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Enfield KS, Colliver E, Lee C, Magness A, Moore DA, Sivakumar M, Grigoriadis K, Pich O, Karasaki T, Hobson PS, Levi D, Veeriah S, Puttick C, Nye EL, Green M, Dijkstra KK, Shimato M, Akarca AU, Marafioti T, Salgado R, Hackshaw A, Jamal-Hanjani M, van Maldegem F, McGranahan N, Glass B, Pulaski H, Walk E, Reading JL, Quezada SA, Hiley CT, Downward J, Sahai E, Swanton C, Angelova M. Spatial Architecture of Myeloid and T Cells Orchestrates Immune Evasion and Clinical Outcome in Lung Cancer. Cancer Discov 2024; 14:1018-1047. [PMID: 38581685 PMCID: PMC11145179 DOI: 10.1158/2159-8290.cd-23-1380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/27/2024] [Accepted: 03/22/2024] [Indexed: 04/08/2024]
Abstract
Understanding the role of the tumor microenvironment (TME) in lung cancer is critical to improving patient outcomes. We identified four histology-independent archetype TMEs in treatment-naïve early-stage lung cancer using imaging mass cytometry in the TRACERx study (n = 81 patients/198 samples/2.3 million cells). In immune-hot adenocarcinomas, spatial niches of T cells and macrophages increased with clonal neoantigen burden, whereas such an increase was observed for niches of plasma and B cells in immune-excluded squamous cell carcinomas (LUSC). Immune-low TMEs were associated with fibroblast barriers to immune infiltration. The fourth archetype, characterized by sparse lymphocytes and high tumor-associated neutrophil (TAN) infiltration, had tumor cells spatially separated from vasculature and exhibited low spatial intratumor heterogeneity. TAN-high LUSC had frequent PIK3CA mutations. TAN-high tumors harbored recently expanded and metastasis-seeding subclones and had a shorter disease-free survival independent of stage. These findings delineate genomic, immune, and physical barriers to immune surveillance and implicate neutrophil-rich TMEs in metastasis. SIGNIFICANCE This study provides novel insights into the spatial organization of the lung cancer TME in the context of tumor immunogenicity, tumor heterogeneity, and cancer evolution. Pairing the tumor evolutionary history with the spatially resolved TME suggests mechanistic hypotheses for tumor progression and metastasis with implications for patient outcome and treatment. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Katey S.S. Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Emma Colliver
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Claudia Lee
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Alastair Magness
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - David A. Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- 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
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Kristiana Grigoriadis
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- 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
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
| | - Philip S. Hobson
- Flow Cytometry, The Francis Crick Institute, London, United Kingdom
| | - Dina Levi
- Flow Cytometry, The Francis Crick Institute, London, United Kingdom
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- 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
| | - Emma L. Nye
- Experimental Histopathology, The Francis Crick Institute, London, United Kingdom
| | - Mary Green
- Experimental Histopathology, The Francis Crick Institute, London, United Kingdom
| | - Krijn K. Dijkstra
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Masako Shimato
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Ayse U. Akarca
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Teresa Marafioti
- Department of Cellular Pathology, University College London Hospitals, London, United Kingdom
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, United Kingdom
| | | | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, United Kingdom
- Department of Oncology, University College London Hospitals, London, United Kingdom
| | - Febe van Maldegem
- Oncogene Biology Laboratory, The Francis Crick 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
| | | | | | | | - James L. Reading
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Pre-cancer Immunology Laboratory, University College London Cancer Institute, London, United Kingdom
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Sergio A. Quezada
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
- Immune Regulation and Tumour Immunotherapy Group, Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Crispin T. Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, United Kingdom
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Erik Sahai
- Tumour Cell Biology Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
- 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
| | - Mihaela Angelova
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, United Kingdom
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Laguna JC, Tagliamento M, Lambertini M, Hiznay J, Mezquita L. Tackling Non-Small Cell Lung Cancer in Young Adults: From Risk Factors and Genetic Susceptibility to Lung Cancer Profile and Outcomes. Am Soc Clin Oncol Educ Book 2024; 44:e432488. [PMID: 38788188 DOI: 10.1200/edbk_432488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Lung cancer has traditionally been associated with advanced age; however, its increasing incidence among young adults raises concerning questions regarding its etiology and unique considerations for this population. In contrast to the older population, the onset of lung cancer at younger age may be attributed to a complex interplay of incompletely understood individual susceptibility and prevalent environmental risk factors beyond tobacco smoke exposure, such as radon gas and air pollution, which are widespread globally. Consequently, this leads to distinct clinical and molecular profiles, requiring a tailored approach. Furthermore, a diagnosis of cancer represents a threatening event during the prime years of a young person's life, prompting concern about career development, social aspects, fertility aspirations, and physical independence. This poses significant additional challenges for health care professionals in a field that remains underexplored. This comprehensive review recognizes lung cancer in young adults as a distinct entity, exploring its clinical and molecular characteristics, diverse predisposing factors, and priorities in terms of quality of life, with the aim of providing practical support to oncologists and enhancing our understanding of this under-researched population.
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Affiliation(s)
- Juan Carlos Laguna
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Marco Tagliamento
- Department of Internal Medicine and Medical Specialties (DIMI), School of Medicine, University of Genova, Genova, Italy
- Department of Medical Oncology, Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | - Matteo Lambertini
- Department of Internal Medicine and Medical Specialties (DIMI), School of Medicine, University of Genova, Genova, Italy
- Department of Medical Oncology, Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
- Department of Medicine, University of Barcelona, Barcelona, Spain
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3
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Hynds RE, Huebner A, Pearce DR, Hill MS, Akarca AU, Moore DA, Ward S, Gowers KHC, Karasaki T, Al Bakir M, Wilson GA, Pich O, Martínez-Ruiz C, Hossain ASMM, Pearce SP, Sivakumar M, Ben Aissa A, Grönroos E, Chandrasekharan D, Kolluri KK, Towns R, Wang K, Cook DE, Bosshard-Carter L, Naceur-Lombardelli C, Rowan AJ, Veeriah S, Litchfield K, Crosbie PAJ, Dive C, Quezada SA, Janes SM, Jamal-Hanjani M, Marafioti T, McGranahan N, Swanton C. Representation of genomic intratumor heterogeneity in multi-region non-small cell lung cancer patient-derived xenograft models. Nat Commun 2024; 15:4653. [PMID: 38821942 PMCID: PMC11143323 DOI: 10.1038/s41467-024-47547-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/28/2024] [Indexed: 06/02/2024] Open
Abstract
Patient-derived xenograft (PDX) models are widely used in cancer research. To investigate the genomic fidelity of non-small cell lung cancer PDX models, we established 48 PDX models from 22 patients enrolled in the TRACERx study. Multi-region tumor sampling increased successful PDX engraftment and most models were histologically similar to their parent tumor. Whole-exome sequencing enabled comparison of tumors and PDX models and we provide an adapted mouse reference genome for improved removal of NOD scid gamma (NSG) mouse-derived reads from sequencing data. PDX model establishment caused a genomic bottleneck, with models often representing a single tumor subclone. While distinct tumor subclones were represented in independent models from the same tumor, individual PDX models did not fully recapitulate intratumor heterogeneity. On-going genomic evolution in mice contributed modestly to the genomic distance between tumors and PDX models. Our study highlights the importance of considering primary tumor heterogeneity when using PDX models and emphasizes the benefit of comprehensive tumor sampling.
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Affiliation(s)
- Robert E Hynds
- 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.
- Epithelial Cell Biology in ENT Research Group (EpiCENTR), Developmental Biology and Cancer, Great Ormond Street University College London Institute of Child Health, 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 R Pearce
- 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
| | - Ayse U Akarca
- Department of Cellular Pathology, University College London Hospitals, 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
| | - 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
| | - Kate H C Gowers
- Lungs for Living Research Centre, UCL Respiratory, University College London, 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
| | - 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
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Oriol Pich
- 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
| | - A S Md Mukarram Hossain
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Simon P Pearce
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
| | - Monica Sivakumar
- 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
| | - Assma Ben Aissa
- Cancer Immunology Unit, Research Department of Haematology, University College London Cancer Institute, London, UK
| | - Eva Grönroos
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Deepak Chandrasekharan
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Krishna K Kolluri
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Rebecca Towns
- Biological Services Unit, University College London, London, UK
| | - Kaiwen Wang
- School of Medicine, University of Leeds, Leeds, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Leticia Bosshard-Carter
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | | | - Andrew J Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- 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
| | - Philip A J Crosbie
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, UK
- Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, UK
| | - Caroline Dive
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University of Manchester, Manchester, 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 Haematology, University College London Cancer Institute, London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, UCL Respiratory, University 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 Oncology, University College London Hospitals, London, UK
| | - Teresa Marafioti
- Department of Cellular Pathology, 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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4
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Arfan S, Thway K, Jones RL, Huang PH. Molecular Heterogeneity in Leiomyosarcoma and Implications for Personalised Medicine. Curr Treat Options Oncol 2024; 25:644-658. [PMID: 38656686 DOI: 10.1007/s11864-024-01204-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
OPINION STATEMENT Leiomyosarcoma (LMS) is one of the more common subtypes of soft tissue sarcomas (STS), accounting for about 20% of cases. Differences in anatomical location, risk of recurrence and histomorphological variants contribute to the substantial clinical heterogeneity in survival outcomes and therapy responses observed in patients. There is therefore a need to move away from the current one-size-fits-all treatment approach towards a personalised strategy tailored for individual patients. Over the past decade, tissue profiling studies have revealed key genomic features and an additional layer of molecular heterogeneity among patients, with potential utility for optimal risk stratification and biomarker-matched therapies. Furthermore, recent studies investigating intratumour heterogeneity and tumour evolution patterns in LMS suggest some key features that may need to be taken into consideration when designing treatment strategies and clinical trials. Moving forward, national and international collaborative efforts to aggregate expertise, data, resources and tools are needed to achieve a step change in improving patient survival outcomes in this disease of unmet need.
