALDH1L2 expression lowers formate and fMet accumulation and limits metastatic capacity, while human breast cancer samples show a consistent reduction of ALDH1L2 expression in metastases. Together, our data suggest that loss of ALDH1L2 can support metastatic progression by promoting formate and fMet production, resulting in enhanced FPR-dependent signaling.
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Affiliation(s)
- Marc Hennequart
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Steven E Pilley
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christiaan F Labuschagne
- Faculty of Natural and Agricultural Sciences, North-West University (Potchefstroom Campus), 11 Hoffman Street, Potchesfstoom 2531, South Africa
| | - Jack Coomes
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Loic Mervant
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paul C Driscoll
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Younghwan Lee
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Peter Kreuzaler
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Yulia Panina
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Julianna Blagih
- Department of Obstetrics-Gynaecology, University of Montreal, Maisonneuve-Rosemont Hospital Research Centre, 5414 Assomption Blvd, Montreal, QC H1T 2M4, Canada
| | | | | | | | - Eva Grönroos
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Eric C Cheung
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mariia Yuneva
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Charles Swanton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Karen H Vousden
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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24
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Carr EJ, Wu MY, Gahir J, Harvey R, Townsley H, Bailey C, Fowler AS, Dowgier G, Hobbs A, Herman L, Ragno M, Miah M, Bawumia P, Smith C, Miranda M, Mears HV, Adams L, Haptipoglu E, O'Reilly N, Warchal S, Sawyer C, Ambrose K, Kelly G, Beale R, Papineni P, Corrah T, Gilson R, Gamblin S, Kassiotis G, Libri V, Williams B, Swanton C, Gandhi S, Lv Bauer D, Wall EC. Neutralising immunity to omicron sublineages BQ.1.1, XBB, and XBB.1.5 in healthy adults is boosted by bivalent BA.1-containing mRNA vaccination and previous Omicron infection. Lancet Infect Dis 2023:S1473-3099(23)00289-X. [PMID: 37290472 DOI: 10.1016/s1473-3099(23)00289-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 05/02/2023] [Indexed: 06/10/2023]
Affiliation(s)
- Edward J Carr
- The Francis Crick Institute, London, UK; University College London, London, UK
| | - Mary Y Wu
- COVID Surveillance Unit, London, UK; The Francis Crick Institute, London, UK
| | - Joshua Gahir
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | - Hermaleigh Townsley
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Chris Bailey
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | | | | | | | | | | | | | | | | | | | | | - Emine Haptipoglu
- The Francis Crick Institute, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | | | | | | | | | | | - Rupert Beale
- The Francis Crick Institute, London, UK; University College London, London, UK
| | | | - Tumena Corrah
- London Northwest University Healthcare NHS Trust, London, UK
| | - Richard Gilson
- Central and North West London NHS Foundation Trust, London, UK
| | | | - George Kassiotis
- The Francis Crick Institute, London, UK; Department of Infectious Disease, St Mary's Hospital, Imperial College London, London, UK
| | - Vincenzo Libri
- University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Bryan Williams
- University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK
| | - Charles Swanton
- The Francis Crick Institute, London, UK; University College London, London, UK
| | - Sonia Gandhi
- The Francis Crick Institute, London, UK; University College London, London, UK
| | | | - Emma C Wall
- The Francis Crick Institute, London, UK; University College London, London, UK; National Institute for Health Research University College London Hospitals Biomedical Research Centre and Clinical Research Facility, London, UK.
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25
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Pearce DR, Akarca AU, De Maeyer RPH, Kostina E, Huebner A, Sivakumar M, Karasaki T, Shah K, Janes SM, McGranahan N, Reddy V, Akbar AN, Moore DA, Marafioti T, Swanton C, Hynds RE. Phenotyping of lymphoproliferative tumours generated in xenografts of non-small cell lung cancer. Front Oncol 2023; 13:1156743. [PMID: 37342197 PMCID: PMC10277614 DOI: 10.3389/fonc.2023.1156743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/11/2023] [Indexed: 06/22/2023] Open
Abstract
Background Patient-derived xenograft (PDX) models involve the engraftment of tumour tissue in immunocompromised mice and represent an important pre-clinical oncology research method. A limitation of non-small cell lung cancer (NSCLC) PDX model derivation in NOD-scid IL2Rgammanull (NSG) mice is that a subset of initial engraftments are of lymphocytic, rather than tumour origin. Methods The immunophenotype of lymphoproliferations arising in the lung TRACERx PDX pipeline were characterised. To present the histology data herein, we developed a Python-based tool for generating patient-level pathology overview figures from whole-slide image files; PATHOverview is available on GitHub (https://github.com/EpiCENTR-Lab/PATHOverview). Results Lymphoproliferations occurred in 17.8% of lung adenocarcinoma and 10% of lung squamous cell carcinoma transplantations, despite none of these patients having a prior or subsequent clinical history of lymphoproliferative disease. Lymphoproliferations were predominantly human CD20+ B cells and had the immunophenotype expected for post-transplantation diffuse large B cell lymphoma with plasma cell features. All lymphoproliferations expressed Epstein-Barr-encoded RNAs (EBER). Analysis of immunoglobulin light chain gene rearrangements in three tumours where multiple tumour regions had resulted in lymphoproliferations suggested that each had independent clonal origins. Discussion Overall, these data suggest that B cell clones with lymphoproliferative potential are present within primary NSCLC tumours, and that these are under continuous immune surveillance. Since these cells can be expanded following transplantation into NSG mice, our data highlight the value of quality control measures to identify lymphoproliferations within xenograft pipelines and support the incorporation of strategies to minimise lymphoproliferations during the early stages of xenograft establishment pipelines.
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Affiliation(s)
- David R. Pearce
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ayse U. Akarca
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | | | - Emily Kostina
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Ariana Huebner
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Monica Sivakumar
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Takahiro Karasaki
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Kavina Shah
- Division of Medicine, University College London, London, United Kingdom
| | - Sam M. Janes
- Lungs for Living Research Centre, UCL Respiratory, Division of Medicine, University College London, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Genome Evolution Research Group, UCL Cancer Institute, University College London, London, United Kingdom
| | - Venkat Reddy
- Division of Medicine, University College London, London, United Kingdom
| | - Arne N. Akbar
- Division of Medicine, University College London, London, United Kingdom
| | - David A. Moore
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Charles Swanton
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Robert E. Hynds
- Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, UCL Cancer Institute, University College London, London, United Kingdom
- Cancer Evolution and Genome Stability Laboratory, The Francis Crick Institute, London, United Kingdom
- Epithelial Cell Biology in ENT Research (EpiCENTR) Group, Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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26
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Spain L, Coulton A, Lobon I, Rowan A, Schnidrig D, Shepherd ST, Shum B, Byrne F, Goicoechea M, Piperni E, Au L, Edmonds K, Carlyle E, Hunter N, Renn A, Messiou C, Hughes P, Nobbs J, Foijer F, van den Bos H, Wardenaar R, Spierings DC, Spencer C, Schmitt AM, Tippu Z, Lingard K, Grostate L, Peat K, Kelly K, Sarker S, Vaughan S, Mangwende M, Terry L, Kelly D, Biano J, Murra A, Korteweg J, Lewis C, O'Flaherty M, Cattin AL, Emmerich M, Gerard CL, Pallikonda HA, Lynch J, Mason R, Rogiers A, Xu H, Huebner A, McGranahan N, Al Bakir M, Murai J, Naceur-Lombardelli C, Borg E, Mitchison M, Moore DA, Falzon M, Proctor I, Stamp GW, Nye EL, Young K, Furness AJ, Pickering L, Stewart R, Mahadeva U, Green A, Larkin J, Litchfield K, Swanton C, Jamal-Hanjani M, Turajlic S. Late-Stage Metastatic Melanoma Emerges through a Diversity of Evolutionary Pathways. Cancer Discov 2023; 13:1364-1385. [PMID: 36977461 PMCID: PMC10236155 DOI: 10.1158/2159-8290.cd-22-1427] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/06/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023]
Abstract
Understanding the evolutionary pathways to metastasis and resistance to immune-checkpoint inhibitors (ICI) in melanoma is critical for improving outcomes. Here, we present the most comprehensive intrapatient metastatic melanoma dataset assembled to date as part of the Posthumous Evaluation of Advanced Cancer Environment (PEACE) research autopsy program, including 222 exome sequencing, 493 panel-sequenced, 161 RNA sequencing, and 22 single-cell whole-genome sequencing samples from 14 ICI-treated patients. We observed frequent whole-genome doubling and widespread loss of heterozygosity, often involving antigen-presentation machinery. We found KIT extrachromosomal DNA may have contributed to the lack of response to KIT inhibitors of a KIT-driven melanoma. At the lesion-level, MYC amplifications were enriched in ICI nonresponders. Single-cell sequencing revealed polyclonal seeding of metastases originating from clones with different ploidy in one patient. Finally, we observed that brain metastases that diverged early in molecular evolution emerge late in disease. Overall, our study illustrates the diverse evolutionary landscape of advanced melanoma. SIGNIFICANCE Despite treatment advances, melanoma remains a deadly disease at stage IV. Through research autopsy and dense sampling of metastases combined with extensive multiomic profiling, our study elucidates the many mechanisms that melanomas use to evade treatment and the immune system, whether through mutations, widespread copy-number alterations, or extrachromosomal DNA. See related commentary by Shain, p. 1294. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Alexander Coulton
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
| | - Irene Lobon
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Desiree Schnidrig
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Scott T.C. Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Maria Goicoechea
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Elisa Piperni
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, Australia
| | - Kim Edmonds
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Nikki Hunter
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Christina Messiou
- The Royal Marsden Hospital, London, United Kingdom
- The Institute of Cancer Research, Kensington and Chelsea, United Kingdom
| | - Peta Hughes
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Jaime Nobbs
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Floris Foijer
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Hilda van den Bos
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Rene Wardenaar
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Diana C.J. Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - Charlotte Spencer
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | | | | | - Kema Peat
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Sarah Sarker
- The Royal Marsden Hospital, London, United Kingdom
| | | | | | - Lauren Terry
- The Royal Marsden Hospital, London, United Kingdom
| | - Denise Kelly
- The Royal Marsden Hospital, London, United Kingdom
| | | | - Aida Murra
- The Royal Marsden Hospital, London, United Kingdom
| | | | | | | | - Anne-Laure Cattin
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Max Emmerich
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- St. John's Institute of Dermatology, Guy's and St Thomas’ Hospital NHS Foundation Trust, London, United Kingdom
| | - Camille L. Gerard
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Precision Oncology Center, Oncology Department, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Joanna Lynch
- The Royal Marsden Hospital, London, United Kingdom
| | - Robert Mason
- Gold Coast University Hospital, Queensland, Australia
| | - Aljosja Rogiers
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- The Royal Marsden Hospital, London, United Kingdom
| | - Hang Xu
- The Francis Crick Institute, London, United Kingdom
| | - Ariana Huebner
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
| | - Jun Murai
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
- Drug Discovery Technology Laboratories, Ono Pharmaceutical Co., Ltd. Osaka, Japan
| | | | - Elaine Borg
- University College London Hospital, London, United Kingdom
| | | | - David A. Moore
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Mary Falzon
- University College London Hospital, London, United Kingdom
| | - Ian Proctor
- University College London Hospital, London, United Kingdom
| | | | - Emma L. Nye
- The Francis Crick Institute, London, United Kingdom
| | - Kate Young
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Andrew J.S. Furness
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
- The Institute of Cancer Research, Kensington and Chelsea, United Kingdom
| | | | - Ruby Stewart
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Ula Mahadeva
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Anna Green
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - James Larkin
- Guy's and St Thomas’ NHS Foundation Trust, London, United Kingdom
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance (TIGI) Lab, UCL Cancer Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, UCL Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Medical Oncology, University College London Hospitals, London, United Kingdom
| | | | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, United Kingdom
- Skin and Renal Unit, Royal Marsden NHS Foundation Trust, London, United Kingdom
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27
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Hessey S, Fessas P, Zaccaria S, Jamal-Hanjani M, Swanton C. Insights into the metastatic cascade through research autopsies. Trends Cancer 2023; 9:490-502. [PMID: 37059687 DOI: 10.1016/j.trecan.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 04/16/2023]
Abstract
Metastasis is a complex process and the leading cause of cancer-related death globally. Recent studies have demonstrated that genomic sequencing data from paired primary and metastatic tumours can be used to trace the evolutionary origins of cells responsible for metastasis. This approach has yielded new insights into the genomic alterations that engender metastatic potential, and the mechanisms by which cancer spreads. Given that the reliability of these approaches is contingent upon how representative the samples are of primary and metastatic tumour heterogeneity, we review insights from studies that have reconstructed the evolution of metastasis within the context of their cohorts and designs. We discuss the role of research autopsies in achieving the comprehensive sampling necessary to advance the current understanding of metastasis.
