1
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Rosano D, Sofyali E, Dhiman H, Ghirardi C, Ivanoiu D, Heide T, Vingiani A, Bertolotti A, Pruneri G, Canale E, Dewhurst HF, Saha D, Slaven N, Barozzi I, Li T, Zemlyanskiy G, Phillips H, James C, Győrffy B, Lynn C, Cresswell GD, Rehman F, Noberini R, Bonaldi T, Sottoriva A, Magnani L. Long-term Multimodal Recording Reveals Epigenetic Adaptation Routes in Dormant Breast Cancer Cells. Cancer Discov 2024:OF1-OF24. [PMID: 38527495 DOI: 10.1158/2159-8290.cd-23-1161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/10/2024] [Accepted: 02/20/2024] [Indexed: 03/27/2024]
Abstract
Patients with estrogen receptor-positive breast cancer receive adjuvant endocrine therapies (ET) that delay relapse by targeting clinically undetectable micrometastatic deposits. Yet, up to 50% of patients relapse even decades after surgery through unknown mechanisms likely involving dormancy. To investigate genetic and transcriptional changes underlying tumor awakening, we analyzed late relapse patients and longitudinally profiled a rare cohort treated with long-term neoadjuvant ETs until progression. Next, we developed an in vitro evolutionary study to record the adaptive strategies of individual lineages in unperturbed parallel experiments. Our data demonstrate that ETs induce nongenetic cell state transitions into dormancy in a stochastic subset of cells via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably in the absence of recurrent genetic alterations. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs. SIGNIFICANCE This study advances the understanding of therapy-induced dormancy with potential clinical implications for breast cancer. Estrogen receptor-positive breast cancer cells adapt to endocrine treatment by entering a dormant state characterized by strong heterochromatinization with no recurrent genetic changes. Targeting the epigenetic rewiring impairs the adaptation of cancer cells to ETs.
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Affiliation(s)
- Dalia Rosano
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Emre Sofyali
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Heena Dhiman
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
| | - Chiara Ghirardi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Diana Ivanoiu
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Timon Heide
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | | | | | - Giancarlo Pruneri
- Istituto Nazionale Tumori, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Eleonora Canale
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Hannah F Dewhurst
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Debjani Saha
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Neil Slaven
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Centre for Cancer Research, Medical University of Vienna, Austria
| | - Tong Li
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Grigory Zemlyanskiy
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Henry Phillips
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Chela James
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Balázs Győrffy
- Department of Bioinformatics, Semmelweis University, Budapest, Hungary
- RCNS Cancer Biomarker Research Group, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pecs, Pecs, Hungary
| | - Claire Lynn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - George D Cresswell
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Farah Rehman
- Charing Cross Hospital, Imperial College NHS Trust, London, United Kingdom
| | - Roberta Noberini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Haematology-Oncology, University of Milano, Milano, Italy
| | - Andrea Sottoriva
- Human Technopole, Milan, Italy
- Centre for Evolution and Cancer, Institute of Cancer Research, London, United Kingdom
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- The Breast Cancer Now Toby Robins Research Center, The Institute of Cancer Research, London, United Kingdom
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2
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Lakatos E, Gunasri V, Zapata L, Househam J, Heide T, Trahearn N, Swinyard O, Cisneros L, Lynn C, Mossner M, Kimberley C, Spiteri I, Cresswell GD, Llibre-Palomar G, Mitchison M, Maley CC, Jansen M, Rodriguez-Justo M, Bridgewater J, Baker AM, Sottoriva A, Graham TA. Epigenome and early selection determine the tumour-immune evolutionary trajectory of colorectal cancer. bioRxiv 2024:2024.02.12.579956. [PMID: 38405882 PMCID: PMC10888923 DOI: 10.1101/2024.02.12.579956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Immune system control is a major hurdle that cancer evolution must circumvent. The relative timing and evolutionary dynamics of subclones that have escaped immune control remain incompletely characterized, and how immune-mediated selection shapes the epigenome has received little attention. Here, we infer the genome- and epigenome-driven evolutionary dynamics of tumour-immune coevolution within primary colorectal cancers (CRCs). We utilise our existing CRC multi-region multi-omic dataset that we supplement with high-resolution spatially-resolved neoantigen sequencing data and highly multiplexed imaging of the tumour microenvironment (TME). Analysis of somatic chromatin accessibility alterations (SCAAs) reveals frequent somatic loss of accessibility at antigen presenting genes, and that SCAAs contribute to silencing of neoantigens. We observe that strong immune escape and exclusion occur at the outset of CRC formation, and that within tumours, including at the microscopic level of individual tumour glands, additional immune escape alterations have negligible consequences for the immunophenotype of cancer cells. Further minor immuno-editing occurs during local invasion and is associated with TME reorganisation, but that evolutionary bottleneck is relatively weak. Collectively, we show that immune evasion in CRC follows a "Big Bang" evolutionary pattern, whereby genetic, epigenetic and TME-driven immune evasion acquired by the time of transformation defines subsequent cancer-immune evolution.