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Affiliation(s)
- Sara Arfan
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK
- The Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Robin L Jones
- The Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
- Division of Clinical Studies, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, SM2 5NG, UK.
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Karras P, Black JRM, McGranahan N, Marine JC. Decoding the interplay between genetic and non-genetic drivers of metastasis. Nature 2024; 629:543-554. [PMID: 38750233 DOI: 10.1038/s41586-024-07302-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 03/12/2024] [Indexed: 05/18/2024]
Abstract
Metastasis is a multistep process by which cancer cells break away from their original location and spread to distant organs, and is responsible for the vast majority of cancer-related deaths. Preventing early metastatic dissemination would revolutionize the ability to fight cancer. Unfortunately, the relatively poor understanding of the molecular underpinnings of metastasis has hampered the development of effective anti-metastatic drugs. Although it is now accepted that disseminating tumour cells need to acquire multiple competencies to face the many obstacles they encounter before reaching their metastatic site(s), whether these competencies are acquired through an accumulation of metastasis-specific genetic alterations and/or non-genetic events is often debated. Here we review a growing body of literature highlighting the importance of both genetic and non-genetic reprogramming events during the metastatic cascade, and discuss how genetic and non-genetic processes act in concert to confer metastatic competencies. We also describe how recent technological advances, and in particular the advent of single-cell multi-omics and barcoding approaches, will help to better elucidate the cross-talk between genetic and non-genetic mechanisms of metastasis and ultimately inform innovative paths for the early detection and interception of this lethal process.
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Affiliation(s)
- Panagiotis Karras
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - James R M Black
- Cancer Genome Evolution Research Group, UCL Cancer Institute, London, UK
| | | | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, VIB Center for Cancer Biology, KU Leuven, Leuven, Belgium.
- Department of Oncology, KU Leuven, Leuven, Belgium.
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6
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Butler G, Amend SR, Axelrod R, Venditti C, Pienta KJ. Punctuational evolution is pervasive in distal site metastatic colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588529. [PMID: 38645078 PMCID: PMC11030309 DOI: 10.1101/2024.04.08.588529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The evolution of metastasis represents a lethal stage of cancer progression. Yet, the evolutionary kinetics of metastatic disease remain unresolved. Here, using single cell CRISPR-Cas9 lineage tracing data, we show that in metastatic disease, gradual molecular evolution is punctuated by episodes of rapid evolutionary change associated with lineage divergence. By measuring punctuational effects across the metastatic cascade, we show that punctuational effects contribute more to the molecular diversity at distal site metastases compared to the paired primary tumor, suggesting qualitatively different modes of evolution may drive primary and metastatic tumor progression. This is the first empirical evidence for distinct patterns of molecular evolution at early and late stages of metastasis and demonstrates the complex interplay of cell intrinsic and extrinsic factors that shape lethal cancer.
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7
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Kutz O, Drukewitz S, Krüger A, Aust D, William D, Oster S, Schröck E, Baretton G, Link T, Wimberger P, Kuhlmann JD. Exploring evolutionary trajectories in ovarian cancer patients by longitudinal analysis of ctDNA. Clin Chem Lab Med 2024; 0:cclm-2023-1266. [PMID: 38577791 DOI: 10.1515/cclm-2023-1266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
OBJECTIVES We analysed whether temporal heterogeneity of ctDNA encodes evolutionary patterns in ovarian cancer. METHODS Targeted sequencing of 275 cancer-associated genes was performed in a primary tumor biopsy and in ctDNA of six longitudinal plasma samples from 15 patients, using the Illumina platform. RESULTS While there was low overall concordance between the mutational spectrum of the primary tumor biopsies vs. ctDNA, TP53 variants were the most commonly shared somatic alterations. Up to three variant clusters were detected in each tumor biopsy, likely representing predominant clones of the primary tumor, most of them harbouring a TP53 variant. By tracing these clusters in ctDNA, we propose that liquid biopsy may allow to assess the contribution of ancestral clones of the tumor to relapsed abdominal masses, revealing two evolutionary patterns. In pattern#1, clusters detected in the primary tumor biopsy were likely relapse seeding clones, as they contributed a major share to ctDNA at relapse. In pattern#2, similar clusters were present in tumors and ctDNA; however, they were entirely cleared from liquid biopsy after chemotherapy and were undetectable at relapse. ctDNA private variants were present among both patterns, with some of them mirroring subclonal expansions after chemotherapy. CONCLUSIONS We demonstrate that tracing the temporal heterogeneity of ctDNA, even below exome scale resolution, deciphers evolutionary trajectories in ovarian cancer. Furthermore, we describe two evolutionary patterns that may help to identify relapse seeding clones for targeted therapy.
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Affiliation(s)
- Oliver Kutz
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute for Clinical Genetics, 9169 University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- ERN GENTURIS, 9169 Hereditary Cancer Syndrome Center , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- 9169 Max Planck Institute of Molecular Cell Biology and Genetics , Dresden, Germany
| | - Stephan Drukewitz
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 Technische Universitat Dresden , Dresden, Sachsen, Germany
| | - Alexander Krüger
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 Technische Universitat Dresden , Dresden, Sachsen, Germany
| | - Daniela Aust
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- Institute for Pathology, 9169 University Hospital Carl Gustav Carus at the TU Dresden , Dresden, Germany
- 9169 Tumor- and Normal Tissue Bank of the NCT/UCC Dresden , Dresden, Germany
| | - Doreen William
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute for Clinical Genetics, 9169 University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- ERN GENTURIS, 9169 Hereditary Cancer Syndrome Center , Dresden, Germany
- 9169 National Center for Tumor Diseases Dresden (NCT/UCC) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- 9169 Max Planck Institute of Molecular Cell Biology and Genetics , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 National Center for Tumor Diseases Dresden (NCT/UCC) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden , Dresden, Germany
| | - Sandra Oster
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 National Center for Tumor Diseases Dresden (NCT/UCC) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden , Dresden, Germany
| | - Evelin Schröck
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- Institute for Clinical Genetics, 9169 University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- ERN GENTURIS, 9169 Hereditary Cancer Syndrome Center , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- 9169 Max Planck Institute of Molecular Cell Biology and Genetics , Dresden, Germany
- Core Unit for Molecular Tumor Diagnostics (CMTD), 9169 Technische Universitat Dresden , Dresden, Sachsen, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus, TU Dresden , Dresden, Germany
| | - Gustavo Baretton
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
- Institute for Pathology, 9169 University Hospital Carl Gustav Carus at the TU Dresden , Dresden, Germany
- 9169 Tumor- and Normal Tissue Bank of the NCT/UCC Dresden , Dresden, Germany
| | - Theresa Link
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
| | - Pauline Wimberger
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
| | - Jan Dominik Kuhlmann
- Department of Gynecology and Obstetrics, Medical Faculty and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 National Center for Tumour Diseases (NCT) , Dresden, Germany
- 9169 German Cancer Research Center (DKFZ) , Heidelberg, Germany
- Faculty of Medicine and University Hospital Carl Gustav Carus, 9169 Technische Universität Dresden , Dresden, Germany
- 9169 Helmholtz-Zentrum Dresden-Rossendorf (HZDR) , Dresden, Germany
- 9169 German Cancer Consortium (DKTK) , Dresden, Germany
- 9169 Faculty of Medicine and University Hospital Carl Gustav Carus at TU Dresden , Dresden, Germany
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8
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Zand H, Pourvali K. The Function of the Immune System, Beyond Strategies Based on Cell-Autonomous Mechanisms, Determines Cancer Development: Immune Response and Cancer Development. Adv Biol (Weinh) 2024; 8:e2300528. [PMID: 38221702 DOI: 10.1002/adbi.202300528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/09/2023] [Indexed: 01/16/2024]
Abstract
Although cancer remains a challenging disease to treat, early detection and removal of primary tumors through surgery or chemotherapy/radiotherapy can offer hope for patients. The privilege paradigm in cancer biology suggests that cell-autonomous mechanisms play a central role in tumorigenesis. According to this paradigm, these cellular mechanisms are the primary focus for the prevention and treatment of cancers. However, this point of view does not present a comprehensive theory for the initiation of cancer and an effective therapeutic strategy. Having an incomplete understanding of the etiology of cancer, it is essential to re-examine previous assumptions about carcinogenesis and develop new, practical theories that can account for all available clinical and experimental evidence. This will not only help to gain a better understanding of the disease, but also offer new avenues for treatment. This review provides evidence suggesting a shift in focus from a cell-autonomous mechanism to systemic mechanisms, particularly the immune system, that are involved in cancer formation.
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Affiliation(s)
- Hamid Zand
- Department of Cellular and Molecular Nutrition, Faculty of Nutrition Science and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, 1981619573, Iran
| | - Katayoun Pourvali
- Department of Cellular and Molecular Nutrition, Faculty of Nutrition Science and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, 1981619573, Iran
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9
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Järvholm B, Hedman L, Landström M, Liv P, Burdorf A, Torén K. Changing smoking habits and the occurrence of lung cancer in Sweden-a population analysis. Eur J Public Health 2024:ckae050. [PMID: 38519451 DOI: 10.1093/eurpub/ckae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND The objective is to estimate the importance of the decrease of smoking habits in Sweden for the occurrence of lung cancer. METHODS The change in smoking habits in the general population was retrieved from surveys and on taxation of sale of cigarettes. We used data from the Swedish Cancer Register on incidence of lung cancer between 1970 and 2021, stratified for sex, age and cell type, and compared the occurrence overtime in ages between 40 and 84 years. RESULTS The sale of cigarettes peaked in 1980 to 1800 cigarettes per person and decreased to 600 per person in 2021. The change in incidence rates of squamous cell cancer and other cell types varied over time, sex, and age in a pattern that partly seems to be explained by change in the prevalence of daily smokers. The incidence of adenocarcinoma was similar in men and women 1970-2021 and increased, e.g. for women and men 75-79 years of age from around 20 cases in early 1970s to around 120 cases per 100 000 person-years in the 2020s. CONCLUSIONS Our data indicate that the risk of lung cancer several years after smoking cessation is less favourable than previously studies have indicated. There is a similar increase in the incidence of adenocarcinoma in men and women which is hard to explain only with changing smoking habits. The change from non-filter to filter cigarettes in the 1960s-1970s may be a contributing factor.