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Affiliation(s)
- Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Petros Fessas
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK; Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
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28
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Chu Y, Dai E, Li Y, Han G, Pei G, Ingram DR, Thakkar K, Qin JJ, Dang M, Le X, Hu C, Deng Q, Sinjab A, Gupta P, Wang R, Hao D, Peng F, Yan X, Liu Y, Song S, Zhang S, Heymach JV, Reuben A, Elamin YY, Pizzi MP, Lu Y, Lazcano R, Hu J, Li M, Curran M, Futreal A, Maitra A, Jazaeri AA, Ajani JA, Swanton C, Cheng XD, Abbas HA, Gillison M, Bhat K, Lazar AJ, Green M, Litchfield K, Kadara H, Yee C, Wang L. Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance. Nat Med 2023; 29:1550-1562. [PMID: 37248301 DOI: 10.1038/s41591-023-02371-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/26/2023] [Indexed: 05/31/2023]
Abstract
Tumor-infiltrating T cells offer a promising avenue for cancer treatment, yet their states remain to be fully characterized. Here we present a single-cell atlas of T cells from 308,048 transcriptomes across 16 cancer types, uncovering previously undescribed T cell states and heterogeneous subpopulations of follicular helper, regulatory and proliferative T cells. We identified a unique stress response state, TSTR, characterized by heat shock gene expression. TSTR cells are detectable in situ in the tumor microenvironment across various cancer types, mostly within lymphocyte aggregates or potential tertiary lymphoid structures in tumor beds or surrounding tumor edges. T cell states/compositions correlated with genomic, pathological and clinical features in 375 patients from 23 cohorts, including 171 patients who received immune checkpoint blockade therapy. We also found significantly upregulated heat shock gene expression in intratumoral CD4/CD8+ cells following immune checkpoint blockade treatment, particularly in nonresponsive tumors, suggesting a potential role of TSTR cells in immunotherapy resistance. Our well-annotated T cell reference maps, web portal and automatic alignment/annotation tool could provide valuable resources for T cell therapy optimization and biomarker discovery.
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Affiliation(s)
- Yanshuo Chu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enyu Dai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yating Li
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangchun Han
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guangsheng Pei
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Davis R Ingram
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krupa Thakkar
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Jiang-Jiang Qin
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Minghao Dang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Can Hu
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ansam Sinjab
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pravesh Gupta
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ruiping Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dapeng Hao
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Fuduan Peng
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinmiao Yan
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shaojun Zhang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexandre Reuben
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Melissa P Pizzi
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Hu
- Department of Human Genetics, Emory School of Medicine, Atlanta, GA, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Curran
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Futreal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Amir A Jazaeri
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Xiang-Dong Cheng
- Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, China
- Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
| | - Hussein A Abbas
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maura Gillison
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krishna Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander J Lazar
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Michael Green
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kevin Litchfield
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Humam Kadara
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Cassian Yee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA.
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29
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Huntley C, Torr B, Sud A, Rowlands CF, Way R, Snape K, Hanson H, Swanton C, Broggio J, Lucassen A, McCartney M, Houlston RS, Hingorani AD, Jones ME, Turnbull C. Utility of polygenic risk scores in UK cancer screening: a modelling analysis. Lancet Oncol 2023; 24:658-668. [PMID: 37178708 DOI: 10.1016/s1470-2045(23)00156-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/28/2023] [Accepted: 03/30/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND It is proposed that, through restriction to individuals delineated as high risk, polygenic risk scores (PRSs) might enable more efficient targeting of existing cancer screening programmes and enable extension into new age ranges and disease types. To address this proposition, we present an overview of the performance of PRS tools (ie, models and sets of single nucleotide polymorphisms) alongside harms and benefits of PRS-stratified cancer screening for eight example cancers (breast, prostate, colorectal, pancreas, ovary, kidney, lung, and testicular cancer). METHODS For this modelling analysis, we used age-stratified cancer incidences for the UK population from the National Cancer Registration Dataset (2016-18) and published estimates of the area under the receiver operating characteristic curve for current, future, and optimised PRS for each of the eight cancer types. For each of five PRS-defined high-risk quantiles (ie, the top 50%, 20%, 10%, 5%, and 1%) and according to each of the three PRS tools (ie, current, future, and optimised) for the eight cancers, we calculated the relative proportion of cancers arising, the odds ratios of a cancer arising compared with the UK population average, and the lifetime cancer risk. We examined maximal attainable rates of cancer detection by age stratum from combining PRS-based stratification with cancer screening tools and modelled the maximal impact on cancer-specific survival of hypothetical new UK programmes of PRS-stratified screening. FINDINGS The PRS-defined high-risk quintile (20%) of the population was estimated to capture 37% of breast cancer cases, 46% of prostate cancer cases, 34% of colorectal cancer cases, 29% of pancreatic cancer cases, 26% of ovarian cancer cases, 22% of renal cancer cases, 26% of lung cancer cases, and 47% of testicular cancer cases. Extending UK screening programmes to a PRS-defined high-risk quintile including people aged 40-49 years for breast cancer, 50-59 years for colorectal cancer, and 60-69 years for prostate cancer has the potential to avert, respectively, a maximum of 102, 188, and 158 deaths annually. Unstratified screening of the full population aged 48-49 years for breast cancer, 58-59 years for colorectal cancer, and 68-69 years for prostate cancer would use equivalent resources and avert, respectively, an estimated maximum of 80, 155, and 95 deaths annually. These maximal modelled numbers will be substantially attenuated by incomplete population uptake of PRS profiling and cancer screening, interval cancers, non-European ancestry, and other factors. INTERPRETATION Under favourable assumptions, our modelling suggests modest potential efficiency gain in cancer case detection and deaths averted for hypothetical new PRS-stratified screening programmes for breast, prostate, and colorectal cancer. Restriction of screening to high-risk quantiles means many or most incident cancers will arise in those assigned as being low-risk. To quantify real-world clinical impact, costs, and harms, UK-specific cluster-randomised trials are required. FUNDING The Wellcome Trust.
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Affiliation(s)
- Catherine Huntley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
| | - Bethany Torr
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; Haemato-oncology Unit, The Royal Marsden Hospital NHS Foundation Trust, Sutton, UK
| | - Charlie F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Rosalind Way
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Katie Snape
- St Georges University of London, London, UK; South West Thames Regional Genetics Service, St George's Hospital, London, UK
| | - Helen Hanson
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; South West Thames Regional Genetics Service, St George's Hospital, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute, London, UK
| | - John Broggio
- National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK
| | - Anneke Lucassen
- Wellcome Centre for Human Genetics and Centre for Personalised Medicine, University of Oxford, Oxford, UK
| | - Margaret McCartney
- Population and Behavioural Science Division, School of Medicine, University of St Andrews, St Andrews, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Aroon D Hingorani
- University College London British Heart Foundation Research Accelerator Centre, London, UK; Health Data Research UK, London, UK; National Institute of Health Research Biomedical Research Centre and Institute of Cardiovascular Science, Faculty of Population Health, University College London, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK.
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30
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Russell TW, Townsley H, Abbott S, Hellewell J, Carr EJ, Chapman L, Pung R, Quilty BJ, Hodgson D, Fowler AS, Adams L, Bailey C, Mears HV, Harvey R, Clayton B, O’Reilly N, Ngai Y, Nicod J, Gamblin S, Williams B, Gandhi S, Swanton C, Beale R, Bauer DLV, Wall EC, Kucharski A. Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants. medRxiv 2023:2023.05.17.23290105. [PMID: 37292842 PMCID: PMC10246130 DOI: 10.1101/2023.05.17.23290105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.