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Affiliation(s)
- Eszter Lakatos
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- UCL Cancer Institute, University College London, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Nicholas Trahearn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ottilie Swinyard
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Luis Cisneros
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences Arizona State University, Tempe, USA
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D. Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Gerard Llibre-Palomar
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Miriam Mitchison
- Histopathology Department, University College London Hospitals NHS Foundation Trust, London, UK
| | - Carlo C. Maley
- Arizona Cancer Evolution Center, Biodesign Institute and School of Life Sciences Arizona State University, Tempe, USA
| | - Marnix Jansen
- UCL Cancer Institute, University College London, London, UK
| | | | | | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, 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
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
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3
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Ciriello G, Magnani L, Aitken SJ, Akkari L, Behjati S, Hanahan D, Landau DA, Lopez-Bigas N, Lupiáñez DG, Marine JC, Martin-Villalba A, Natoli G, Obenauf AC, Oricchio E, Scaffidi P, Sottoriva A, Swarbrick A, Tonon G, Vanharanta S, Zuber J. Cancer Evolution: A Multifaceted Affair. Cancer Discov 2024; 14:36-48. [PMID: 38047596 PMCID: PMC10784746 DOI: 10.1158/2159-8290.cd-23-0530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/23/2023] [Indexed: 12/05/2023]
Abstract
Cancer cells adapt and survive through the acquisition and selection of molecular modifications. This process defines cancer evolution. Building on a theoretical framework based on heritable genetic changes has provided insights into the mechanisms supporting cancer evolution. However, cancer hallmarks also emerge via heritable nongenetic mechanisms, including epigenetic and chromatin topological changes, and interactions between tumor cells and the tumor microenvironment. Recent findings on tumor evolutionary mechanisms draw a multifaceted picture where heterogeneous forces interact and influence each other while shaping tumor progression. A comprehensive characterization of the cancer evolutionary toolkit is required to improve personalized medicine and biomarker discovery. SIGNIFICANCE Tumor evolution is fueled by multiple enabling mechanisms. Importantly, genetic instability, epigenetic reprogramming, and interactions with the tumor microenvironment are neither alternative nor independent evolutionary mechanisms. As demonstrated by findings highlighted in this perspective, experimental and theoretical approaches must account for multiple evolutionary mechanisms and their interactions to ultimately understand, predict, and steer tumor evolution.
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Affiliation(s)
- Giovanni Ciriello
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Luca Magnani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Epigenetic Plasticity and Evolution Laboratory, Division of Breast Cancer Research, The Institute of Cancer Research, London, United Kingdom
- Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Sarah J. Aitken
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, United Kingdom
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Leila Akkari
- Division of Tumor Biology and Immunology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
| | - Douglas Hanahan
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Dan A. Landau
- New York Genome Center, New York, New York
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, New York
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Darío G. Lupiáñez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Jean-Christophe Marine
- Laboratory for Molecular Cancer Biology, Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Molecular Cancer Biology, Department of Oncology, KULeuven, Leuven, Belgium
| | - Ana Martin-Villalba
- Department of Molecular Neurobiology, German Cancer Research Center (DFKZ), Heidelberg, Germany
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Anna C. Obenauf
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Elisa Oricchio
- Swiss Cancer Center Leman, Lausanne, Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Paola Scaffidi
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Cancer Epigenetic Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Sottoriva
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
| | - Giovanni Tonon
- Vita-Salute San Raffaele University, Milan, Italy
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sakari Vanharanta
- Translational Cancer Medicine Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
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4
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Chen B, Ramazzotti D, Heide T, Spiteri I, Fernandez-Mateos J, James C, Magnani L, Graham TA, Sottoriva A. Contribution of pks + E. coli mutations to colorectal carcinogenesis. Nat Commun 2023; 14:7827. [PMID: 38030613 PMCID: PMC10687070 DOI: 10.1038/s41467-023-43329-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
The dominant mutational signature in colorectal cancer genomes is C > T deamination (COSMIC Signature 1) and, in a small subgroup, mismatch repair signature (COSMIC signatures 6 and 44). Mutations in common colorectal cancer driver genes are often not consistent with those signatures. Here we perform whole-genome sequencing of normal colon crypts from cancer patients, matched to a previous multi-omic tumour dataset. We analyse normal crypts that were distant vs adjacent to the cancer. In contrast to healthy individuals, normal crypts of colon cancer patients have a high incidence of pks + (polyketide synthases) E.coli (Escherichia coli) mutational and indel signatures, and this is confirmed by metagenomics. These signatures are compatible with many clonal driver mutations detected in the corresponding cancer samples, including in chromatin modifier genes, supporting their role in early tumourigenesis. These results provide evidence that pks + E.coli is a potential driver of carcinogenesis in the human gut.