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Affiliation(s)
- Bengt Järvholm
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Linnea Hedman
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Maréne Landström
- Pathology Section, Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - Per Liv
- Department of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
| | - Alex Burdorf
- Department of Public Health, Erasmus MC, Rotterdam, The Netherlands
| | - Kjell Torén
- Section of Occupational and Environmental Medicine, University of Gothenburg, Gothenburg, Sweden
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10
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Long Y, Yang B, Lei Q, Gao F, Chen L, Chen W, Chen S, Ren W, Cao Y, Xu L, Wu D, Qu J, Li H, Yu Y, Zhang A, Wang S, Chen W, Wang H, Chen T, Chen Z, Li Q. Targeting Senescent Alveolar Epithelial Cells Using Engineered Mesenchymal Stem Cell-Derived Extracellular Vesicles To Treat Pulmonary Fibrosis. ACS NANO 2024; 18:7046-7063. [PMID: 38381372 PMCID: PMC10919282 DOI: 10.1021/acsnano.3c10547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/09/2024] [Accepted: 02/13/2024] [Indexed: 02/22/2024]
Abstract
Type 2 alveolar epithelial cell (AEC2) senescence is crucial to the pathogenesis of pulmonary fibrosis (PF). The nicotinamide adenine dinucleotide (NAD+)-consuming enzyme cluster of differentiation 38 (CD38) is a marker of senescent cells and is highly expressed in AEC2s of patients with PF, thus rendering it a potential treatment target. Umbilical cord mesenchymal stem cell (MSC)-derived extracellular vesicles (MSC-EVs) have emerged as a cell-free treatment with clinical application prospects in antiaging and antifibrosis treatments. Herein, we constructed CD38 antigen receptor membrane-modified MSC-EVs (CD38-ARM-MSC-EVs) by transfecting MSCs with a lentivirus loaded with a CD38 antigen receptor-CD8 transmembrane fragment fusion plasmid to target AEC2s and alleviate PF. Compared with MSC-EVs, the CD38-ARM-MSC-EVs engineered in this study showed a higher expression of the CD38 antigen receptor and antifibrotic miRNAs and targeted senescent AEC2s cells highly expressing CD38 in vitro and in naturally aged mouse models after intraperitoneal administration. CD38-ARM-MSC-EVs effectively restored the NAD+ levels, reversed the epithelial-mesenchymal transition phenotype, and rejuvenated senescent A549 cells in vitro, thereby mitigating multiple age-associated phenotypes and alleviating PF in aged mice. Thus, this study provides a technology to engineer MSC-EVs and support our CD38-ARM-MSC-EVs to be developed as promising agents with high clinical potential against PF.
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Affiliation(s)
- Yaoying Long
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Bianlei Yang
- Department
of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qian Lei
- West
China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fei Gao
- Department
of Hematology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Li Chen
- Department
of Hematology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Wenlan Chen
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Siyi Chen
- Department
of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Wenxiang Ren
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yulin Cao
- Department
of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Liuyue Xu
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Di Wu
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Jiao Qu
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - He Li
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Yali Yu
- Department
of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Anyuan Zhang
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Shan Wang
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Weiqun Chen
- Key
Laboratory for Molecular Diagnosis of Hubei Province, The Central
Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Hongxiang Wang
- Department
of Hematology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430014, China
| | - Ting Chen
- Hubei Engineering
Research Center for Application of Extracellular Vesicle, Hubei University of Science and Technology, Xianning 437100, China
| | - Zhichao Chen
- Department
of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Qiubai Li
- Department
of Rheumatology and Immunology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
- Hubei Engineering
Research Center for Application of Extracellular Vesicle, Hubei University of Science and Technology, Xianning 437100, China
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11
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Chang E, An JY. Whole-genome doubling is a double-edged sword: the heterogeneous role of whole-genome doubling in various cancer types. BMB Rep 2024; 57:125-134. [PMID: 38449300 PMCID: PMC10979346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome doubling (WGD), characterized by the duplication of an entire set of chromosomes, is commonly observed in various tumors, occurring in approximately 30-40% of patients with different cancer types. The effect of WGD on tumorigenesis varies depending on the context, either promoting or suppressing tumor progression. Recent advances in genomic technologies and large-scale clinical investigations have led to the identification of the complex patterns of genomic alterations underlying WGD and their functional consequences on tumorigenesis progression and prognosis. Our comprehensive review aims to summarize the causes and effects of WGD on tumorigenesis, highlighting its dualistic influence on cancer cells. We then introduce recent findings on WGD-associated molecular signatures and genetic aberrations and a novel subtype related to WGD. Finally, we discuss the clinical implications of WGD in cancer subtype classification and future therapeutic interventions. Overall, a comprehensive understanding of WGD in cancer biology is crucial to unraveling its complex role in tumorigenesis and identifying novel therapeutic strategies. [BMB Reports 2024; 57(3): 125-134].
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Affiliation(s)
- Eunhyong Chang
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul 02841, Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul 02841, Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Korea
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12
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Kunimasa K, Tamiya M, Inoue T, Kawamura T, Miyazaki A, Kojitani Y, Honma K, Nishino K. Clinical application of the Lung Cancer Compact Panel TM using various types of cytological specimens in patients with lung cancer. Lung Cancer 2024; 189:107498. [PMID: 38324922 DOI: 10.1016/j.lungcan.2024.107498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND The Lung Cancer Compact PanelTM (compact panel) is a gene panel that can detect driver alterations with high sensitivity in liquid samples, including tumor cells. This study examined the ability of a compact panel to detect genetic mutations in liquid specimens used in clinical practice. METHODS Three cohorts, bronchoscopic biopsy forceps washing (washing cohort), pleural effusion (pleural cohort), and spinal fluid (spinal cohort), were analyzed using the compact panel. Liquid samples were added into the GM (Genemetrics) tubes and analyzed. The washing cohort assessed the concordance rate of gene panel analysis outcomes in tissue specimens derived from the primary tumor. Meanwhile, the pleural cohort investigated the impact of storing specimens for 8 weeks and more on nucleic acid and mutation detection rates. RESULTS In the washing cohort (n = 79), the concordance rate with mutations detected in tissues was 75/79 (94.9 %). This rate reached 100 % when focusing solely on driver alterations for treatment. The pleural cohort (n = 8) showed no deterioration in nucleic acid quality or quantity after 8 weeks of storage in GM tubes. Similarly, in the spinal cohort (n = 9), spinal fluid with malignant cells exhibited driver alterations similar to those in the primary tumor. These findings underscore the efficacy of the compact panel in accurately identifying genetic mutations in different liquid specimens. CONCLUSIONS The compact panel is a reliable tool for detecting driver alterations in various cytological specimens. Its consistent performance across diverse sample types emphasizes its potential for guiding targeted therapies for patients with lung cancer and enhancing precision medicine approaches.
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Affiliation(s)
- Kei Kunimasa
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan.
| | - Motohiro Tamiya
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takako Inoue
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Takahisa Kawamura
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Akito Miyazaki
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Yoshiki Kojitani
- Department of Medical Oncology, Osaka International Cancer Institute, Osaka, Japan
| | - Keiichiro Honma
- Department of Diagnostic Pathology & Cytology, Osaka International Cancer Institute, Osaka, Japan
| | - Kazumi Nishino
- Department of Thoracic Oncology, Osaka International Cancer Institute, Osaka, Japan
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13
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Wang X, Yang K, Yang Y, Wang X, Yuan K. Immunotherapy rechallenge of advanced lung adenocarcinoma with cadonilimab (PD-1/CTLA-4 Bi-specific antibody): a case report. Anticancer Drugs 2024; 35:288-291. [PMID: 37982205 DOI: 10.1097/cad.0000000000001557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2023]
Abstract
Lung adenocarcinoma (ADC) is a common pulmonary malignant disease with poor prognosis. Immunotherapeutic strategies are the current cornerstone of first-line therapy in driver-negative advanced lung ADC, but there is no treatment standard once the disease has progressed after the first-line application of immune checkpoint inhibitors (ICIs). Clinically, immunotherapy rechallenges are being attempted. However, it is undeniable that there are still great limitations to rechallenging patients with single- or double-ICI immunotherapy though immunotherapy rechallenges can bring new benefits. Cadonilimab (AK104), a unique bi-specific antibody targeting PD-1/CTLA-4, has similar biological activity but lower toxicity than the combination of CTLA-4 and PD-1 antibodies. Herein, we report a case of advanced lung ADC rechallenged with cadonilimab as a posterior-line therapy. The condition of the patient was maintained at stable disease for 6 months. This might provide a new idea and choice for the challenge of immunotherapy resistance.