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Affiliation(s)
- Timothy W. Russell
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Hermaleigh Townsley
- The Francis Crick Institute, 1 Midland Road, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
| | - Sam Abbott
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Joel Hellewell
- European Molecular Biology Laboratory-European Bioinformatics Institute, Cambridge, UK
| | - Edward J Carr
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Lloyd Chapman
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Lancaster University, Bailrigg, Lancaster
| | - Rachael Pung
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Billy J. Quilty
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - David Hodgson
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Lorin Adams
- The Francis Crick Institute, 1 Midland Road, London, UK
| | | | | | - Ruth Harvey
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Bobbi Clayton
- The Francis Crick Institute, 1 Midland Road, London, UK
| | | | - Yenting Ngai
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Jerome Nicod
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Steve Gamblin
- The Francis Crick Institute, 1 Midland Road, London, UK
| | - Bryan Williams
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
- University College London, Gower Street, London
| | - Sonia Gandhi
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Charles Swanton
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
| | - Rupert Beale
- The Francis Crick Institute, 1 Midland Road, London, UK
- University College London, Gower Street, London
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - David LV Bauer
- The Francis Crick Institute, 1 Midland Road, London, UK
- Genotype-to-Phenotype UK National Virology Consortium (G2P-UK)
| | - Emma C Wall
- The Francis Crick Institute, 1 Midland Road, London, UK
- National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility, London, UK
- University College London, Gower Street, London
| | - Adam Kucharski
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, UK
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31
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Wu MY, Shepherd STC, Fendler A, Carr EJ, Au L, Harvey R, Dowgier G, Hobbs A, Herman LS, Ragno M, Adams L, Schmitt AM, Tippu Z, Shum B, Farag S, Rogiers A, O'Reilly N, Bawumia P, Smith C, Carlyle E, Edmonds K, Del Rosario L, Lingard K, Mangwende M, Holt L, Ahmod H, Korteweg J, Foley T, Barber T, Hepworth S, Emslie-Henry A, Caulfield-Lynch N, Byrne F, Deng D, Williams B, Brown M, Caidan S, Gavrielides M, MacRae JI, Kelly G, Peat K, Kelly D, Murra A, Kelly K, O'Flaherty M, Popat S, Yousaf N, Jhanji S, Tatham K, Cunningham D, Van As N, Young K, Furness AJS, Pickering L, Beale R, Swanton C, Gandhi S, Gamblin S, Bauer DLV, Kassiotis G, Howell M, Walker S, Nicholson E, Larkin J, Wall EC, Turajlic S. Sotrovimab restores neutralization against current Omicron subvariants in patients with blood cancer. Cancer Cell 2023; 41:821-823. [PMID: 37116490 PMCID: PMC10113515 DOI: 10.1016/j.ccell.2023.04.005] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/30/2023]
Abstract
Wu et al. report that patients with hematologic malignancies have reduced immunity against SARS-CoV-2 Omicron subvariants and Sotrovimab retains neutralizing capacity against all tested Omicron subvariants.
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Affiliation(s)
- Mary Y Wu
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Annika Fendler
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Department of Urology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Edward J Carr
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London NW1 2PG, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK; Department of Medical Oncology, Peter MacCallum Cancer Centre, VIC 3010, Melbourne, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, VIC 3010, Melbourne, Australia
| | - Ruth Harvey
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Agnieszka Hobbs
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Lou S Herman
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Martina Ragno
- COVID Surveillance Unit, The Francis Crick Institute, London NW1 1AT, UK
| | - Lorin Adams
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Andreas M Schmitt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Zayd Tippu
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Benjamin Shum
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Sheima Farag
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Aljosja Rogiers
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Nicola O'Reilly
- Worldwide Influenza Centre, The Francis Crick Institute, London NW1 1AT, UK
| | - Philip Bawumia
- Human Biology Science and Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Callie Smith
- Human Biology Science and Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Eleanor Carlyle
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kim Edmonds
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lyra Del Rosario
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Karla Lingard
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Mary Mangwende
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Lucy Holt
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Hamid Ahmod
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Justine Korteweg
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Tara Foley
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Taja Barber
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Stephanie Hepworth
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | | | | | - Fiona Byrne
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Daqi Deng
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Bryan Williams
- School of Life and Medical Sciences, University College London, 235 Euston Road, London NW1 2BU, UK; University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London WC1E 6BT, UK
| | - Michael Brown
- University College London Hospitals NHS Foundation Trust Biomedical Research Centre, London WC1E 6BT, UK; Clinical Research Department, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - Simon Caidan
- Safety, Health & Sustainability, The Francis Crick Institute, London NW1 1AT, UK
| | - Mike Gavrielides
- Scientific Computing Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - James I MacRae
- Metabolomics Scientific Technology Platform, The Francis Crick Institute, London NW1 1AT, UK
| | - Gavin Kelly
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Kema Peat
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Denise Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Aida Murra
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kayleigh Kelly
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Molly O'Flaherty
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Sanjay Popat
- Lung Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Nadia Yousaf
- Lung Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Acute Oncology Service, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Shaman Jhanji
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Kate Tatham
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - David Cunningham
- Gastrointestinal Unit, The Royal Marsden NHS Foundation Trust, London and Surrey, SM2 5PT, UK
| | - Nicholas Van As
- Clincal Oncology Unit, The Royal Marsden NHS Foundation Trust, London NW1 1AT, UK
| | - Kate Young
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Andrew J S Furness
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Lisa Pickering
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Rupert Beale
- Cell Biology of Infection Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Division of Medicine, University College London, London NW1 2PG, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London NW1 1AT, UK; University College London Cancer Institute, London WC1E 6DD, UK
| | - Sonia Gandhi
- Neurodegeneration Biology Laboratory, The Francis Crick Institute, London NW1 1AT, UK; UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Steve Gamblin
- Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - David L V Bauer
- RNA Virus Replication Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Michael Howell
- High Throughput Screening Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Susanna Walker
- Anaesthetics, Perioperative Medicine and Pain Department, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Emma Nicholson
- Haemato-oncology Unit, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Haemato-oncology Unit, The Institute of Cancer Research, London SW7 3RP, UK
| | - James Larkin
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK
| | - Emma C Wall
- School of Life and Medical Sciences, University College London, 235 Euston Road, London NW1 2BU, UK; The Francis Crick Institute, London NW1 1AT, UK.
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London NW1 1AT, UK; Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London SW7 3RP, UK.
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32
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Zhang H, AbdulJabbar K, Moore DA, Akarca A, Enfield KS, Jamal-Hanjani M, Raza SEA, Veeriah S, Salgado R, McGranahan N, Le Quesne J, Swanton C, Marafioti T, Yuan Y. Spatial Positioning of Immune Hotspots Reflects the Interplay between B and T Cells in Lung Squamous Cell Carcinoma. Cancer Res 2023; 83:1410-1425. [PMID: 36853169 PMCID: PMC10152235 DOI: 10.1158/0008-5472.can-22-2589] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 01/05/2023] [Accepted: 02/24/2023] [Indexed: 03/01/2023]
Abstract
Beyond tertiary lymphoid structures, a significant number of immune-rich areas without germinal center-like structures are observed in non-small cell lung cancer. Here, we integrated transcriptomic data and digital pathology images to study the prognostic implications, spatial locations, and constitution of immune rich areas (immune hotspots) in a cohort of 935 patients with lung cancer from The Cancer Genome Atlas. A high intratumoral immune hotspot score, which measures the proportion of immune hotspots interfacing with tumor islands, was correlated with poor overall survival in lung squamous cell carcinoma but not in lung adenocarcinoma. Lung squamous cell carcinomas with high intratumoral immune hotspot scores were characterized by consistent upregulation of B-cell signatures. Spatial statistical analyses conducted on serial multiplex IHC slides further revealed that only 4.87% of peritumoral immune hotspots and 0.26% of intratumoral immune hotspots were tertiary lymphoid structures. Significantly lower densities of CD20+CXCR5+ and CD79b+ B cells and less diverse immune cell interactions were found in intratumoral immune hotspots compared with peritumoral immune hotspots. Furthermore, there was a negative correlation between the percentages of CD8+ T cells and T regulatory cells in intratumoral but not in peritumoral immune hotspots, with tertiary lymphoid structures excluded. These findings suggest that the intratumoral immune hotspots reflect an immunosuppressive niche compared with peritumoral immune hotspots, independent of the distribution of tertiary lymphoid structures. A balance toward increased intratumoral immune hotspots is indicative of a compromised antitumor immune response and poor outcome in lung squamous cell carcinoma. SIGNIFICANCE Intratumoral immune hotspots beyond tertiary lymphoid structures reflect an immunosuppressive microenvironment, different from peritumoral immune hotspots, warranting further study in the context of immunotherapies.
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Affiliation(s)
- Hanyun Zhang
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - David A. Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Ayse Akarca
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Katey S.S. Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Department of Oncology, University College London Hospitals, London, United Kingdom
- Cancer Metastasis Lab, University College London Cancer Institute, London, United Kingdom
| | - Shan E. Ahmed Raza
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | | | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Glasgow, United Kingdom
- School of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
- NHS Greater Glasgow and Clyde Pathology Department, Queen Elizabeth University Hospital, London, United Kingdom
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Oncology, University College London Hospitals, London, United Kingdom
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
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33
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Javitt A, Shmueli MD, Kramer MP, Kolodziejczyk AA, Cohen IJ, Radomir L, Sheban D, Kamer I, Litchfield K, Bab-Dinitz E, Zadok O, Neiens V, Ulman A, Wolf-Levy H, Eisenberg-Lerner A, Kacen A, Alon M, Rêgo AT, Stacher-Priehse E, Lindner M, Koch I, Bar J, Swanton C, Samuels Y, Levin Y, da Fonseca PCA, Elinav E, Friedman N, Meiners S, Merbl Y. The proteasome regulator PSME4 modulates proteasome activity and antigen diversity to abrogate antitumor immunity in NSCLC. Nat Cancer 2023; 4:629-647. [PMID: 37217651 DOI: 10.1038/s43018-023-00557-4] [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] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 04/10/2023] [Indexed: 05/24/2023]
Abstract
Immunotherapy revolutionized treatment options in cancer, yet the mechanisms underlying resistance in many patients remain poorly understood. Cellular proteasomes have been implicated in modulating antitumor immunity by regulating antigen processing, antigen presentation, inflammatory signaling and immune cell activation. However, whether and how proteasome complex heterogeneity may affect tumor progression and the response to immunotherapy has not been systematically examined. Here, we show that proteasome complex composition varies substantially across cancers and impacts tumor-immune interactions and the tumor microenvironment. Through profiling of the degradation landscape of patient-derived non-small-cell lung carcinoma samples, we find that the proteasome regulator PSME4 is upregulated in tumors, alters proteasome activity, attenuates presented antigenic diversity and associates with lack of response to immunotherapy. Collectively, our approach affords a paradigm by which proteasome composition heterogeneity and function should be examined across cancer types and targeted in the context of precision oncology.