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Affiliation(s)
- Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangzhou, China
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Luca Magnani
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Trevor A Graham
- 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.
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5
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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Zapata L, Caravagna G, Williams MJ, Lakatos E, AbdulJabbar K, Werner B, Chowell D, James C, Gourmet L, Milite S, Acar A, Riaz N, Chan TA, Graham TA, Sottoriva A. Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. Nat Genet 2023; 55:451-460. [PMID: 36894710 PMCID: PMC10011129 DOI: 10.1038/s41588-023-01313-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/25/2023] [Indexed: 03/11/2023]
Abstract
In cancer, evolutionary forces select for clones that evade the immune system. Here we analyzed >10,000 primary tumors and 356 immune-checkpoint-treated metastases using immune dN/dS, the ratio of nonsynonymous to synonymous mutations in the immunopeptidome, to measure immune selection in cohorts and individuals. We classified tumors as immune edited when antigenic mutations were removed by negative selection and immune escaped when antigenicity was covered up by aberrant immune modulation. Only in immune-edited tumors was immune predation linked to CD8 T cell infiltration. Immune-escaped metastases experienced the best response to immunotherapy, whereas immune-edited patients did not benefit, suggesting a preexisting resistance mechanism. Similarly, in a longitudinal cohort, nivolumab treatment removes neoantigens exclusively in the immunopeptidome of nonimmune-edited patients, the group with the best overall survival response. Our work uses dN/dS to differentiate between immune-edited and immune-escaped tumors, measuring potential antigenicity and ultimately helping predict response to treatment.
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Affiliation(s)
- Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Cancer Data Science Laboratory, Dipartimento di Matematica e Geoscienze, Università degli Studi di Trieste, Trieste, Italy
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan 10 Kettering Cancer Center, New York, NY, USA
| | - Eszter Lakatos
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Khalid AbdulJabbar
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Benjamin Werner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Diego Chowell
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Lucie Gourmet
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Salvatore Milite
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah, Ankara, Turkey
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Timothy A Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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7
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Heide T, Househam J, Cresswell GD, Spiteri I, Lynn C, Mossner M, Kimberley C, Fernandez-Mateos J, Chen B, Zapata L, James C, Barozzi I, Chkhaidze K, Nichol D, Gunasri V, Berner A, Schmidt M, Lakatos E, Baker AM, Costa H, Mitchinson M, Piazza R, Jansen M, Caravagna G, Ramazzotti D, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Graham TA, Sottoriva A. The co-evolution of the genome and epigenome in colorectal cancer. Nature 2022; 611:733-743. [PMID: 36289335 PMCID: PMC9684080 DOI: 10.1038/s41586-022-05202-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 08/05/2022] [Indexed: 12/13/2022]
Abstract
Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the co-evolution of the genome and epigenome of colorectal tumours at single-clone resolution using spatial multi-omic profiling of individual glands. We collected 1,370 samples from 30 primary cancers and 8 concomitant adenomas and generated 1,207 chromatin accessibility profiles, 527 whole genomes and 297 whole transcriptomes. We found positive selection for DNA mutations in chromatin modifier genes and recurrent somatic chromatin accessibility alterations, including in regulatory regions of cancer driver genes that were otherwise devoid of genetic mutations. Genome-wide alterations in accessibility for transcription factor binding involved CTCF, downregulation of interferon and increased accessibility for SOX and HOX transcription factor families, suggesting the involvement of developmental genes during tumourigenesis. Somatic chromatin accessibility alterations were heritable and distinguished adenomas from cancers. Mutational signature analysis showed that the epigenome in turn influences the accumulation of DNA mutations. This study provides a map of genetic and epigenetic tumour heterogeneity, with fundamental implications for understanding colorectal cancer biology.