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Affiliation(s)
- Xuan Wang
- Department of Pharmacology, School of Basic Medicine, Qingdao University, Qingdao
| | - Kunning Yang
- Department of Respiratory Medicine, Weifang Second People's Hospital, Weifang
| | - Yang Yang
- Institute of Nutrition and Health, School of Public Health, Qingdao University, Qingdao, China
| | - Xinling Wang
- Department of Respiratory Medicine, Weifang Second People's Hospital, Weifang
| | - Kede Yuan
- Department of Respiratory Medicine, Weifang Second People's Hospital, Weifang
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14
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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. NATURE 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] [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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15
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Li L, Jiang H, Zeng B, Wang X, Bao Y, Chen C, Ma L, Yuan J. Liquid biopsy in lung cancer. Clin Chim Acta 2024; 554:117757. [PMID: 38184141 DOI: 10.1016/j.cca.2023.117757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/08/2024]
Abstract
Lung cancer is a highly prevalent malignancy worldwide and the primary cause of mortality. The absence of systematic and standardized diagnostic approaches for identifying potential pulmonary nodules, early-stage cancers, and indeterminate tumors has led clinicians to consider tissue biopsy and pathological sections as the preferred method for clinical diagnosis, often regarded as the gold standard. The conventional tissue biopsy is an invasive procedure that does not adequately capture the diverse characteristics and evolving nature of tumors. Recently, the concept of 'liquid biopsy' has gained considerable attention as a promising solution. Liquid biopsy is a non-invasive approach that facilitates repeated analysis, enabling real-time monitoring of tumor recurrence, metastasis, and response to treatment. Currently, liquid biopsy includes circulating tumor cells, circulating cell-free DNA, circulating tumor DNA, circulating cell-free RNA, extracellular vesicles, and other proteins and metabolites. With rapid progress in molecular technology, liquid biopsy has emerged as a highly promising and intriguing approach, yielding compelling results. This article critically examines the significant role and potential clinical implications of liquid biopsy in the diagnosis, treatment, and prognosis of lung cancer.
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Affiliation(s)
- Lan Li
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Haixia Jiang
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Bingjie Zeng
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Xianzhao Wang
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Yunxia Bao
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China
| | - Changqiang Chen
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China.
| | - Lifang Ma
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China.
| | - Jin Yuan
- Department of Laboratory Medicine, Shanghai Chest Hospital Shanghai Jiao Tong University School of Medicine Shanghai China, Shanghai 200030, China; Academy of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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16
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Li Z, Lv H, Zhang F, Zhu Z, Guo Q, Wang M, Huang C, Guo L, Meng F, Tian Z. Using molecular characteristics to distinguish multiple primary lung cancers and intrapulmonary metastases. PeerJ 2024; 12:e16808. [PMID: 38313018 PMCID: PMC10838092 DOI: 10.7717/peerj.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/29/2023] [Indexed: 02/06/2024] Open
Abstract
Objectives Multiple lung cancers may present as multiple primary lung cancers (MPLC) or intrapulmonary metastasis (IPM) with variations in clinical stage, treatment, and prognosis. However, the existing differentiation criteria based on histology do not fully meet the clinical needs. Next-generation sequencing (NGS) may play an important role in assisting the identification of different pathologies. Here, we extended the relevant data by combining histology and NGS to develop detailed identification criteria for MPLC and IPM. Materials and Methods Patients with lung cancer (each patient had ≥2 tumors) were enrolled in the training (n = 22) and validation (n = 13) cohorts. Genomic profiles obtained from 450-gene-targeted NGS were analyzed, and the new criteria were developed based on our findings and pre-existing Martini & Melamed criteria and molecular benchmarks. Results The analysis of the training cohort indicated that patients identified with MPLC had no (or <2) trunk or shared mutations. However, 98.02% of mutations were branch mutations, and 69.23% of MPLC had no common mutations. In contrast, a higher percentage of trunk (33.08%) or shared (9.02%) mutations were identified in IPM, suggesting significant differences among mutated components. Subsequently, eight MPLC and five IPM cases were identified in the validation cohort, aligning with the independent imaging and pathologic distinction. Overall, the percentage of trunk and shared mutations was higher in patients with IPM than in patients with MPLC. Based on these results and the establishment of new determination criteria for MPLC and IPM, we emphasize that the type and number of shared variants based on histologic consistency assist in identification. Conclusion Determining genetic alterations may be an effective method for differentiating MPLC and IPM, and NGS can be used as a valuable assisting tool.
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Affiliation(s)
- Zhenhua Li
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Huilai Lv
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Fan Zhang
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ziming Zhu
- Department of Thoracic Surgery, The First Hospital of Xingtai, Xingtai, China
| | - Qiang Guo
- Department of Thoracic Surgery, Affiliated Hospital of Hebei University, Baoding, China
| | - Mingbo Wang
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | - Chao Huang
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
| | | | | | - Ziqiang Tian
- Department of Thoracic Surgery, Fourth Hospital of Hebei Medical University, Shijiazhuang, China
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17
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Hariprakash JM, Salviato E, La Mastra F, Sebestyén E, Tagliaferri I, Silva RS, Lucini F, Farina L, Cinquanta M, Rancati I, Riboni M, Minardi SP, Roz L, Gorini F, Lanzuolo C, Casola S, Ferrari F. Leveraging Tissue-Specific Enhancer-Target Gene Regulatory Networks Identifies Enhancer Somatic Mutations That Functionally Impact Lung Cancer. Cancer Res 2024; 84:133-153. [PMID: 37855660 PMCID: PMC10758689 DOI: 10.1158/0008-5472.can-23-1129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/29/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
Enhancers are noncoding regulatory DNA regions that modulate the transcription of target genes, often over large distances along with the genomic sequence. Enhancer alterations have been associated with various pathological conditions, including cancer. However, the identification and characterization of somatic mutations in noncoding regulatory regions with a functional effect on tumorigenesis and prognosis remain a major challenge. Here, we present a strategy for detecting and characterizing enhancer mutations in a genome-wide analysis of patient cohorts, across three lung cancer subtypes. Lung tissue-specific enhancers were defined by integrating experimental data and public epigenomic profiles, and the genome-wide enhancer-target gene regulatory network of lung cells was constructed by integrating chromatin three-dimensional architecture data. Lung cancers possessed a similar mutation burden at tissue-specific enhancers and exons but with differences in their mutation signatures. Functionally relevant alterations were prioritized on the basis of the pathway-level integration of the effect of a mutation and the frequency of mutations on individual enhancers. The genes enriched for mutated enhancers converged on the regulation of key biological processes and pathways relevant to tumor biology. Recurrent mutations in individual enhancers also affected the expression of target genes, with potential relevance for patient prognosis. Together, these findings show that noncoding regulatory mutations have a potential relevance for cancer pathogenesis and can be exploited for patient classification. SIGNIFICANCE Mapping enhancer-target gene regulatory interactions and analyzing enhancer mutations at the level of their target genes and pathways reveal convergence of recurrent enhancer mutations on biological processes involved in tumorigenesis and prognosis.
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Affiliation(s)
| | - Elisa Salviato
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Endre Sebestyén
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Federica Lucini
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Lorenzo Farina
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | - Ilaria Rancati
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | | | | | - Luca Roz
- Fondazione IRCCS—Istituto Nazionale Tumori, Milan, Italy
| | - Francesca Gorini
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
| | - Chiara Lanzuolo
- INGM, National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi,” Milan, Italy
- Institute of Biomedical Technologies, National Research Council (ITB-CNR), Segrate, Italy
| | - Stefano Casola
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesco Ferrari
- IFOM-ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza,” National Research Council (IGM-CNR), Pavia, Italy
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18
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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] [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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19
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Jongbloed M, Khosla AA, Bartolomeo V, Jatwani K, Singh R, De Ruysscher DKM, Hendriks LEL, Desai A. Measured Steps: Navigating the Path of Oligoprogressive Lung Cancer with Targeted and Immunotherapies. Curr Oncol Rep 2024; 26:80-89. [PMID: 38175464 DOI: 10.1007/s11912-023-01490-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
PURPOSE OF REVIEW This review discusses the definitions, treatment modalities, management, future directions, and ongoing clinical trials of oligoprogressive disease in oncogene-driven and non-oncogene-driven NSCLC. RECENT FINDINGS During the last decades, diagnostic and treatment modalities for oligometastatic NSCLC have advanced significantly, leading to improved survival. Additionally, our understanding of the tumor biology of oligoprogressive disease has expanded. However, despite the efforts of organizations, such as EORTC, ESTRO, and ASTRO proposing definitions for oligometastatic and oligoprogressive disease, heterogeneity in definitions persists in (ongoing) trials. Recognizing the significance of subclassification within oligoprogressive disease in NSCLC and the varying risks associated with subsequent metastatic spread, there is a call for tailored management strategies. A consensus on standardized criteria for the definition of oligoprogressive disease is urgently needed and will not only facilitate meaningful comparisons between studies but also pave the way for the development of personalized treatment plans that take into account the heterogeneous nature of oligoprogressive disease.
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Affiliation(s)
- Mandy Jongbloed
- Department of Pulmonary Diseases, GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Atulya A Khosla
- Division of Internal Medicine, William Beaumont University Hospital, Royal Oak, MI, USA
| | - Valentina Bartolomeo
- Radiation Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
- Department of Clinical Surgical, Diagnostic and Pediatric Sciences, Pavia University, Pavia, Italy
- Department of Radiation Oncology (Maastro Clinic), Maastricht University Medical Center, GROW School for Oncology and Reproduction (GROW), Maastricht, Netherlands
| | - Karan Jatwani
- Division of Hematology-Oncology, Roswell Park Cancer Center, Buffalo, NY, USA
| | - Rohit Singh
- Division of Hematology-Oncology, University of Vermont, Burlington, VT, USA
| | - Dirk K M De Ruysscher
- Department of Radiation Oncology (Maastro Clinic), Maastricht University Medical Center, GROW School for Oncology and Reproduction (GROW), Maastricht, Netherlands
| | - Lizza E L Hendriks
- Department of Pulmonary Diseases, GROW School for Oncology and Reproduction, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Aakash Desai
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, 1824 6th Ave S, Birmingham, AL, 35233, USA.
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20
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Begg KAG, Braun H, Ghaddar N, Wu L, Downs JA. Defects in DNA damage responses in SWI/SNF mutant cells and their impact on immune responses. DNA Repair (Amst) 2024; 133:103609. [PMID: 38101147 DOI: 10.1016/j.dnarep.2023.103609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
The mammalian SWI/SNF chromatin remodelling complexes are commonly dysregulated in cancer. These complexes contribute to maintaining genome stability through a variety of pathways. Recent research has highlighted an important interplay between genome instability and immune signalling, and evidence suggests that this interplay can modulate the response to immunotherapy. Here, we review emerging studies where direct evidence of this relationship has been uncovered in SWI/SNF deficient cells. We also highlight genome maintenance activities of SWI/SNF that could potentially shape immune responses and discuss potential therapeutic implications.