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Affiliation(s)
- Aaron Javitt
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Merav D Shmueli
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
| | - Matthias P Kramer
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ivan J Cohen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lihi Radomir
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Daoud Sheban
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Iris Kamer
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Kevin Litchfield
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Oranit Zadok
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - Vanessa Neiens
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum Muenchen, Munich, Germany
- Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Adi Ulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Wolf-Levy
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Assaf Kacen
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Alon
- Department of Molecular and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | | | | | - Ina Koch
- Member of the German Center for Lung Research (DZL), Munich, Germany
- Asklepios Lung Clinic Munich-Gauting, Gauting, Germany
| | - Jair Bar
- Institute of Oncology, Sheba Medical Center, Ramat Gan, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Charles Swanton
- UCL Cancer Institute, CRUK Lung Cancer Centre of Excellence, Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Yardena Samuels
- Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Paula C A da Fonseca
- Department of Molecular and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- School of Molecular Biosciences, University of Glasgow, Glasgow, UK
| | - Eran Elinav
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
- Division of Cancer-Microbiome Research, DKFZ, Heidelberg, Germany
| | - Nir Friedman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Silke Meiners
- Comprehensive Pneumology Center (CPC), University Hospital, Ludwig-Maximilians University, Helmholtz Zentrum Muenchen, Munich, Germany
- Member of the German Center for Lung Research (DZL), Munich, Germany
- Research Center Borstel, Borstel, Germany
- Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Borstel, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, Kiel, Germany
| | - Yifat Merbl
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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34
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Weeden CE, Gayevskiy V, Marceaux C, Batey D, Tan T, Yokote K, Ribera NT, Clatch A, Christo S, Teh CE, Mitchell AJ, Trussart M, Rankin LC, Obers A, McDonald JA, Sutherland KD, Sharma VJ, Starkey G, D'Costa R, Antippa P, Leong T, Steinfort D, Irving L, Swanton C, Gordon CL, Mackay LK, Speed TP, Gray DHD, Asselin-Labat ML. Early immune pressure initiated by tissue-resident memory T cells sculpts tumor evolution in non-small cell lung cancer. Cancer Cell 2023; 41:837-852.e6. [PMID: 37086716 DOI: 10.1016/j.ccell.2023.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 02/05/2023] [Accepted: 03/24/2023] [Indexed: 04/24/2023]
Abstract
Tissue-resident memory T (TRM) cells provide immune defense against local infection and can inhibit cancer progression. However, it is unclear to what extent chronic inflammation impacts TRM activation and whether TRM cells existing in tissues before tumor onset influence cancer evolution in humans. We performed deep profiling of healthy lungs and lung cancers in never-smokers (NSs) and ever-smokers (ESs), finding evidence of enhanced immunosurveillance by cells with a TRM-like phenotype in ES lungs. In preclinical models, tumor-specific or bystander TRM-like cells present prior to tumor onset boosted immune cell recruitment, causing tumor immune evasion through loss of MHC class I protein expression and resistance to immune checkpoint inhibitors. In humans, only tumors arising in ES patients underwent clonal immune evasion, unrelated to tobacco-associated mutagenic signatures or oncogenic drivers. These data demonstrate that enhanced TRM-like activity prior to tumor development shapes the evolution of tumor immunogenicity and can impact immunotherapy outcomes.
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Affiliation(s)
- Clare E Weeden
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Velimir Gayevskiy
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Claire Marceaux
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel Batey
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Tania Tan
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Kenta Yokote
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Nina Tubau Ribera
- Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Allison Clatch
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Susan Christo
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Charis E Teh
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andrew J Mitchell
- Materials Characterisation and Fabrication Platform, Department of Chemical Engineering, the University of Melbourne, Parkville, VIC, Australia
| | - Marie Trussart
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Lucille C Rankin
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Andreas Obers
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Jackson A McDonald
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Kate D Sutherland
- ACRF Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia
| | - Varun J Sharma
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia; Department of Cardiothoracic Surgery, Austin Health, Heidelberg, VIC, Australia
| | - Graham Starkey
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; Liver and Intestinal Transplant Unit, Austin Health, Heidelberg, VIC, Australia
| | - Rohit D'Costa
- DonateLife Victoria, Carlton, VIC, Australia; Department of Intensive Care Medicine, Melbourne Health, Melbourne, VIC, Australia
| | - Phillip Antippa
- Department of Surgery, University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Tracy Leong
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia; Department of Respiratory and Sleep Medicine, Austin Health, Heidelberg, VIC, Australia
| | - Daniel Steinfort
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Louis Irving
- Department of Medicine, the University of Melbourne, Parkville, VIC, Australia; The Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Claire L Gordon
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Infectious Diseases, Austin Health, Heidelberg, VIC, Australia; North Eastern Public Health Unit, Austin Health, Heidelberg, VIC, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; School of Mathematics and Statistics, the University of Melbourne, Parkville, VIC, Australia
| | - Daniel H D Gray
- Immunology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
| | - Marie-Liesse Asselin-Labat
- Personalised Oncology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Department of Medical Biology, the University of Melbourne, Parkville, VIC, Australia.
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35
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Weeden CE, Hill W, Lim EL, Grönroos E, Swanton C. Impact of risk factors on early cancer evolution. Cell 2023; 186:1541-1563. [PMID: 37059064 DOI: 10.1016/j.cell.2023.03.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/31/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
Recent identification of oncogenic cells within healthy tissues and the prevalence of indolent cancers found incidentally at autopsies reveal a greater complexity in tumor initiation than previously appreciated. The human body contains roughly 40 trillion cells of 200 different types that are organized within a complex three-dimensional matrix, necessitating exquisite mechanisms to restrain aberrant outgrowth of malignant cells that have the capacity to kill the host. Understanding how this defense is overcome to trigger tumorigenesis and why cancer is so extraordinarily rare at the cellular level is vital to future prevention therapies. In this review, we discuss how early initiated cells are protected from further tumorigenesis and the non-mutagenic pathways by which cancer risk factors promote tumor growth. By nature, the absence of permanent genomic alterations potentially renders these tumor-promoting mechanisms clinically targetable. Finally, we consider existing strategies for early cancer interception with perspectives on the next steps for molecular cancer prevention.
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Affiliation(s)
- Clare E Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Center of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK.
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36
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Dijkstra KK, Wu Y, Swanton C. The Effects of Clonal Heterogeneity on Cancer Immunosurveillance. Annu Rev Cancer Biol 2023. [DOI: 10.1146/annurev-cancerbio-061521-101910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Intratumor heterogeneity (ITH) is associated with tumor progression in several clinical and experimental settings and contributes to therapeutic resistance. Its relation to cancer immunosurveillance is complex. Clonally heterogeneous tumors are associated with decreased immunosurveillance and are less responsive to immune checkpoint inhibition, but the mechanistic basis underlying these observations remains unclear. One possibility is that tumors that are under active immunosurveillance are relatively homogeneous because immunosurveillance prevents the outgrowth of immunogenic subclones. Alternatively, high ITH might directly impair immunosurveillance due to lower dosages of subclonal antigens, competition between antigens and immunodominance, the induction of detrimental T cell differentiation programs, or negative feedback loops. Here we review the evidence for these scenarios and outline hypotheses that could underlie the negative association between clonal heterogeneity and cancer immunosurveillance. Expected final online publication date for the Annual Review of Cancer Biology, Volume 7 is April 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Krijn K. Dijkstra
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom;,
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Yin Wu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom;,
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Peter Gorer Department of Immunobiology and Centre for Inflammation Biology and Cancer Immunology, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
- Immunosurveillance Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom;,
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
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37
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Lucas O, Ward S, Zaidi R, Hill M, Lim E, Zhai H, Bunkum A, Hessey S, Dietzen M, Rowan A, Naceur-Lombardelli C, Kanu N, Jamal-Hanjani M, Swanton C, Zaccaria S. Abstract 4277: Measuring proliferation rates of distinct tumour clones using single-cell DNA sequencing. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background:
Tumour proliferation rate is a key phenotypic feature of cancer, with higher rates linked to poorer clinical outcomes. Thus far, proliferation rates have been measured using pathological or experimental techniques on bulk tumour samples. However, while tumours are heterogeneous compositions of distinct clones with varying levels of fitness, measuring the proliferation of individual clones has not been possible to date. We hypothesise that enabling the identification of the most proliferative clones would reveal genomic hallmarks of aggressive clones, or the prediction of their potential phenotype, e.g., metastatic potential.
Methods:
We have developed SPRINTER (Single-cell Proliferation Rate Inference in Neoplasms Through Evolutionary Routes), a novel computational method to measure proliferation rates in individual tumour clones using single-cell whole-genome DNA sequencing. To assess the accuracy and power of SPRINTER, we have also developed an experimental approach to DNA sequence >18,000 single cells, accurately separated in different DNA-replication phases. We have sequenced and applied SPRINTER to >10,000 non-small cell lung cancer cells from longitudinal and metastatic tumour samples within the TRACERx study and PEACE autopsy programme. We have further analysed published data from >10,000 breast cancer cells.
Results:
We demonstrate that SPRINTER can accurately identify subpopulations of cells with different proliferation rates using relatively small numbers of cells, in contrast to previous preliminary approaches. While our estimates are concordant with previous bulk experimental studies (5-40%), we importantly have identified clonal heterogeneity in proliferation rates. Using bulk analysis, we have identified patterns of dissemination of tumour clones in non-small cell lung cancer. Integrating this with single-cell data, our results indicate that more widely disseminating tumour clones have higher proliferation rates, suggesting a link between proliferation and dissemination potential. We additionally find that clones are more proliferative in the metastatic versus the primary setting. Furthermore, we have identified high proliferation clones that may have a selective advantage in a breast tumour, and have inferred that they likely arose recently in cancer evolution.
Conclusions:
We have developed a novel method that enables accurate identification of proliferation rates of individual tumour clones using single-cell DNA sequencing data, allowing the investigation of genomic hallmarks in highly proliferative clones that might lead to higher fitness.
Citation Format: Olivia Lucas, Sophie Ward, Rija Zaidi, Mark Hill, Emilia Lim, Haoran Zhai, Abigail Bunkum, Sonya Hessey, Michelle Dietzen, Andrew Rowan, Cristina Naceur-Lombardelli, Nnenna Kanu, Mariam Jamal-Hanjani, Charles Swanton, Simone Zaccaria. Measuring proliferation rates of distinct tumour clones using single-cell DNA sequencing. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4277.
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Affiliation(s)
- Olivia Lucas
- 1University College London, London, United Kingdom
| | - Sophie Ward
- 2Francis Crick Institute, London, United Kingdom
| | - Rija Zaidi
- 1University College London, London, United Kingdom
| | - Mark Hill
- 2Francis Crick Institute, London, United Kingdom
| | - Emilia Lim
- 2Francis Crick Institute, London, United Kingdom
| | - Haoran Zhai
- 1University College London, London, United Kingdom
| | | | - Sonya Hessey
- 1University College London, London, United Kingdom
| | | | - Andrew Rowan
- 2Francis Crick Institute, London, United Kingdom
| | | | - Nnenna Kanu
- 1University College London, London, United Kingdom
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38
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Cha H, Simpson B, Swanton C, Litchfield K, Consortium GER. Abstract 3137: Somatic structure variants as a biomarker to predict immune checkpoint inhibitor response by generating anti-tumour antigen. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-3137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
The introduction of checkpoint inhibitors (CPI) has revolutionised the treatment of advanced cancers, which act to ameliorate the anti-tumour response through blocking inhibitive immune checkpoint receptors. Whole-exome sequencing (WES) based estimates of tumour mutational burden (TMB) has been robustly associated with response to CPI therapy across multiple tumour types and a threshold of ≥10 mutations per megabase (Mb) is now an FDA-approved biomarker for treatment with pembrolizumab. However, studies to date have been limited to whole exome sequencing (WES), with no data yet reported on the utility of whole genome sequencing (WGS) as a biomarker to predict CPI response. WGS data can identify non-coding alterations which impact the expression of immune regulatory genes, variants likely to form non-coding epitopes, including novel open reading frame mutations especially structure variants (SV). Here, we have identified a pan-cancer cohort of n=364 patients treated with CPI from Genomics England 100,000 Genomes Project (GEL). We find that SV burden is highly associated with worse CPI response (HR =1.3 (1.0-1.8) , p-value = 0.037) and high SV burden group have low tumour-infiltrating lymphocyte (TIL) score (P-value < 0.0001). However, we found that patients who have high proportion of SV derived neoantigen group improved overall survival (HR = 0.44 (0.27-0.73) , p-value = 0.002). In addition, enhancer region alteration of antigen present gene was observed in 43 patients (12%) and was associated with worse CPI response. (HR = 1.5 (1.0-2.2), P-value = 0.034). We further explored the SV derived neoantigen generate neoantigen-specific T cell response.