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Affiliation(s)
- Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Chris Kimberley
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
- Centre for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Ketevan Chkhaidze
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Helena Costa
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Marnix Jansen
- Department of Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Triest, Triest, Italy
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Computational Biology Research Centre, Human Technopole, Milan, Italy.
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8
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Househam J, Heide T, Cresswell GD, Spiteri I, Kimberley C, Zapata L, Lynn C, James C, Mossner M, Fernandez-Mateos J, Vinceti A, Baker AM, Gabbutt C, Berner A, Schmidt M, Chen B, Lakatos E, Gunasri V, Nichol D, Costa H, Mitchinson M, Ramazzotti D, Werner B, Iorio F, Jansen M, Caravagna G, Barnes CP, Shibata D, Bridgewater J, Rodriguez-Justo M, Magnani L, Sottoriva A, Graham TA. Phenotypic plasticity and genetic control in colorectal cancer evolution. Nature 2022; 611:744-753. [PMID: 36289336 PMCID: PMC9684078 DOI: 10.1038/s41586-022-05311-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/01/2022] [Indexed: 12/12/2022]
Abstract
Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain unknown. Here we show that intratumour genetic ancestry only infrequently affects gene expression traits and subclonal evolution in colorectal cancer (CRC). Using spatially resolved paired whole-genome and transcriptome sequencing, we find that the majority of intratumour variation in gene expression is not strongly heritable but rather 'plastic'. Somatic expression quantitative trait loci analysis identified a number of putative genetic controls of expression by cis-acting coding and non-coding mutations, the majority of which were clonal within a tumour, alongside frequent structural alterations. Consistently, computational inference on the spatial patterning of tumour phylogenies finds that a considerable proportion of CRCs did not show evidence of subclonal selection, with only a subset of putative genetic drivers associated with subclone expansions. Spatial intermixing of clones is common, with some tumours growing exponentially and others only at the periphery. Together, our data suggest that most genetic intratumour variation in CRC has no major phenotypic consequence and that transcriptional plasticity is, instead, widespread within a tumour.
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Affiliation(s)
- Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chris Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Claire Lynn
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chela James
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Maximilian Mossner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | | | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Calum Gabbutt
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Alison Berner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Schmidt
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Bingjie Chen
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Eszter Lakatos
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Vinaya Gunasri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Daniel Nichol
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Helena Costa
- UCL Cancer Institute, University College London, London, UK
| | - Miriam Mitchinson
- Histopathology Department, University College London Hospitals NHS Foundation Trust, London, UK
| | - Daniele Ramazzotti
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Benjamin Werner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Francesco Iorio
- Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Marnix Jansen
- UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
| | - Darryl Shibata
- Department of Pathology, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | | | | | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, 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.
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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9
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Ingles Russo Garces A, Milite S, Oliveira E, Fernandez-Mateos J, Chen B, Pickard L, Stewart A, Lau R, De Haven Brandon A, Paranjape E, Sottoriva A, Banerjee S, Banerji U. 1697P Drug-induced evolutionary dynamics in BRCA-mutant/non-mutant ovarian cancer models. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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10
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Tari H, Kessler K, Trahearn N, Werner B, Vinci M, Jones C, Sottoriva A. Quantification of spatial subclonal interactions enhancing the invasive phenotype of pediatric glioma. Cell Rep 2022; 40:111283. [PMID: 36044867 PMCID: PMC9449134 DOI: 10.1016/j.celrep.2022.111283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/21/2022] [Accepted: 08/08/2022] [Indexed: 11/25/2022] Open
Abstract
Diffuse midline gliomas (DMGs) are highly aggressive, incurable childhood brain tumors. They present a clinical challenge due to many factors, including heterogeneity and diffuse infiltration, complicating disease management. Recent studies have described the existence of subclonal populations that may co-operate to drive pro-tumorigenic processes such as cellular invasion. However, a precise quantification of subclonal interactions is lacking, a problem that extends to other cancers. In this study, we combine spatial computational modeling of cellular interactions during invasion with co-evolution experiments of clonally disassembled patient-derived DMG cells. We design a Bayesian inference framework to quantify spatial subclonal interactions between molecular and phenotypically distinct lineages with different patterns of invasion. We show how this approach could discriminate genuine interactions, where one clone enhanced the invasive phenotype of another, from those apparently only due to the complex dynamics of spatially restricted growth. This study provides a framework for the quantification of subclonal interactions in DMG.