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Affiliation(s)
- Katheryn A G Begg
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Hanna Braun
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Nagham Ghaddar
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Lillian Wu
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Jessica A Downs
- Division of Cancer Biology, The Institute of Cancer Research, London, UK.
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21
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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22
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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] [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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23
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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 : THE PREPRINT SERVER FOR BIOLOGY 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] [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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24
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Vittoria MA, Quinton RJ, Ganem NJ. Whole-genome doubling in tissues and tumors. Trends Genet 2023; 39:954-967. [PMID: 37714734 PMCID: PMC10840902 DOI: 10.1016/j.tig.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
The overwhelming majority of proliferating somatic human cells are diploid, and this genomic state is typically maintained across successive cell divisions. However, failures in cell division can induce a whole-genome doubling (WGD) event, in which diploid cells transition to a tetraploid state. While some WGDs are developmentally programmed to produce nonproliferative tetraploid cells with specific cellular functions, unscheduled WGDs can be catastrophic: erroneously arising tetraploid cells are ill-equipped to cope with their doubled cellular and chromosomal content and quickly become genomically unstable and tumorigenic. Deciphering the genetics that underlie the genesis, physiology, and evolution of whole-genome doubled (WGD+) cells may therefore reveal therapeutic avenues to selectively eliminate pathological WGD+ cells.
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Affiliation(s)
- Marc A Vittoria
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Ryan J Quinton
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Neil J Ganem
- Department of Medicine, Division of Hematology and Oncology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA; Department of Pharmacology, Physiology, and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA.
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25
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Fick CN, Dunne EG, Lankadasari MB, Mastrogiacomo B, Asao T, Vanstraelen S, Liu Y, Sanchez-Vega F, Jones DR. Genomic profiling and metastatic risk in early-stage non-small cell lung cancer. JTCVS OPEN 2023; 16:9-16. [PMID: 38204702 PMCID: PMC10775106 DOI: 10.1016/j.xjon.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/02/2023] [Accepted: 10/11/2023] [Indexed: 01/12/2024]
Affiliation(s)
- Cameron N. Fick
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Elizabeth G. Dunne
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Manendra B. Lankadasari
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Brooke Mastrogiacomo
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Tetsuhiko Asao
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Stijn Vanstraelen
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yuan Liu
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Francisco Sanchez-Vega
- Computational Oncology Service, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - David R. Jones
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
- Druckenmiller Center for Lung Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY
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26
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Lakhani AA, Thompson SL, Sheltzer JM. Aneuploidy in human cancer: new tools and perspectives. Trends Genet 2023; 39:968-980. [PMID: 37778926 PMCID: PMC10715718 DOI: 10.1016/j.tig.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Chromosome copy number imbalances, otherwise known as aneuploidies, are a common but poorly understood feature of cancer. Here, we describe recent advances in both detecting and manipulating aneuploidies that have greatly advanced our ability to study their role in tumorigenesis. In particular, new clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have been developed that allow the creation of isogenic cell lines with specific chromosomal changes, thereby facilitating experiments in genetically controlled backgrounds to uncover the consequences of aneuploidy. These approaches provide increasing evidence that aneuploidy is a key driver of cancer development and enable the identification of multiple dosage-sensitive genes encoded on aneuploid chromosomes. Consequently, measuring aneuploidy may inform clinical prognosis, while treatment strategies that target aneuploidy could represent a novel method to counter malignant growth.
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Affiliation(s)
- Asad A Lakhani
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring, Harbor, NY 11724, USA
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27
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Cohen Shvefel S, Pai JA, Cao Y, Pal LR, Levy R, Yao W, Cheng K, Zemanek M, Bartok O, Weller C, Yin Y, Du PP, Yakubovich E, Orr I, Ben-Dor S, Oren R, Fellus-Alyagor L, Golani O, Goliand I, Ranmar D, Savchenko I, Ketrarou N, Schäffer AA, Ruppin E, Satpathy AT, Samuels Y. Temporal genomic analysis of melanoma rejection identifies regulators of tumor immune evasion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.29.569032. [PMID: 38077050 PMCID: PMC10705560 DOI: 10.1101/2023.11.29.569032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Decreased intra-tumor heterogeneity (ITH) correlates with increased patient survival and immunotherapy response. However, even highly homogenous tumors may display variability in their aggressiveness, and how immunologic-factors impinge on their aggressiveness remains understudied. Here we studied the mechanisms responsible for the immune-escape of murine tumors with low ITH. We compared the temporal growth of homogeneous, genetically-similar single-cell clones that are rejected vs. those that are not-rejected after transplantation in-vivo using single-cell RNA sequencing and immunophenotyping. Non-rejected clones showed high infiltration of tumor-associated-macrophages (TAMs), lower T-cell infiltration, and increased T-cell exhaustion compared to rejected clones. Comparative analysis of rejection-associated gene expression programs, combined with in-vivo CRISPR knockout screens of candidate mediators, identified Mif (macrophage migration inhibitory factor) as a regulator of immune rejection. Mif knockout led to smaller tumors and reversed non-rejection-associated immune composition, particularly, leading to the reduction of immunosuppressive macrophage infiltration. Finally, we validated these results in melanoma patient data.
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Affiliation(s)
- Sapir Cohen Shvefel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joy A Pai
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yingying Cao
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Lipika R Pal
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ronen Levy
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Winnie Yao
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Kuoyuan Cheng
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- MSD R&D (China) Co., Ltd
| | - Marie Zemanek
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Osnat Bartok
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Weller
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Peter P Du
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Elizabeta Yakubovich
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Irit Orr
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Shifra Ben-Dor
- Bioinformatics Unit, Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Roni Oren
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Liat Fellus-Alyagor
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Inna Goliand
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Dean Ranmar
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Ilya Savchenko
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Nadav Ketrarou
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
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28
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Li C, Shao J, Li P, Feng J, Li J, Wang C. Circulating tumor DNA as liquid biopsy in lung cancer: Biological characteristics and clinical integration. Cancer Lett 2023; 577:216365. [PMID: 37634743 DOI: 10.1016/j.canlet.2023.216365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 08/29/2023]
Abstract
Lung cancer maintains high morbidity and mortality rate globally despite significant advancements in diagnosis and treatment in the era of precision medicine. Pathological analysis of tumor tissue, the current gold standard for lung cancer diagnosis, is intrusive and intrinsically confined to evaluating the limited amount of tissues that could be physically extracted. However, tissue biopsy has several limitations, including the invasiveness of the procedure and difficulty in obtaining samples for patients at advanced stages., there Additionally,has been no major breakthrough in tumor biomarkers with high specificity and sensitivity, particularly for early-stage lung cancer. Liquid biopsy has been considered a feasible auxiliary tool for tearly dianosis, evaluating treatment responses and monitoring prognosis of lung cancer. Circulating tumor DNA (ctDNA), an ideal biomarker of liquid biopsy, has emerged as one of the most reliable tools for monitoring tumor processes at molecular levels. Herein, this review focuses on tumor heterogeneity to elucidate the superiority of liquid biopsy and retrospectively discussdeciphersolution. We systematically elaborate ctDNA biological characteristics, introduce methods for ctDNA detection, and discuss the current role of plasma ctDNA in lung cancer management. Finally, we summarize the drawbacks of ctDNA analysis and highlight its potential clinical application in lung cancer.
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Affiliation(s)
- Changshu Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Jun Shao
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Peiyi Li
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwei Li
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Chengdi Wang
- Department of Pulmonary and Critical Care Medicine, Med-X Center for Manufacturing, Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Respiratory Health and Multimorbidity, West China School of Medicine, West China Hospital, Sichuan University, Chengdu, China.
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29
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Whiting FJH, Househam J, Baker AM, Sottoriva A, Graham TA. Phenotypic noise and plasticity in cancer evolution. Trends Cell Biol 2023:S0962-8924(23)00206-4. [PMID: 37968225 DOI: 10.1016/j.tcb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023]
Abstract
Non-genetic alterations can produce changes in a cell's phenotype. In cancer, these phenomena can influence a cell's fitness by conferring access to heritable, beneficial phenotypes. Herein, we argue that current discussions of 'phenotypic plasticity' in cancer evolution ignore a salient feature of the original definition: namely, that it occurs in response to an environmental change. We suggest 'phenotypic noise' be used to distinguish non-genetic changes in phenotype that occur independently from the environment. We discuss the conceptual and methodological techniques used to identify these phenomena during cancer evolution. We propose that the distinction will guide efforts to define mechanisms of phenotype change, accelerate translational work to manipulate phenotypes through treatment, and, ultimately, improve patient outcomes.