Summary of Cox Model from structure variant Variables No. patients HR (95% CI) P Sex Female 164 Male 200 1.15 ( 0.87-1.52) 0.3285 Cancer Type Others 59 Lung 88 1.39 (0.91-2.14) 0.1255 Melanoma 155 0.84 (0.56-1.28) 0.4267 Renal 62 0.84 (0.52-1.38) 0.495 TMB estimated WGS 364 0.98 (0.97-0.99) 0.0036 SV burden Low 182 High 182 1.36 (1.02-1.81) 0.0358 Proportion of anti-tumour antigen from SV Low 49 High 47 0.48 (0.29-0.8) 0.0045 antigen non-generate 268 0.49 (0.35-0.7) < 0.0001
Citation Format: Hongui Cha, Benjamin Simpson, Charles Swanton, Kevin Litchfield, Genomics England Research Consortium. Somatic structure variants as a biomarker to predict immune checkpoint inhibitor response by generating anti-tumour antigen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3137.
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Affiliation(s)
- Hongui Cha
- 1University College London, London, United Kingdom
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Hessey S, Huebner A, Pich O, Bunkum A, Liu W, Moore DA, Naceur-Lombardelli C, Veeriah S, Ward S, Salgado R, McGranahan N, Zaccaria S, Swanton C, Jamal-Hanjani M. Abstract 2037: Tracking the emergence of immunotherapy resistance in lung cancer metastases. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-2037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Metastatic non-small cell lung cancer (NSCLC) results from a complex evolutionary process in which cancer cells migrate from a primary tumour to a new anatomical site. Immunotherapy is frequently used to treat NSCLC, but drug resistance is frequent (>50%) and metastasis remains the most common cause of death. Recent studies of primary and metastatic tumours suggest that anti-cancer treatments can impact cancer evolutionary dynamics by applying selective pressures that promote the development of treatment resistance in genetically distinct subpopulations of cancer cells, or tumour clones. However, the relationship between metastatic progression and the development of resistance to immunotherapy has not been fully explored. In particular, whether metastases become resistant to immunotherapy as a result of the migration of resistant cells or whether distinct metastatic sites converge in parallel toward an immunotherapy resistance phenotype irrespective of cell migration, is not known.
In this work, we investigate the role of metastatic cell migration in the development of immunotherapy resistance using DNA sequencing data from primary and metastatic tumour samples from twelve immunotherapy-treated patients with NSCLC co-recruited to the national TRACERx and PEACE studies. Using computational approaches, we identified distinct tumour clones in primary and metastatic tumours and used these to reconstruct tumour phylogenies for each patient. By evaluating tumour clonal dynamics in relation to treatment, we classified tumour clones as either sensitive or resistant to immunotherapy. We reconstructed the metastatic migration histories of these clones using existing computational methods based on somatic single nucleotide variants. Our results suggest that heterogeneous mechanisms of immune evasion develop in parallel at distinct metastatic sites. The ongoing analysis of the genetic changes that distinguish resistant from sensitive clones, and migrating from non-migrating clones, will provide further detail regarding the impact of metastatic migrations on immunotherapy resistance.
Using this approach to map the evolutionary history of metastatic NSCLC, we provide insight into the mechanism by which immunotherapy resistance develops at distinct metastatic sites.
Citation Format: Sonya Hessey, Ariana Huebner, Oriol Pich, Abi Bunkum, Wing Liu, David A. Moore, Cristina Naceur-Lombardelli, Selvaraju Veeriah, Sophie Ward, Roberto Salgado, Nicholas McGranahan, Simone Zaccaria, Charles Swanton, Mariam Jamal-Hanjani. Tracking the emergence of immunotherapy resistance in lung cancer metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2037.
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Affiliation(s)
- Sonya Hessey
- 1University College London (UCL), London, United Kingdom
| | - Ariana Huebner
- 1University College London (UCL), London, United Kingdom
| | - Oriol Pich
- 2Francis Crick Institute, London, United Kingdom
| | - Abi Bunkum
- 1University College London (UCL), London, United Kingdom
| | - Wing Liu
- 1University College London (UCL), London, United Kingdom
| | - David A. Moore
- 1University College London (UCL), London, United Kingdom
| | | | | | - Sophie Ward
- 2Francis Crick Institute, London, United Kingdom
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40
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Frankell AM, Dietzen M, Al Bakir M, Lim EL, Karasaki T, Ward S, Veeriah S, Colliver E, Huebner A, Bunkum A, Hill MS, Grigoriadis K, Moore DA, Black JRM, Liu WK, Thol K, Pich O, Watkins TBK, Naceur-Lombardelli C, Cook DE, Salgado R, Wilson GA, Bailey C, Angelova M, Bentham R, Martínez-Ruiz C, Abbosh C, Nicholson AG, Le Quesne J, Biswas D, Rosenthal R, Puttick C, Hessey S, Lee C, Prymas P, Toncheva A, Smith J, Xing W, Nicod J, Price G, Kerr KM, Naidu B, Middleton G, Blyth KG, Fennell DA, Forster MD, Lee SM, Falzon M, Hewish M, Shackcloth MJ, Lim E, Benafif S, Russell P, Boleti E, Krebs MG, Lester JF, Papadatos-Pastos D, Ahmad T, Thakrar RM, Lawrence D, Navani N, Janes SM, Dive C, Blackhall FH, Summers Y, Cave J, Marafioti T, Herrero J, Quezada SA, Peggs KS, Schwarz RF, Van Loo P, Miedema DM, Birkbak NJ, Hiley CT, Hackshaw A, Zaccaria S, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of lung cancer and impact of subclonal selection in TRACERx. Nature 2023; 616:525-533. [PMID: 37046096 PMCID: PMC10115649 DOI: 10.1038/s41586-023-05783-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 02/02/2023] [Indexed: 04/14/2023]
Abstract
Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource.
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Affiliation(s)
- Alexander M Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Wing Kin Liu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Robert Bentham
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Pathology Department, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Dhruva Biswas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Division of Medicine, University College London, London, UK
| | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Jon Smith
- Scientific Computing, The Francis Crick Institute, London, UK
| | - Wei Xing
- Scientific Computing, The Francis Crick Institute, London, UK
| | - Jerome Nicod
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Gillian Price
- Department of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
- University of Aberdeen, Aberdeen, UK
| | - Keith M Kerr
- University of Aberdeen, Aberdeen, UK
- Department of Pathology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
| | - Babu Naidu
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Gary Middleton
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Kevin G Blyth
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Queen Elizabeth University Hospital, Glasgow, UK
| | - Dean A Fennell
- University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Mary Falzon
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Madeleine Hewish
- Royal Surrey Hospital, Royal Surrey Hospitals NHS Foundation Trust, Guilford, UK
- University of Surrey, Guilford, UK
| | | | - Eric Lim
- Academic Division of Thoracic Surgery, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sarah Benafif
- Department of Oncology, University College London Hospitals, London, UK
| | - Peter Russell
- Princess Alexandra Hospital, The Princess Alexandra Hospital NHS Trust, Harlow, UK
| | - Ekaterini Boleti
- Royal Free Hospital, Royal Free London NHS Foundation Trust, London, UK
| | - Matthew G Krebs
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Jason F Lester
- Singleton Hospital, Swansea Bay University Health Board, Swansea, UK
| | | | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, London, UK
| | - Ricky M Thakrar
- Department of Thoracic Medicine, University College London Hospitals, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - David Lawrence
- Department of Thoracic Surgery, University College London Hospital NHS Trust, London, UK
| | - Neal Navani
- Department of Thoracic Medicine, University College London Hospitals, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Fiona H Blackhall
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Yvonne Summers
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Judith Cave
- Department of Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Javier Herrero
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Department of Haematology, University College London Hospitals, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Roland F Schwarz
- Institute for Computational Cancer Biology, Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin, Germany
| | - Peter Van Loo
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Daniël M Miedema
- LEXOR, Center for Experimental and Molecular Medicine, Cancer Center Amsterdam and Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Amsterdam, The Netherlands
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Allan Hackshaw
- Cancer Research UK and UCL Cancer Trials Centre, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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41
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Ng KW, Boumelha J, Enfield KSS, Almagro J, Cha H, Pich O, Karasaki T, Moore DA, Salgado R, Sivakumar M, Young G, Molina-Arcas M, de Carné Trécesson S, Anastasiou P, Fendler A, Au L, Shepherd STC, Martínez-Ruiz C, Puttick C, Black JRM, Watkins TBK, Kim H, Shim S, Faulkner N, Attig J, Veeriah S, Magno N, Ward S, Frankell AM, Al Bakir M, Lim EL, Hill MS, Wilson GA, Cook DE, Birkbak NJ, Behrens A, Yousaf N, Popat S, Hackshaw A, Hiley CT, Litchfield K, McGranahan N, Jamal-Hanjani M, Larkin J, Lee SH, Turajlic S, Swanton C, Downward J, Kassiotis G. Antibodies against endogenous retroviruses promote lung cancer immunotherapy. Nature 2023; 616:563-573. [PMID: 37046094 PMCID: PMC10115647 DOI: 10.1038/s41586-023-05771-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/30/2023] [Indexed: 04/14/2023]
Abstract
B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)1,2. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive1,2. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma3. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response.
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Affiliation(s)
- Kevin W Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Katey S S Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Queensland, Australia
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - George Young
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, UK
| | | | | | | | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hyemin Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seohee Shim
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Nikhil Faulkner
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jan Attig
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Neil Magno
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
- CRUK Convergence Science Centre, Imperial College, London, UK
| | - Nadia Yousaf
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Lung Unit, The Royal Marsden Hospital, London, UK
| | - Sanjay Popat
- Lung Unit, The Royal Marsden Hospital, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK.