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Affiliation(s)
- Haider Tari
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Glioma Team, The Institute of Cancer Research, London, UK
| | - Ketty Kessler
- Glioma Team, The Institute of Cancer Research, London, UK
| | - Nick Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Benjamin Werner
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Vinci
- Department of Haematology/Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Chris Jones
- Glioma Team, The Institute of Cancer Research, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Research Centre for Computational Biology, Human Technopole, Milan, Italy.
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11
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Berner AM, Gabbutt C, Nowinski S, Househam J, Trahearn N, Cresswell GD, Nadhamuni VS, Kimberley C, Fassan M, Baker AM, Sottoriva A, Thirlwell C, Bridgewater J, Graham T. Abstract A045: Multiple roles for plasticity in metastasis and therapy resistance in long-term survivors of metastatic colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.evodyn22-a045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Long-term survivors (LS) of metastatic colorectal cancer (mCRC) who experience multiple recurrences with resectable oligometastatic disease provide an opportunity to explore co-evolution of the tumor and immune microenvironment. We profiled 16 LS of mCRC with a median follow-up of 9.3 years and median of 3 biopsies/resections per patient (range 2-7). We performed multi-omic profiling of 56 primary and 176 metastatic samples from formalin-fixed paraffin-embedded tissue using low pass whole genome sequencing, 3’ RNA sequencing and DNA methylation arrays. A machine learning cell classifier was used to quantify immune cell and fibroblast infiltration from hematoxylin and eosin staining. Copy number profiling showed that the fraction of genome altered remained relatively stable across time and tissue type but that already-altered segments underwent progressive fragmentation. Inter-timepoint divergence of copy number alterations was significantly higher than intra-timepoint divergence, and intra-timepoint divergence was lower for liver and lung metastases than for primary tumors. Chemotherapy treatment did not significantly affect either divergence type. Differential expression and gene set enrichment analysis (GSEA) revealed common pathways dysregulated in metastases compared to primaries, including reductions in E2F (important in G1/S checkpoint) and G2M checkpoint, suggestive of the onset of senescence in metastases. Tumors underwent progressive hypomethylation over time and analysis of genes with concordant changes in promoter methylation and expression revealed dysregulation in pathways related to endocytosis, cell adhesion and migration. This suggests an important role for phenotypic plasticity in driving the metastatic phenotype. There were transient increases in the proportion of macrophages, lymphocytes and neutrophils in tumors that had undergone neoadjuvant chemotherapy in the 6 months prior to resection and slight increases in M1 macrophage activity (by GSEA) in tumors that were previously therapy naïve. There were concordant transient increases in pathways associated with immune response (MYC V1 and MTORC1), as well as xenobiotic metabolism. The latter is a known mechanism of drug resistance to both the platinum- and fluoropyridine-based therapies used in CRC. There were also more sustained increases post-chemotherapy in inflammatory and immune pathways associated with the adaptive immune response and tissue injury and repair. These findings were corroborated by concordant changes in promoter methylation. These data suggest that there is a threshold level of aneuploidy required to facilitate CRC metastasis but the migratory phenotype and adaptation to the metastatic niche are driven by plasticity. Chemotherapy induces differing short-term and long-term anti-tumor immune responses in the local microenvironment. We see evidence that mCRCs are able to mount plastic pro-survival mechanisms in response to chemotherapy.
Citation Format: Alison May Berner, Calum Gabbutt, Salpie Nowinski, Jacob Househam, Nick Trahearn, George D. Cresswell, Vinaya Srirangam Nadhamuni, Christopher Kimberley, Matteo Fassan, Ann-Marie Baker, Andrea Sottoriva, Christina Thirlwell, John Bridgewater, Trevor Graham. Multiple roles for plasticity in metastasis and therapy resistance in long-term survivors of metastatic colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A045.