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Affiliation(s)
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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30
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Zhang S, Liu X, Zhou L, Wang K, Shao J, Shi J, Wang X, Mu J, Gao T, Jiang Z, Chen K, Wang C, Wang G. Intelligent prognosis evaluation system for stage I-III resected non-small-cell lung cancer patients on CT images: a multi-center study. EClinicalMedicine 2023; 65:102270. [PMID: 38106558 PMCID: PMC10725055 DOI: 10.1016/j.eclinm.2023.102270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 12/19/2023] Open
Abstract
Background Prognosis is crucial for personalized treatment and surveillance suggestion of the resected non-small-cell lung cancer (NSCLC) patients in stage I-III. Although the tumor-node-metastasis (TNM) staging system is a powerful predictor, it is not perfect enough to accurately distinguish all the patients, especially within the same TNM stage. In this study, we developed an intelligent prognosis evaluation system (IPES) using pre-therapy CT images to assist the traditional TNM staging system for more accurate prognosis prediction of resected NSCLC patients. Methods 20,333 CT images of 6371 patients from June 12, 2009 to March 24, 2022 in West China Hospital of Sichuan University, Mianzhu People's Hospital, Peking University People's Hospital, Chengdu Shangjin Nanfu Hospital and Guangan Peoples' Hospital were included in this retrospective study. We developed the IPES based on self-supervised pre-training and multi-task learning, which aimed to predict an overall survival (OS) risk for each patient. We further evaluated the prognostic accuracy of the IPES and its ability to stratify NSCLC patients with the same TNM stage and with the same EGFR genotype. Findings The IPES was able to predict OS risk for stage I-III resected NSCLC patients in the training set (C-index 0.806; 95% CI: 0.744-0.846), internal validation set (0.783; 95% CI: 0.744-0.825) and external validation set (0.817; 95% CI: 0.786-0.849). In addition, IPES performed well in early-stage (stage I) and EGFR genotype prediction. Furthermore, by adopting IPES-based survival score (IPES-score), resected NSCLC patients in the same stage or with the same EGFR genotype could be divided into low- and high-risk subgroups with good and poor prognosis, respectively (p < 0.05 for all). Interpretation The IPES provided a non-invasive way to obtain prognosis-related information from patients. The identification of IPES for resected NSCLC patients with low and high prognostic risk in the same TNM stage or with the same EGFR genotype suggests that IPES have potential to offer more personalized treatment and surveillance suggestion for NSCLC patients. Funding This study was funded by the National Natural Science Foundation of China (grant 62272055, 92259303, 92059203), New Cornerstone Science Foundation through the XPLORER PRIZE, Young Elite Scientists Sponsorship Program by CAST (2021QNRC001), Clinical Medicine Plus X - Young Scholars Project, Peking University, the Fundamental Research Funds for the Central Universities (K.C.), Research Unit of Intelligence Diagnosis and Treatment in Early Non-small Cell Lung Cancer, Chinese Academy of Medical Sciences (2021RU002), BUPT Excellent Ph.D. Students Foundation (CX2022104).
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Affiliation(s)
- Siqi Zhang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Xiaohong Liu
- UCL Cancer Institute, University College London, London, WC1E 6DD, UK
| | - Lixin Zhou
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Kai Wang
- College of Future Technology, Peking University and Peking-Tsinghua Center for Life Sciences, Beijing, 100871, China
| | - Jun Shao
- State Key Laboratory of Respiratory Health and Multimorbidity, Department of Pulmonary and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jianyu Shi
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Xuan Wang
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Jiaxing Mu
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Tianrun Gao
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Zeyu Jiang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Kezhong Chen
- Thoracic Oncology Institute and Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
| | - Chengdi Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, Department of Pulmonary and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Guangyu Wang
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, 100876, China
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31
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Chen S, Zhou Z, Li Y, Du Y, Chen G. Application of single-cell sequencing to the research of tumor microenvironment. Front Immunol 2023; 14:1285540. [PMID: 37965341 PMCID: PMC10641410 DOI: 10.3389/fimmu.2023.1285540] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Single-cell sequencing is a technique for detecting and analyzing genomes, transcriptomes, and epigenomes at the single-cell level, which can detect cellular heterogeneity lost in conventional sequencing hybrid samples, and it has revolutionized our understanding of the genetic heterogeneity and complexity of tumor progression. Moreover, the tumor microenvironment (TME) plays a crucial role in the formation, development and response to treatment of tumors. The application of single-cell sequencing has ushered in a new age for the TME analysis, revealing not only the blueprint of the pan-cancer immune microenvironment, but also the heterogeneity and differentiation routes of immune cells, as well as predicting tumor prognosis. Thus, the combination of single-cell sequencing and the TME analysis provides a unique opportunity to unravel the molecular mechanisms underlying tumor development and progression. In this review, we summarize the recent advances in single-cell sequencing and the TME analysis, highlighting their potential applications in cancer research and clinical translation.
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Affiliation(s)
| | | | | | | | - Guoan Chen
- Department of Human Cell Biology and Genetics, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, China
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Fielding D, Dalley AJ, Singh M, Nandakumar L, Lakis V, Chittoory H, Fairbairn D, Patch AM, Kazakoff SH, Ferguson K, Bashirzadeh F, Bint M, Pahoff C, Son JH, Ryan K, Hodgson A, Sharma S, Pearson JV, Waddell N, Lakhani SR, Hartel G, Simpson PT, Nones K. Discrepancies in tumor mutation burden reporting from sequential endobronchial ultrasound transbronchial needle aspiration samples within single lymph node stations - brief report. Front Oncol 2023; 13:1259882. [PMID: 37927461 PMCID: PMC10620689 DOI: 10.3389/fonc.2023.1259882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/29/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Tumour Mutation Burden (TMB) is a potential biomarker for immune cancer therapies. Here we investigated parameters that might affect TMB using duplicate cytology smears obtained from endobronchial ultrasound transbronchial needle aspiration (EBUS TBNA)-sampled malignant lymph nodes. Methods Individual Diff-Quik cytology smears were prepared for each needle pass. DNA extracted from each smear underwent sequencing using large gene panel (TruSight Oncology 500 (TSO500 - Illumina)). TMB was estimated using the TSO500 Local App v. 2.0 (Illumina). Results Twenty patients had two or more Diff-Quik smears (total 45 smears) which passed sequencing quality control. Average smear TMB was 8.7 ± 5.0 mutations per megabase (Mb). Sixteen of the 20 patients had paired samples with minimal differences in TMB score (average difference 1.3 ± 0.85). Paired samples from 13 patients had concordant TMB (scores below or above a threshold of 10 mutations/Mb). Markedly discrepant TMB was observed in four cases, with an average difference of 11.3 ± 2.7 mutations/Mb. Factors affecting TMB calling included sample tumour content, the amount of DNA used in sequencing, and bone fide heterogeneity of node tumour between paired samples. Conclusion TMB assessment is feasible from EBUS-TBNA smears from a single needle pass. Repeated samples of a lymph node station have minimal variation in TMB in most cases. However, this novel data shows how tumour content and minor change in site of node sampling can impact TMB. Further study is needed on whether all node aspirates should be combined in 1 sample, or whether testing independent nodes using smears is needed.
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Affiliation(s)
- David Fielding
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Andrew J. Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Mahendra Singh
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Lakshmy Nandakumar
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David Fairbairn
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Kaltin Ferguson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Michael Bint
- Department of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, QLD, Australia
| | - Carl Pahoff
- Department of Respiratory Medicine, Gold Coast University Hospital, Southport, QLD, Australia
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Kimberley Ryan
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Alan Hodgson
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Sowmya Sharma
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- ACL Pathology, Sydney, NSW, Australia
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
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Li Z, Lu S. Integrating minimal residual disease monitoring into clinical practice for NSCLC: Is the era upon us? Cancer Cell 2023; 41:1699-1701. [PMID: 37816330 DOI: 10.1016/j.ccell.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023]
Abstract
In this issue of Cancer Cell, Chen et al. and Pan et al. employ personalized, tumor-informed technology to detect minimal residual disease in non-small-cell lung cancer and demonstrate the clinical promise of integrating liquid biopsy techniques to improve the assessment of cancer progression and metastasis risk.
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Affiliation(s)
- Ziming Li
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Shun Lu
- Department of Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China.
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Bai K, Chen X, Qi X, Zhang Y, Zou Y, Li J, Yu L, Li Y, Jiang J, Yang Y, Liu Y, Feng S, Bu H. Cerebrospinal fluid circulating tumour DNA genotyping and survival analysis in lung adenocarcinoma with leptomeningeal metastases. J Neurooncol 2023; 165:149-160. [PMID: 37897649 PMCID: PMC10638181 DOI: 10.1007/s11060-023-04471-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023]
Abstract
PURPOSE The prognosis of patients with leptomeningeal metastasis (LM) remains poor. Circulating tumour DNA (ctDNA) has been proven to be abundantly present in cerebrospinal fluid (CSF); hence, its clinical implication as a biomarker needs to be further verified. METHODS We conducted a retrospective study of 35 lung adenocarcinoma (LUAD) patients with LM, and matched CSF and plasma samples were collected from all patients. All paired samples underwent next-generation sequencing (NGS) of 139 lung cancer-associated genes. The clinical characteristics and genetic profiling of LM were analysed in association with survival prognosis. RESULTS LM showed genetic heterogeneity, in which CSF had a higher detection rate of ctDNA (P = 0.003), a higher median mutation count (P < 0.0001), a higher frequency of driver mutations (P < 0.01), and more copy number variation (CNV) alterations (P < 0.001) than plasma. The mutation frequencies of the EGFR, TP53, CDKN2A, MYC and CDKN2B genes were easier to detect in CSF than in LUAD tissue (P < 0.05), possibly reflecting the underlying mechanism of LM metastasis. CSF ctDNA is helpful for analysing the mechanism of EGFR-TKI resistance. In cohort 1, which comprised patients who received 1/2 EGFR-TKIs before the diagnosis of LM, TP53 and CDKN2A were the most common EGFR-independent resistant mutations. In cohort 2, comprising those who progressed after osimertinib and developed LM, 7 patients (43.75%) had EGFR CNV detected in CSF but not plasma. Furthermore, patient characteristics and various genes were included for interactive survival analysis. Patients with EGFR-mutated LUAD (P = 0.042) had a higher median OS, and CSF ctDNA mutation with TERT (P = 0.013) indicated a lower median OS. Last, we reported an LM case in which CSF ctDNA dynamic changes were well correlated with clinical treatment. CONCLUSIONS CSF ctDNA could provide a more comprehensive genetic landscape of LM, indicating the potential metastasis-related and EGFR-TKI resistance mechanisms of LM patients. In addition, genotyping of CSF combined with clinical outcomes can predict the prognosis of LUAD patients with LM.
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Affiliation(s)
- Kaixuan Bai
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Xin Chen
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- Department of Neurology, Xingtai People's Hospital, Xingtai, China
| | - Xuejiao Qi
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Yu Zhang
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Yueli Zou
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Jian Li
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- Department of General Practice, Hengshui People's Hospital, Hengshui, China
| | - Lili Yu
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Yuanyuan Li
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Jiajia Jiang
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Yi Yang
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Yajing Liu
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Shuanghao Feng
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China
- Neurological Laboratory of Hebei Province, Shijiazhuang, China
| | - Hui Bu
- Department of Neurology, The Second Hospital of Hebei Medical University, 215 Heping West Road, Xinhua District, Shijiazhuang, Hebei Province, China.