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
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42
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Al Bakir M, Huebner A, Martínez-Ruiz C, Grigoriadis K, Watkins TBK, Pich O, Moore DA, Veeriah S, Ward S, Laycock J, Johnson D, Rowan A, Razaq M, Akther M, Naceur-Lombardelli C, Prymas P, Toncheva A, Hessey S, Dietzen M, Colliver E, Frankell AM, Bunkum A, Lim EL, Karasaki T, Abbosh C, Hiley CT, Hill MS, Cook DE, Wilson GA, Salgado R, Nye E, Stone RK, Fennell DA, Price G, Kerr KM, Naidu B, Middleton G, Summers Y, Lindsay CR, Blackhall FH, Cave J, Blyth KG, Nair A, Ahmed A, Taylor MN, Procter AJ, Falzon M, Lawrence D, Navani N, Thakrar RM, Janes SM, Papadatos-Pastos D, Forster MD, Lee SM, Ahmad T, Quezada SA, Peggs KS, Van Loo P, Dive C, Hackshaw A, Birkbak NJ, Zaccaria S, Jamal-Hanjani M, McGranahan N, Swanton C. The evolution of non-small cell lung cancer metastases in TRACERx. Nature 2023; 616:534-542. [PMID: 37046095 PMCID: PMC10115651 DOI: 10.1038/s41586-023-05729-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/12/2023] [Indexed: 04/14/2023]
Abstract
Metastatic disease is responsible for the majority of cancer-related deaths1. We report the longitudinal evolutionary analysis of 126 non-small cell lung cancer (NSCLC) tumours from 421 prospectively recruited patients in TRACERx who developed metastatic disease, compared with a control cohort of 144 non-metastatic tumours. In 25% of cases, metastases diverged early, before the last clonal sweep in the primary tumour, and early divergence was enriched for patients who were smokers at the time of initial diagnosis. Simulations suggested that early metastatic divergence more frequently occurred at smaller tumour diameters (less than 8 mm). Single-region primary tumour sampling resulted in 83% of late divergence cases being misclassified as early, highlighting the importance of extensive primary tumour sampling. Polyclonal dissemination, which was associated with extrathoracic disease recurrence, was found in 32% of cases. Primary lymph node disease contributed to metastatic relapse in less than 20% of cases, representing a hallmark of metastatic potential rather than a route to subsequent recurrences/disease progression. Metastasis-seeding subclones exhibited subclonal expansions within primary tumours, probably reflecting positive selection. Our findings highlight the importance of selection in metastatic clone evolution within untreated primary tumours, the distinction between monoclonal versus polyclonal seeding in dictating site of recurrence, the limitations of current radiological screening approaches for early diverging tumours and the need to develop strategies to target metastasis-seeding subclones before relapse.
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Affiliation(s)
- Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Joanne Laycock
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Diana Johnson
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Maryam Razaq
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mita Akther
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Abigail Bunkum
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Emma Nye
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | | | - Dean A Fennell
- University of Leicester, Leicester, UK
- University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Gillian Price
- Department of Medical Oncology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
- University of Aberdeen, Aberdeen, UK
| | - Keith M Kerr
- University of Aberdeen, Aberdeen, UK
- Department of Pathology, Aberdeen Royal Infirmary NHS Grampian, Aberdeen, UK
| | - Babu Naidu
- Birmingham Acute Care Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - Gary Middleton
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Yvonne Summers
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Colin R Lindsay
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Fiona H Blackhall
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester, UK
| | - Judith Cave
- Department of Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Kevin G Blyth
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Cancer Research UK Beatson Institute, Glasgow, UK
- Queen Elizabeth University Hospital, Glasgow, UK
| | - Arjun Nair
- Department of Radiology, University College London Hospitals, London, UK
- UCL Respiratory, Department of Medicine, University College London, London, UK
| | - Asia Ahmed
- Department of Radiology, University College London Hospitals, London, UK
| | - Magali N Taylor
- Department of Radiology, University College London Hospitals, London, UK
| | | | - Mary Falzon
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - David Lawrence
- Department of Thoracic Surgery, University College London Hospital NHS Trust, London, UK
| | - Neal Navani
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospitals, London, UK
| | - Ricky M Thakrar
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
- Department of Thoracic Medicine, University College London Hospitals, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Martin D Forster
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Siow Ming Lee
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Tanya Ahmad
- Department of Oncology, University College London Hospitals, London, UK
| | - Sergio A Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Karl S Peggs
- Department of Haematology, University College London Hospitals, London, UK
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline Dive
- Cancer Research UK Manchester Institute Cancer Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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43
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Martínez-Ruiz C, Black JRM, Puttick C, Hill MS, Demeulemeester J, Larose Cadieux E, Thol K, Jones TP, Veeriah S, Naceur-Lombardelli C, Toncheva A, Prymas P, Rowan A, Ward S, Cubitt L, Athanasopoulou F, Pich O, Karasaki T, Moore DA, Salgado R, Colliver E, Castignani C, Dietzen M, Huebner A, Al Bakir M, Tanić M, Watkins TBK, Lim EL, Al-Rashed AM, Lang D, Clements J, Cook DE, Rosenthal R, Wilson GA, Frankell AM, de Carné Trécesson S, East P, Kanu N, Litchfield K, Birkbak NJ, Hackshaw A, Beck S, Van Loo P, Jamal-Hanjani M, Swanton C, McGranahan N. Genomic-transcriptomic evolution in lung cancer and metastasis. Nature 2023; 616:543-552. [PMID: 37046093 PMCID: PMC10115639 DOI: 10.1038/s41586-023-05706-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/04/2023] [Indexed: 04/14/2023]
Abstract
Intratumour heterogeneity (ITH) fuels lung cancer evolution, which leads to immune evasion and resistance to therapy1. Here, using paired whole-exome and RNA sequencing data, we investigate intratumour transcriptomic diversity in 354 non-small cell lung cancer tumours from 347 out of the first 421 patients prospectively recruited into the TRACERx study2,3. Analyses of 947 tumour regions, representing both primary and metastatic disease, alongside 96 tumour-adjacent normal tissue samples implicate the transcriptome as a major source of phenotypic variation. Gene expression levels and ITH relate to patterns of positive and negative selection during tumour evolution. We observe frequent copy number-independent allele-specific expression that is linked to epigenomic dysfunction. Allele-specific expression can also result in genomic-transcriptomic parallel evolution, which converges on cancer gene disruption. We extract signatures of RNA single-base substitutions and link their aetiology to the activity of the RNA-editing enzymes ADAR and APOBEC3A, thereby revealing otherwise undetected ongoing APOBEC activity in tumours. Characterizing the transcriptomes of primary-metastatic tumour pairs, we combine multiple machine-learning approaches that leverage genomic and transcriptomic variables to link metastasis-seeding potential to the evolutionary context of mutations and increased proliferation within primary tumour regions. These results highlight the interplay between the genome and transcriptome in influencing ITH, lung cancer evolution and metastasis.
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Affiliation(s)
- Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Integrative Cancer Genomics Laboratory, Department of Oncology, KU Leuven, Leuven, Belgium
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Elizabeth Larose Cadieux
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Kerstin Thol
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas P Jones
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Laura Cubitt
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Foteini Athanasopoulou
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Carla Castignani
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Miljana Tanić
- Medical Genomics, University College London Cancer Institute, London, UK
- Experimental Oncology, Institute for Oncology and Radiology of Serbia, Belgrade, Serbia
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Ali M Al-Rashed
- Centre for Nephrology, Division of Medicine, University College London, London, UK
| | - Danny Lang
- Scientific Computing STP, Francis Crick Institute, London, UK
| | - James Clements
- Scientific Computing STP, Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Rachel Rosenthal
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
| | | | - Philip East
- Bioinformatics and Biostatistics, The Francis Crick Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Stephan Beck
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute and University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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44
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Hill W, Lim EL, Weeden CE, Lee C, Augustine M, Chen K, Kuan FC, Marongiu F, Evans EJ, Moore DA, Rodrigues FS, Pich O, Bakker B, Cha H, Myers R, van Maldegem F, Boumelha J, Veeriah S, Rowan A, Naceur-Lombardelli C, Karasaki T, Sivakumar M, De S, Caswell DR, Nagano A, Black JRM, Martínez-Ruiz C, Ryu MH, Huff RD, Li S, Favé MJ, Magness A, Suárez-Bonnet A, Priestnall SL, Lüchtenborg M, Lavelle K, Pethick J, Hardy S, McRonald FE, Lin MH, Troccoli CI, Ghosh M, Miller YE, Merrick DT, Keith RL, Al Bakir M, Bailey C, Hill MS, Saal LH, Chen Y, George AM, Abbosh C, Kanu N, Lee SH, McGranahan N, Berg CD, Sasieni P, Houlston R, Turnbull C, Lam S, Awadalla P, Grönroos E, Downward J, Jacks T, Carlsten C, Malanchi I, Hackshaw A, Litchfield K, DeGregori J, Jamal-Hanjani M, Swanton C. Lung adenocarcinoma promotion by air pollutants. Nature 2023; 616:159-167. [PMID: 37020004 PMCID: PMC7614604 DOI: 10.1038/s41586-023-05874-3] [Citation(s) in RCA: 97] [Impact Index Per Article: 97.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 02/21/2023] [Indexed: 04/07/2023]
Abstract
A complete understanding of how exposure to environmental substances promotes cancer formation is lacking. More than 70 years ago, tumorigenesis was proposed to occur in a two-step process: an initiating step that induces mutations in healthy cells, followed by a promoter step that triggers cancer development1. Here we propose that environmental particulate matter measuring ≤2.5 μm (PM2.5), known to be associated with lung cancer risk, promotes lung cancer by acting on cells that harbour pre-existing oncogenic mutations in healthy lung tissue. Focusing on EGFR-driven lung cancer, which is more common in never-smokers or light smokers, we found a significant association between PM2.5 levels and the incidence of lung cancer for 32,957 EGFR-driven lung cancer cases in four within-country cohorts. Functional mouse models revealed that air pollutants cause an influx of macrophages into the lung and release of interleukin-1β. This process results in a progenitor-like cell state within EGFR mutant lung alveolar type II epithelial cells that fuels tumorigenesis. Ultradeep mutational profiling of histologically normal lung tissue from 295 individuals across 3 clinical cohorts revealed oncogenic EGFR and KRAS driver mutations in 18% and 53% of healthy tissue samples, respectively. These findings collectively support a tumour-promoting role for PM2.5 air pollutants and provide impetus for public health policy initiatives to address air pollution to reduce disease burden.
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Affiliation(s)
- William Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare E Weeden
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Division of Medicine, University College London, London, UK
| | - Marcellus Augustine
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Division of Medicine, University College London, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Kezhong Chen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Thoracic Surgery and Thoracic Oncology Institute, Peking University People's Hospital, Beijing, China
| | - Feng-Che Kuan
- Department of Hematology and Oncology, Chang Gung Memorial Hospital, Chiayi Branch, Chiayi, Taiwan
- Graduate Institute of Clinical Medical Sciences, Chang-Gung University, Taoyuan, Taiwan
| | - Fabio Marongiu
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Edward J Evans
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Felipe S Rodrigues
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Bjorn Bakker
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hongui Cha
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Renelle Myers
- BC Cancer Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Febe van Maldegem
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Swapnanil De
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Deborah R Caswell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ai Nagano
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- 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, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Min Hyung Ryu
- Department of Medicine, Division of Respiratory Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease, Vancouver Coastal Health Research Institute, UBC, Vancouver, British Columbia, Canada
| | - Ryan D Huff
- Department of Medicine, Division of Respiratory Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease, Vancouver Coastal Health Research Institute, UBC, Vancouver, British Columbia, Canada
| | - Shijia Li
- Department of Medicine, Division of Respiratory Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease, Vancouver Coastal Health Research Institute, UBC, Vancouver, British Columbia, Canada
| | | | - Alastair Magness
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Alejandro Suárez-Bonnet
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Simon L Priestnall
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, UK
- Experimental Histopathology, The Francis Crick Institute, London, UK
| | - Margreet Lüchtenborg
- National Disease Registration Service (NDRS), NHS England, Leeds, UK
- Centre for Cancer, Society and Public Health, Comprehensive Cancer Centre, School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Katrina Lavelle
- National Disease Registration Service (NDRS), NHS England, Leeds, UK
| | - Joanna Pethick
- National Disease Registration Service (NDRS), NHS England, Leeds, UK
| | - Steven Hardy
- National Disease Registration Service (NDRS), NHS England, Leeds, UK
| | - Fiona E McRonald
- National Disease Registration Service (NDRS), NHS England, Leeds, UK
| | - Meng-Hung Lin
- Health Information and Epidemiology Laboratory, Chang-Gung Memorial Hospital, Chiayi, Taiwan
| | - Clara I Troccoli
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Flagship Biosciences, Boulder, CO, USA
| | - Moumita Ghosh
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - York E Miller
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Veterans Affairs Eastern Colorado Healthcare System, Aurora, CO, USA
| | - Daniel T Merrick
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Robert L Keith
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Veterans Affairs Eastern Colorado Healthcare System, Aurora, CO, USA
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Chris Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Lao H Saal
- SAGA Diagnostics, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Yilun Chen
- SAGA Diagnostics, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Anthony M George
- SAGA Diagnostics, Lund, Sweden
- Division of Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Peter Sasieni
- Comprehensive Cancer Centre, King's College London, London, UK
| | - Richard Houlston
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Stephen Lam
- BC Cancer Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Tyler Jacks
- David H. Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher Carlsten
- Department of Medicine, Division of Respiratory Medicine, Chan-Yeung Centre for Occupational and Environmental Respiratory Disease, Vancouver Coastal Health Research Institute, UBC, Vancouver, British Columbia, Canada
| | - Ilaria Malanchi
- Tumour-Host Interaction Laboratory, The Francis Crick Institute, London, UK
| | - Allan Hackshaw
- Cancer Research UK and UCL Cancer Trials Centre, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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Abbosh C, Frankell AM, Harrison T, Kisistok J, Garnett A, Johnson L, Veeriah S, Moreau M, Chesh A, Chaunzwa TL, Weiss J, Schroeder MR, Ward S, Grigoriadis K, Shahpurwalla A, Litchfield K, Puttick C, Biswas D, Karasaki T, Black JRM, Martínez-Ruiz C, Bakir MA, Pich O, Watkins TBK, Lim EL, Huebner A, Moore DA, Godin-Heymann N, L'Hernault A, Bye H, Odell A, Roberts P, Gomes F, Patel AJ, Manzano E, Hiley CT, Carey N, Riley J, Cook DE, Hodgson D, Stetson D, Barrett JC, Kortlever RM, Evan GI, Hackshaw A, Daber RD, Shaw JA, Aerts HJWL, Licon A, Stahl J, Jamal-Hanjani M, Birkbak NJ, McGranahan N, Swanton C. Tracking early lung cancer metastatic dissemination in TRACERx using ctDNA. Nature 2023; 616:553-562. [PMID: 37055640 PMCID: PMC7614605 DOI: 10.1038/s41586-023-05776-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 01/30/2023] [Indexed: 04/15/2023]
Abstract
Circulating tumour DNA (ctDNA) can be used to detect and profile residual tumour cells persisting after curative intent therapy1. The study of large patient cohorts incorporating longitudinal plasma sampling and extended follow-up is required to determine the role of ctDNA as a phylogenetic biomarker of relapse in early-stage non-small-cell lung cancer (NSCLC). Here we developed ctDNA methods tracking a median of 200 mutations identified in resected NSCLC tissue across 1,069 plasma samples collected from 197 patients enrolled in the TRACERx study2. A lack of preoperative ctDNA detection distinguished biologically indolent lung adenocarcinoma with good clinical outcome. Postoperative plasma analyses were interpreted within the context of standard-of-care radiological surveillance and administration of cytotoxic adjuvant therapy. Landmark analyses of plasma samples collected within 120 days after surgery revealed ctDNA detection in 25% of patients, including 49% of all patients who experienced clinical relapse; 3 to 6 monthly ctDNA surveillance identified impending disease relapse in an additional 20% of landmark-negative patients. We developed a bioinformatic tool (ECLIPSE) for non-invasive tracking of subclonal architecture at low ctDNA levels. ECLIPSE identified patients with polyclonal metastatic dissemination, which was associated with a poor clinical outcome. By measuring subclone cancer cell fractions in preoperative plasma, we found that subclones seeding future metastases were significantly more expanded compared with non-metastatic subclones. Our findings will support (neo)adjuvant trial advances and provide insights into the process of metastatic dissemination using low-ctDNA-level liquid biopsy.
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Affiliation(s)
- Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Judit Kisistok
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | | | | | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | | | - Tafadzwa L Chaunzwa
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Jakob Weiss
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Radiology, Freiburg University Hospital, Freiburg, Germany
| | | | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | | | | | | | | | | | - Fabio Gomes
- The Christie NHS Foundation Trust, Manchester, UK
| | - Akshay J Patel
- University Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Manzano
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nicolas Carey
- Cancer Research Centre, University of Leicester, Leicester, UK
| | - Joan Riley
- Cancer Research Centre, University of Leicester, Leicester, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | | | | | | | - Gerard I Evan
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | | | - Jacqui A Shaw
- Cancer Research Centre, University of Leicester, Leicester, UK
| | - Hugo J W L Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| | | | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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46
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Al-Sawaf O, Weiss J, Skrzypski M, Lam JM, Karasaki T, Zambrana F, Kidd AC, Frankell AM, Watkins TBK, Martínez-Ruiz C, Puttick C, Black JRM, Huebner A, Bakir MA, Sokač M, Collins S, Veeriah S, Magno N, Naceur-Lombardelli C, Prymas P, Toncheva A, Ward S, Jayanth N, Salgado R, Bridge CP, Christiani DC, Mak RH, Bay C, Rosenthal M, Sattar N, Welsh P, Liu Y, Perrimon N, Popuri K, Beg MF, McGranahan N, Hackshaw A, Breen DM, O'Rahilly S, Birkbak NJ, Aerts HJWL, Jamal-Hanjani M, Swanton C. Body composition and lung cancer-associated cachexia in TRACERx. Nat Med 2023; 29:846-858. [PMID: 37045997 PMCID: PMC7614477 DOI: 10.1038/s41591-023-02232-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 01/24/2023] [Indexed: 04/14/2023]
Abstract
Cancer-associated cachexia (CAC) is a major contributor to morbidity and mortality in individuals with non-small cell lung cancer. Key features of CAC include alterations in body composition and body weight. Here, we explore the association between body composition and body weight with survival and delineate potential biological processes and mediators that contribute to the development of CAC. Computed tomography-based body composition analysis of 651 individuals in the TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy (Rx)) study suggested that individuals in the bottom 20th percentile of the distribution of skeletal muscle or adipose tissue area at the time of lung cancer diagnosis, had significantly shorter lung cancer-specific survival and overall survival. This finding was validated in 420 individuals in the independent Boston Lung Cancer Study. Individuals classified as having developed CAC according to one or more features at relapse encompassing loss of adipose or muscle tissue, or body mass index-adjusted weight loss were found to have distinct tumor genomic and transcriptomic profiles compared with individuals who did not develop such features. Primary non-small cell lung cancers from individuals who developed CAC were characterized by enrichment of inflammatory signaling and epithelial-mesenchymal transitional pathways, and differentially expressed genes upregulated in these tumors included cancer-testis antigen MAGEA6 and matrix metalloproteinases, such as ADAMTS3. In an exploratory proteomic analysis of circulating putative mediators of cachexia performed in a subset of 110 individuals from TRACERx, a significant association between circulating GDF15 and loss of body weight, skeletal muscle and adipose tissue was identified at relapse, supporting the potential therapeutic relevance of targeting GDF15 in the management of CAC.
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Affiliation(s)
- Othman Al-Sawaf
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jakob Weiss
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Department of Diagnostic and Interventional Radiology, University Freiburg, Freiburg, Germany
| | - Marcin Skrzypski
- Department of Oncology and Radiotherapy, Medical University of Gdańsk, Gdańsk, Poland
| | - Jie Min Lam
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | | | - Andrew C Kidd
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Mateo Sokač
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Susie Collins
- Early Clinical Development, Pfizer UK Ltd, Cambridge, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Neil Magno
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Paulina Prymas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Nick Jayanth
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - David C Christiani
- Department of Medicine, Massachusetts General Hospital/Harvard Medicine School, and Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Raymond H Mak
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Camden Bay
- Department of Radiology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA, USA
| | - Michael Rosenthal
- Department of Radiology, Brigham and Women's Hospital and Dana-Farber Cancer Institute, and Harvard Medical School, Boston, MA, USA
| | - Naveed Sattar
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Paul Welsh
- School of Cardiovascular and Metabolic Health, University of Glasgow, Glasgow, UK
| | - Ying Liu
- Department of Genetics, Harvard Medical School, Boston, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Boston, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, USA
| | - Karteek Popuri
- Department of Computer Science, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Burnaby, Canada
| | - Mirza Faisal Beg
- School of Engineering Science, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Danna M Breen
- Internal Medicine Research Unit, Pfizer, Cambridge, MA, USA
| | - Stephen O'Rahilly
- Wellcome Trust-MRC Institute of Metabolic Science and NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Nicolai J Birkbak
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Hugo J W L Aerts
- Artificial Intelligence in Medicine (AIM) Program, Mass General Brigham, Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Radiology and Nuclear Medicine, CARIM & GROW, Maastricht University, Maastricht, The Netherlands
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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Karasaki T, Moore DA, Veeriah S, Naceur-Lombardelli C, Toncheva A, Magno N, Ward S, Bakir MA, Watkins TBK, Grigoriadis K, Huebner A, Hill MS, Frankell AM, Abbosh C, Puttick C, Zhai H, Gimeno-Valiente F, Saghafinia S, Kanu N, Dietzen M, Pich O, Lim EL, Martínez-Ruiz C, Black JRM, Biswas D, Campbell BB, Lee C, Colliver E, Enfield KSS, Hessey S, Hiley CT, Zaccaria S, Litchfield K, Birkbak NJ, Cadieux EL, Demeulemeester J, Van Loo P, Adusumilli PS, Tan KS, Cheema W, Sanchez-Vega F, Jones DR, Rekhtman N, Travis WD, Hackshaw A, Marafioti T, Salgado R, Le Quesne J, Nicholson AG, McGranahan N, Swanton C, Jamal-Hanjani M. Evolutionary characterization of lung adenocarcinoma morphology in TRACERx. Nat Med 2023; 29:833-845. [PMID: 37045996 PMCID: PMC7614478 DOI: 10.1038/s41591-023-02230-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 01/24/2023] [Indexed: 04/14/2023]
Abstract
Lung adenocarcinomas (LUADs) display a broad histological spectrum from low-grade lepidic tumors through to mid-grade acinar and papillary and high-grade solid, cribriform and micropapillary tumors. How morphology reflects tumor evolution and disease progression is poorly understood. Whole-exome sequencing data generated from 805 primary tumor regions and 121 paired metastatic samples across 248 LUADs from the TRACERx 421 cohort, together with RNA-sequencing data from 463 primary tumor regions, were integrated with detailed whole-tumor and regional histopathological analysis. Tumors with predominantly high-grade patterns showed increased chromosomal complexity, with higher burden of loss of heterozygosity and subclonal somatic copy number alterations. Individual regions in predominantly high-grade pattern tumors exhibited higher proliferation and lower clonal diversity, potentially reflecting large recent subclonal expansions. Co-occurrence of truncal loss of chromosomes 3p and 3q was enriched in predominantly low-/mid-grade tumors, while purely undifferentiated solid-pattern tumors had a higher frequency of truncal arm or focal 3q gains and SMARCA4 gene alterations compared with mixed-pattern tumors with a solid component, suggesting distinct evolutionary trajectories. Clonal evolution analysis revealed that tumors tend to evolve toward higher-grade patterns. The presence of micropapillary pattern and 'tumor spread through air spaces' were associated with intrathoracic recurrence, in contrast to the presence of solid/cribriform patterns, necrosis and preoperative circulating tumor DNA detection, which were associated with extra-thoracic recurrence. These data provide insights into the relationship between LUAD morphology, the underlying evolutionary genomic landscape, and clinical and anatomical relapse risk.