- The Key Laboratory of Neurology (Hebei Medical University), Ministry of Education, Shijiazhuang, China.
- Neurological Laboratory of Hebei Province, Shijiazhuang, China.
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Holme JA, Vondráček J, Machala M, Lagadic-Gossmann D, Vogel CFA, Le Ferrec E, Sparfel L, Øvrevik J. Lung cancer associated with combustion particles and fine particulate matter (PM 2.5) - The roles of polycyclic aromatic hydrocarbons (PAHs) and the aryl hydrocarbon receptor (AhR). Biochem Pharmacol 2023; 216:115801. [PMID: 37696458 PMCID: PMC10543654 DOI: 10.1016/j.bcp.2023.115801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Air pollution is the leading cause of lung cancer after tobacco smoking, contributing to 20% of all lung cancer deaths. Increased risk associated with living near trafficked roads, occupational exposure to diesel exhaust, indoor coal combustion and cigarette smoking, suggest that combustion components in ambient fine particulate matter (PM2.5), such as polycyclic aromatic hydrocarbons (PAHs), may be central drivers of lung cancer. Activation of the aryl hydrocarbon receptor (AhR) induces expression of xenobiotic-metabolizing enzymes (XMEs) and increase PAH metabolism, formation of reactive metabolites, oxidative stress, DNA damage and mutagenesis. Lung cancer tissues from smokers and workers exposed to high combustion PM levels contain mutagenic signatures derived from PAHs. However, recent findings suggest that ambient air PM2.5 exposure primarily induces lung cancer development through tumor promotion of cells harboring naturally acquired oncogenic mutations, thus lacking typical PAH-induced mutations. On this background, we discuss the role of AhR and PAHs in lung cancer development caused by air pollution focusing on the tumor promoting properties including metabolism, immune system, cell proliferation and survival, tumor microenvironment, cell-to-cell communication, tumor growth and metastasis. We suggest that the dichotomy in lung cancer patterns observed between smoking and outdoor air PM2.5 represent the two ends of a dose-response continuum of combustion PM exposure, where tumor promotion in the peripheral lung appears to be the driving factor at the relatively low-dose exposures from ambient air PM2.5, whereas genotoxicity in the central airways becomes increasingly more important at the higher combustion PM levels encountered through smoking and occupational exposure.
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Affiliation(s)
- Jørn A Holme
- Department of Air Quality and Noise, Division of Climate and Environmental Health, Norwegian Institute of Public Health, PO Box PO Box 222 Skøyen, 0213 Oslo, Norway
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic
| | - Miroslav Machala
- Department of Pharmacology and Toxicology, Veterinary Research Institute, 62100 Brno, Czech Republic
| | - Dominique Lagadic-Gossmann
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Christoph F A Vogel
- Department of Environmental Toxicology and Center for Health and the Environment, University of California, Davis, CA 95616, USA
| | - Eric Le Ferrec
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Lydie Sparfel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S 1085, F-35000, Rennes, France
| | - Johan Øvrevik
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway; Division of Climate and Environmental Health, Norwegian Institute of Public Health, PO Box 222 Skøyen, 0213 Oslo, Norway.
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36
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Garbo E, Del Rio B, Ferrari G, Cani M, Napoli VM, Bertaglia V, Capelletto E, Rolfo C, Novello S, Passiglia F. Exploring the Potential of Non-Coding RNAs as Liquid Biopsy Biomarkers for Lung Cancer Screening: A Literature Review. Cancers (Basel) 2023; 15:4774. [PMID: 37835468 PMCID: PMC10571819 DOI: 10.3390/cancers15194774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Lung cancer represent the leading cause of cancer mortality, so several efforts have been focused on the development of a screening program. To address the issue of high overdiagnosis and false positive rates associated to LDCT-based screening, there is a need for new diagnostic biomarkers, with liquid biopsy ncRNAs detection emerging as a promising approach. In this scenario, this work provides an updated summary of the literature evidence about the role of non-coding RNAs in lung cancer screening. A literature search on PubMed was performed including studies which investigated liquid biopsy non-coding RNAs biomarker lung cancer patients and a control cohort. Micro RNAs were the most widely studied biomarkers in this setting but some preliminary evidence was found also for other non-coding RNAs, suggesting that a multi-biomarker based liquid biopsy approach could enhance their efficacy in the screening context. However, further studies are needed in order to optimize detection techniques as well as diagnostic accuracy before introducing novel biomarkers in the early diagnosis setting.
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Affiliation(s)
- Edoardo Garbo
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Benedetta Del Rio
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Giorgia Ferrari
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Massimiliano Cani
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Valerio Maria Napoli
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Valentina Bertaglia
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Enrica Capelletto
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Christian Rolfo
- Center for Thoracic Oncology, Tisch Cancer Institute, Mount Sinai Health System, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Silvia Novello
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
| | - Francesco Passiglia
- Department of Oncology, University of Turin, San Luigi Hospital, 10124 Orbassano, Italy; (E.G.); (B.D.R.); (G.F.); (M.C.); (V.M.N.); (V.B.); (E.C.); (S.N.)
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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Jones TP, McGranahan N. Deciphering the landscape of transcriptional heterogeneity across cancer. Cancer Cell 2023; 41:1548-1550. [PMID: 37595585 DOI: 10.1016/j.ccell.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/20/2023]
Abstract
By integrating scRNA-seq datasets across 77 studies and 24 cancer types, in Nature, Gavish et al. uncover recurrent patterns of gene expression that explain a significant proportion of transcriptomic heterogeneity observed in cancer and explore their functional significance.
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Affiliation(s)
- Thomas P Jones
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer 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, University College London Cancer Institute, London, UK.
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Qiu X, Ni B, Shen Y, Zhang Y, Xia X, Cao H, Zhang Z, Zhu C. Synchronous primary colorectal mucinous adenocarcinoma and pancreatic ductal adenocarcinoma: A case report. Oncol Lett 2023; 26:405. [PMID: 37600331 PMCID: PMC10436161 DOI: 10.3892/ol.2023.13991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
The present study reports a rare case of synchronous colorectal mucinous adenocarcinoma (CMAC) and pancreatic ductal adenocarcinoma (PDAC). A 61-year-old man complained of hematochezia for half a month. Colonoscopy and biopsy in a local hospital revealed mucinous adenocarcinoma in the sigmoid colon, and a subsequent abdominal computed tomography examination in Ren Ji Hospital (Shanghai, China) identified an unexpectedly hypovascular lesion in the body and tail of the pancreas, in addition to a mass in the colon. The patient then underwent combined surgery consisting of a distal pancreaticosplenectomy and a sigmoidectomy, and the postoperative pathological tests confirmed the co-occurrence of CMAC and PDAC. Next-generation sequencing demonstrated no deleterious germline mutations, but did find some critical somatic mutations concerning both tumors. The patient received 12 cycles of a combination of 5-fluorouracil, leucovorin, irinotecan and oxaliplatin (modified FOLFIRINOX regimen) as adjuvant chemotherapy thereafter. Complete remission was achieved at 1 year after the surgery. To the best of our knowledge, this is the first documented case of such synchronous malignances (CMAC and PDAC) in the literature, and its publication therefore improves our overall understanding in this field.
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Affiliation(s)
- Xudong Qiu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Bo Ni
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yanying Shen
- Department of Pathology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Yeqian Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Xiang Xia
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Hui Cao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
| | - Chunchao Zhu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P.R. China
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Krebs MG, Popat S. RETaliation-Tackling Rare Resistance Alterations to Osimertinib. Clin Cancer Res 2023; 29:2951-2953. [PMID: 37314773 DOI: 10.1158/1078-0432.ccr-23-0993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/16/2023] [Accepted: 05/25/2023] [Indexed: 06/15/2023]
Abstract
RET fusions occur as a rare mechanism of acquired resistance to osimertinib in patients with EGFR mutation-positive non-small cell lung cancer. Inhibiting RET alongside osimertinib shows promising clinical activity, but innovative approaches are needed to seek regulatory approvals in these rare treatment resistance settings. See related article by Rotow et al., p. 2979.
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Affiliation(s)
- Matthew G Krebs
- Division of Cancer Sciences, The University of Manchester and The Christie NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, United Kingdom
| | - Sanjay Popat
- Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
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41
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Lorenz C, Hillmer AM, Brägelmann J. Predicting the next move: tracking the complexity of lung cancer evolution and metastasis. Signal Transduct Target Ther 2023; 8:291. [PMID: 37553337 PMCID: PMC10409755 DOI: 10.1038/s41392-023-01567-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 08/10/2023] Open
Affiliation(s)
- Carina Lorenz
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Mildred Scheel School of Oncology Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
| | - Axel M Hillmer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Johannes Brägelmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany.
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Mildred Scheel School of Oncology Cologne, Cologne, Germany.
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Center for Molecular Medicine Cologne, Cologne, Germany.
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Liu M, Jin S, Agabiti SS, Jensen TB, Yang T, Radda JSD, Ruiz CF, Baldissera G, Muzumdar MD, Wang S. A genome-wide single-cell 3D genome atlas of lung cancer progression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.23.550157. [PMID: 37546882 PMCID: PMC10401964 DOI: 10.1101/2023.07.23.550157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Alterations in three-dimensional (3D) genome structures are associated with cancer1-5. However, how genome folding evolves and diversifies during subclonal cancer progression in the native tissue environment remains unknown. Here, we leveraged a genome-wide chromatin tracing technology to directly visualize 3D genome folding in situ in a faithful Kras-driven mouse model of lung adenocarcinoma (LUAD)6, generating the first single-cell 3D genome atlas of any cancer. We discovered stereotypical 3D genome alterations during cancer development, including a striking structural bottleneck in preinvasive adenomas prior to progression to LUAD, indicating a stringent selection on the 3D genome early in cancer progression. We further showed that the 3D genome precisely encodes cancer states in single cells, despite considerable cell-to-cell heterogeneity. Finally, evolutionary changes in 3D genome compartmentalization - partially regulated by polycomb group protein Rnf2 through its ubiquitin ligase-independent activity - reveal novel genetic drivers and suppressors of LUAD progression. Our results demonstrate the importance of mapping the single-cell cancer 3D genome and the potential to identify new diagnostic and therapeutic biomarkers from 3D genomic architectures.