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Affiliation(s)
- Takahiro Karasaki
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | | | - Antonia Toncheva
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Neil Magno
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Maise Al Bakir
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Kristiana Grigoriadis
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Ariana Huebner
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Christopher Abbosh
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Haoran Zhai
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Francisco Gimeno-Valiente
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sadegh Saghafinia
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Nnennaya Kanu
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, 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, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Dhruva Biswas
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Bill Lyons Informatics Centre, University College London Cancer Institute, London, UK
| | - Brittany B Campbell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Katey S S Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Sonya Hessey
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Crispin T Hiley
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Simone Zaccaria
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Elizabeth Larose Cadieux
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Medical Genomics, University College London Cancer Institute, London, UK
| | - Jonas Demeulemeester
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Integrative Cancer Genomics Laboratory, Department of Oncology, KU Leuven, Leuven, Belgium
- VIB - KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Peter Van Loo
- Cancer Genomics Laboratory, The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prasad S Adusumilli
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Center for Cell Engineering, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kay See Tan
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Waseem Cheema
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francisco Sanchez-Vega
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David R Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William D Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Allan Hackshaw
- Cancer Research UK & UCL Cancer Trials Centre, London, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - John Le Quesne
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
- Pathology Department, Queen Elizabeth University Hospital, NHS Greater Glasgow and Clyde, Glasgow, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
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48
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Virassamy B, Caramia F, Savas P, Sant S, Wang J, Christo SN, Byrne A, Clarke K, Brown E, Teo ZL, von Scheidt B, Freestone D, Gandolfo LC, Weber K, Teply-Szymanski J, Li R, Luen SJ, Denkert C, Loibl S, Lucas O, Swanton C, Speed TP, Darcy PK, Neeson PJ, Mackay LK, Loi S. Intratumoral CD8 + T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer. Cancer Cell 2023; 41:585-601.e8. [PMID: 36827978 DOI: 10.1016/j.ccell.2023.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 10/17/2022] [Accepted: 01/13/2023] [Indexed: 02/25/2023]
Abstract
CD8+ tumor-infiltrating lymphocytes with a tissue-resident memory T (TRM) cell phenotype are associated with favorable prognosis in patients with triple-negative breast cancer (TNBC). However, the relative contribution of CD8+ TRM cells to anti-tumor immunity and immune checkpoint blockade efficacy in breast cancer remains unknown. Here, we show that intratumoral CD8+ T cells in murine mammary tumors transcriptionally resemble those from TNBC patients. Phenotypic and transcriptional studies established two intratumoral sub-populations: one more enriched in markers of terminal exhaustion (TEX-like) and the other with a bona fide resident phenotype (TRM-like). Treatment with anti-PD-1 and anti-CTLA-4 therapy resulted in expansion of these intratumoral populations, with the TRM-like subset displaying significantly enhanced cytotoxic capacity. TRM-like CD8+ T cells could also provide local immune protection against tumor rechallenge and a TRM gene signature extracted from tumor-free tissue was significantly associated with improved clinical outcomes in TNBC patients treated with checkpoint inhibitors.
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Affiliation(s)
- Balaji Virassamy
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Franco Caramia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Peter Savas
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Sneha Sant
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jianan Wang
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - Susan N Christo
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Ann Byrne
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Kylie Clarke
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Emmaline Brown
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Zhi Ling Teo
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca von Scheidt
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David Freestone
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Luke C Gandolfo
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Karsten Weber
- German Breast Cancer Group, GBG-Forschungs GmbH, Neu-Isenburg, Germany
| | - Julia Teply-Szymanski
- German Breast Cancer Group, GBG-Forschungs GmbH, Neu-Isenburg, Germany; Department of Pathology, University Marburg-Giessen, Campus Marburg, Germany
| | - Ran Li
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Stephen J Luen
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Carsten Denkert
- German Breast Cancer Group, GBG-Forschungs GmbH, Neu-Isenburg, Germany; Department of Pathology, University Marburg-Giessen, Campus Marburg, Germany
| | - Sibylle Loibl
- German Breast Cancer Group, GBG-Forschungs GmbH, Neu-Isenburg, Germany
| | - Olivia Lucas
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Computational Cancer Genomics Research Group, University College London Cancer Institute, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Terence P Speed
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC, Australia
| | - Phillip K Darcy
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia.
| | - Paul J Neeson
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia.
| | - Laura K Mackay
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Sherene Loi
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, VIC, Australia.
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49
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Bassey-Archibong BI, Rajendra Chokshi C, Aghaei N, Kieliszek AM, Tatari N, McKenna D, Singh M, Kalpana Subapanditha M, Parmar A, Mobilio D, Savage N, Lam F, Tokar T, Provias J, Lu Y, Chafe SC, Swanton C, Hynds RE, Venugopal C, Singh SK. An HLA-G/SPAG9/STAT3 axis promotes brain metastases. Proc Natl Acad Sci U S A 2023; 120:e2205247120. [PMID: 36780531 PMCID: PMC9974476 DOI: 10.1073/pnas.2205247120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 09/18/2022] [Indexed: 02/15/2023] Open
Abstract
Brain metastases (BM) are the most common brain neoplasm in adults. Current BM therapies still offer limited efficacy and reduced survival outcomes, emphasizing the need for a better understanding of the disease. Herein, we analyzed the transcriptional profile of brain metastasis initiating cells (BMICs) at two distinct stages of the brain metastatic cascade-the "premetastatic" or early stage when they first colonize the brain and the established macrometastatic stage. RNA sequencing was used to obtain the transcriptional profiles of premetastatic and macrometastatic (non-premetastatic) lung, breast, and melanoma BMICs. We identified that lung, breast, and melanoma premetastatic BMICs share a common transcriptomic signature that is distinct from their non-premetastatic counterparts. Importantly, we show that premetastatic BMICs exhibit increased expression of HLA-G, which we further demonstrate functions in an HLA-G/SPAG9/STAT3 axis to promote the establishment of brain metastatic lesions. Our findings suggest that unraveling the molecular landscape of premetastatic BMICs allows for the identification of clinically relevant targets that can possibly inform the development of preventive and/or more efficacious BM therapies.
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Affiliation(s)
| | - Chirayu Rajendra Chokshi
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nikoo Aghaei
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Agata Monika Kieliszek
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Nazanin Tatari
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Dillon McKenna
- Department of Surgery, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Mohini Singh
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | | | - Arun Parmar
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Daniel Mobilio
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Neil Savage
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Fred Lam
- Department of Surgery, Division of Neurosurgery, McMaster University Faculty of Health Sciences, Hamilton General Hospital, Hamilton, ON, L8S 4K1, Canada
| | - Tomas Tokar
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, M5T 2S8, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, University Health Network, Toronto, ON, M5T 2S8, Canada
| | - John Provias
- Department of Anatomical Pathology (Neuropathology), Hamilton General Hospital, Hamilton, ON, L8L 2X2, Canada
- Department of Pathology and Molecular Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Yu Lu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | | | - Charles Swanton
- The Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, University College London, London, WC1E 6DD, United Kingdom
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Robert Edward Hynds
- The Cancer Research UK (CRUK) Lung Cancer Centre of Excellence, University College London (UCL) Cancer Institute, University College London, London, WC1E 6DD, United Kingdom
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Chitra Venugopal
- Department of Surgery, McMaster University, Hamilton, ON, L8S 4K1, Canada
| | - Sheila Kumari Singh
- Department of Surgery, McMaster University, Hamilton, ON, L8S 4K1, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada
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50
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Caswell D, Swanton C. Distinct Mutagenic Activity of APOBEC3G Cytidine Deaminase Identified in Bladder Cancer. Cancer Res 2023; 83:487-488. [PMID: 36789568 DOI: 10.1158/0008-5472.can-22-3598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 02/16/2023]
Abstract
The APOBEC cytidine deaminase enzyme family is linked to mutational signatures identified in cancer. While previous work has provided insights into the role of APOBEC3A and APOBEC3B in mutational processes in cancer, understanding of the mutational signatures induced by other APOBEC family members is limited. In this issue of Cancer Research, Liu and colleagues investigated the role of APOBEC3G (A3G) in bladder cancer. The authors revealed that transgenic expression of A3G in a murine bladder cancer model promotes tumorigenesis and induces a unique mutational signature distinct from previously identified APOBEC signatures. Expression of this A3G-related mutational signature correlated with significantly worse survival in patients with urothelial bladder carcinoma, and A3G expression was identified in 21 different cancer types. These findings suggest that different APOBEC3 enzymes induce unique mutation signatures and play distinct roles in cancer evolution. More complete understanding of the function of each APOBEC3 enzyme will improve anticancer therapy. See related article by Liu et al., p. 506.
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Affiliation(s)
- Deborah Caswell
- Cancer Evaluation and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evaluation and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
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