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Affiliation(s)
- Miao Liu
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Shengyan Jin
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Sherry S. Agabiti
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
| | - Tyler B. Jensen
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
| | - Tianqi Yang
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Jonathan S. D. Radda
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Christian F. Ruiz
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
| | - Gabriel Baldissera
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
| | - Mandar Deepak Muzumdar
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Biology Institute, Yale University; West Haven, CT 06516, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
- Department of Internal Medicine, Section of Medical Oncology, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Yale Cancer Center, Smilow Cancer Hospital, New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University; New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics and Development Program, Yale University; New Haven, CT 06510, USA
| | - Siyuan Wang
- Department of Genetics, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- M.D.-Ph.D. Program, Yale University; New Haven, CT 06510, USA
- Yale Combined Program in the Biological and Biomedical Sciences, Yale University; New Haven, CT 06510, USA
- Molecular Cell Biology, Genetics and Development Program, Yale University; New Haven, CT 06510, USA
- Department of Cell Biology, Yale School of Medicine, Yale University; New Haven, CT 06510, USA
- Biochemistry, Quantitative Biology, Biophysics, and Structural Biology Program, Yale University; New Haven, CT 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine; New Haven, CT 06510, USA
- Yale Liver Center, Yale University School of Medicine; New Haven, CT 06510, USA
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Du Y, Zhang S, Zhang G, Hu J, Zhao L, Xiong Y, Shen L, Chen R, Ye K, Xu Y. Mutational profiling of Chinese patients with thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1156999. [PMID: 37465126 PMCID: PMC10351985 DOI: 10.3389/fendo.2023.1156999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Background The incidence of thyroid cancer in China has rapidly increased in recent decades. As the genetic profiles of thyroid cancer vary dramatically between different geographical regions, a comprehensive genetic landscape of thyroid cancer in the Chinese population is urgently needed. Methods We retrospectively included thyroid cancer patients from three Chinese medical centers between February 2015 and August 2020. To dissect the genomic profiling of these patients, we performed targeted next-generation sequencing on their tumor tissues using a 1,021-gene panel. Results A total of 458 Chinese patients with thyroid cancer were enrolled, including four malignant histological subtypes arising from follicular epithelial thyroid cells. BRAF driver mutations were identified in 76.0% of patients, followed by RET rearrangements (7.6%) and RAS driver mutations (4.1%). Tumors with more somatic mutations correlated with worse clinical characteristics, including older age at diagnosis, less differentiation of tumor, larger tumor size, lymph node metastasis and distal metastasis. Subclonal BRAF mutations occurred in 20% (6/30) of patients and were frequent in poorly differentiated or anaplastic tumors (33.3% [2/6] vs. 4.2% [1/24], P = 0.09) and those with distal metastasis (50.0% [2/4] vs. 8.7% [2/23], P = 0.09). Tumors with TERT promoter mutations had significantly more somatic mutations (average: 6.5 vs. 1.8, P < 0.001). Moreover, TERT promoter mutations were not associated with lymph node metastasis but significantly associated with older age at diagnosis and poorly differentiated or anaplastic tumors, regardless of their clonal architecture. Conclusion Our results shed light on the molecular pathogenesis and clinical characteristics of thyroid cancer in the Chinese population. The number of somatic mutations, TERT promoter mutations, and the clonal architecture of BRAF mutations should be considered in the risk stratification of thyroid cancer.
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Affiliation(s)
- Yaying Du
- Department of Thyroid and Breast Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Gang Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Jiaying Hu
- Ultrasound Diagnostic Department, Daping Hospital, Army Military Medical University, Chongqing, China
| | - Lianhua Zhao
- Department of Pathology, Daping Hospital, Army Military Medical University, Chongqing, China
| | | | - Lu Shen
- Geneplus-Beijing, Beijing, China
| | | | - Ke Ye
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yan Xu
- Department of Breast and Thyroid Surgery, Daping Hospital, Army Military Medical University, Chongqing, China
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Qiu T, Zhi X, Ren S. Recent advance of next-generation sequencing in patients with lung cancer. Expert Rev Mol Diagn 2023; 23:959-970. [PMID: 37750512 DOI: 10.1080/14737159.2023.2260755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION Precision medicine based on the driver genes mutation status is the current systemic therapeutic paradigm in patients with lung cancer. Next-generation sequencing (NGS) has emerged as a powerful platform for molecular diagnosis by virtue of high-throughput and massively parallel sequencing. Liquid biopsy also enabled the dynamic monitoring and comprehensive profiling of lung cancer in a noninvasive manner. However, challenges remain in the field of technology and clinical applications, especially in the era of immunotherapy. AREAS COVERED Here, we update the role of NGS in the context of lung cancer screening, molecular diagnosis, predictive and prognostic biomarkers, and guiding personalized treatment. EXPERT OPINION The NGS application for actable genomic alternation has greatly changed the therapeutic landscape in patients with lung cancer including perioperative setting and advanced stage. Meanwhile, emerging evidence has shown the potential of other applications such as early screening and detection, and MRD. However, challenges remain such as the lack of standardized protocols across different platforms and bioinformatics analysis pipelines, and the complexity of interpreting and leveraging numerous genomic mutation messages for therapy selection. Future research is needed to overcome these challenges and expand the applications of NGS to other aspects such as immunotherapy.
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Affiliation(s)
- Tianyu Qiu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinxin Zhi
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shengxiang Ren
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Malapelle U, Tabbò F, Muscarella LA. Editorial: Concomitant pathogenic mutations in oncogene-driven subgroups: when next generation biology meets targeted therapy in NSCLC. Front Oncol 2023; 13:1239304. [PMID: 37427122 PMCID: PMC10325716 DOI: 10.3389/fonc.2023.1239304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, Italy
| | - Fabrizio Tabbò
- SC Oncologia ASLCN2 Alba e BRA, PO Michele e Pietro Ferrero, Verduno, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
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Vredevoogd DW, Peeper DS. Heterogeneity in functional genetic screens: friend or foe? Front Immunol 2023; 14:1162706. [PMID: 37398651 PMCID: PMC10312307 DOI: 10.3389/fimmu.2023.1162706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Functional genetic screens to uncover tumor-intrinsic nodes of immune resistance have uncovered numerous mechanisms by which tumors evade our immune system. However, due to technical limitations, tumor heterogeneity is imperfectly captured with many of these analyses. Here, we provide an overview of the nature and sources of heterogeneity that are relevant for tumor-immune interactions. We argue that this heterogeneity may actually contribute to the discovery of novel mechanisms of immune evasion, given a sufficiently large and heterogeneous set of input data. Taking advantage of tumor cell heterogeneity, we provide proof-of-concept analyses of mechanisms of TNF resistance. Thus, consideration of tumor heterogeneity is imperative to increase our understanding of immune resistance mechanisms.
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47
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Sanz-Gómez N, González-Álvarez M, De Las Rivas J, de Cárcer G. Whole-Genome Doubling as a source of cancer: how, when, where, and why? Front Cell Dev Biol 2023; 11:1209136. [PMID: 37342233 PMCID: PMC10277508 DOI: 10.3389/fcell.2023.1209136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Chromosome instability is a well-known hallmark of cancer, leading to increased genetic plasticity of tumoral cells, which favors cancer aggressiveness, and poor prognosis. One of the main sources of chromosomal instability are events that lead to a Whole-Genome Duplication (WGD) and the subsequently generated cell polyploidy. In recent years, several studies showed that WGD occurs at the early stages of cell transformation, which allows cells to later become aneuploid, thus leading to cancer progression. On the other hand, other studies convey that polyploidy plays a tumor suppressor role, by inducing cell cycle arrest, cell senescence, apoptosis, and even prompting cell differentiation, depending on the tissue cell type. There is still a gap in understanding how cells that underwent WGD can overcome the deleterious effect on cell fitness and evolve to become tumoral. Some laboratories in the chromosomal instability field recently explored this paradox, finding biomarkers that modulate polyploid cells to become oncogenic. This review brings a historical view of how WGD and polyploidy impact cell fitness and cancer progression, and bring together the last studies that describe the genes helping cells to adapt to polyploidy.
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Affiliation(s)
- Natalia Sanz-Gómez
- Cell Cycle and Cancer Biomarkers Laboratory, Cancer Biology Department, Instituto de Investigaciones Biomédicas “Alberto Sols“. (IIBM) CSIC-UAM, Madrid, Spain
| | - María González-Álvarez
- Cell Cycle and Cancer Biomarkers Laboratory, Cancer Biology Department, Instituto de Investigaciones Biomédicas “Alberto Sols“. (IIBM) CSIC-UAM, Madrid, Spain
| | - Javier De Las Rivas
- Bioinformatics and Functional Genomics Group, Cancer Research Center (CiC-IBMCC), Consejo Superior de Investigaciones Científicas (CSIC), University of Salamanca (USAL), Salamanca, Spain
| | - Guillermo de Cárcer
- Cell Cycle and Cancer Biomarkers Laboratory, Cancer Biology Department, Instituto de Investigaciones Biomédicas “Alberto Sols“. (IIBM) CSIC-UAM, Madrid, Spain
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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: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [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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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] [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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Hayes TK, Meyerson M. Molecular portraits of lung cancer evolution. Nature 2023; 616:435-436. [PMID: 37045956 DOI: 10.1038/d41586-023-00934-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
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