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Affiliation(s)
- Alison May Berner
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Calum Gabbutt
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Salpie Nowinski
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Jacob Househam
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | - Nick Trahearn
- Institute of Cancer Research, London, United Kingdom,
| | | | | | | | | | - Ann-Marie Baker
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
| | | | | | | | - Trevor Graham
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom,
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12
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Palles C, West HD, Chew E, Galavotti S, Flensburg C, Grolleman JE, Jansen EAM, Curley H, Chegwidden L, Arbe-Barnes EH, Lander N, Truscott R, Pagan J, Bajel A, Sherwood K, Martin L, Thomas H, Georgiou D, Fostira F, Goldberg Y, Adams DJ, van der Biezen SAM, Christie M, Clendenning M, Thomas LE, Deltas C, Dimovski AJ, Dymerska D, Lubinski J, Mahmood K, van der Post RS, Sanders M, Weitz J, Taylor JC, Turnbull C, Vreede L, van Wezel T, Whalley C, Arnedo-Pac C, Caravagna G, Cross W, Chubb D, Frangou A, Gruber AJ, Kinnersley B, Noyvert B, Church D, Graham T, Houlston R, Lopez-Bigas N, Sottoriva A, Wedge D, Jenkins MA, Kuiper RP, Roberts AW, Cheadle JP, Ligtenberg MJL, Hoogerbrugge N, Koelzer VH, Rivas AD, Winship IM, Ponte CR, Buchanan DD, Power DG, Green A, Tomlinson IPM, Sampson JR, Majewski IJ, de Voer RM. Germline MBD4 deficiency causes a multi-tumor predisposition syndrome. Am J Hum Genet 2022; 109:953-960. [PMID: 35460607 PMCID: PMC9118112 DOI: 10.1016/j.ajhg.2022.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
We report an autosomal recessive, multi-organ tumor predisposition syndrome, caused by bi-allelic loss-of-function germline variants in the base excision repair (BER) gene MBD4. We identified five individuals with bi-allelic MBD4 variants within four families and these individuals had a personal and/or family history of adenomatous colorectal polyposis, acute myeloid leukemia, and uveal melanoma. MBD4 encodes a glycosylase involved in repair of G:T mismatches resulting from deamination of 5'-methylcytosine. The colorectal adenomas from MBD4-deficient individuals showed a mutator phenotype attributable to mutational signature SBS1, consistent with the function of MBD4. MBD4-deficient polyps harbored somatic mutations in similar driver genes to sporadic colorectal tumors, although AMER1 mutations were more common and KRAS mutations less frequent. Our findings expand the role of BER deficiencies in tumor predisposition. Inclusion of MBD4 in genetic testing for polyposis and multi-tumor phenotypes is warranted to improve disease management.
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Affiliation(s)
- Claire Palles
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Edward Chew
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Sara Galavotti
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Judith E Grolleman
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Erik A M Jansen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Helen Curley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Laura Chegwidden
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Edward H Arbe-Barnes
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Nicola Lander
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Rebekah Truscott
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Judith Pagan
- Molecular Genetics Laboratory, South East Scotland Genetic Service, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ashish Bajel
- Peter MacCallum Cancer Center and Royal Melbourne Hospital, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Kitty Sherwood
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Lynn Martin
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Huw Thomas
- St Mark's Hospital, Imperial College London, London, UK
| | - Demetra Georgiou
- Genomic Medicine, Imperial College Healthcare Trust and North West Thames Regional Genetics Service, Northwick Park, Harrow, UK
| | | | - Yael Goldberg
- Raphael Recanati Genetic Institute, Rabin Medical Center - Beilinson Hospital, Petach Tikva, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Simone A M van der Biezen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Michael Christie
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Laura E Thomas
- Institute of Life Sciences, Swansea University, Swansea SA28PP, UK
| | - Constantinos Deltas
- Center of Excellence in Biobanking and Biomedical Research and Molecular Medicine Research Center, University of Cyprus Medical School, Nicosia, Cyprus
| | - Aleksandar J Dimovski
- Center for Biomolecular Pharmaceutical Analyzes, UKIM Faculty of Pharmacy, 1000 Skopje, Republic of Macedonia
| | - Dagmara Dymerska
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Jan Lubinski
- Hereditary Cancer Center, Department of Genetics and Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Khalid Mahmood
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia
| | - Rachel S van der Post
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Mathijs Sanders
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Jürgen Weitz
- Department of Surgical Research, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jenny C Taylor
- Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Clare Turnbull
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Lilian Vreede
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, 2300 Leiden, the Netherlands
| | - Celina Whalley
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Claudia Arnedo-Pac
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Giulio Caravagna
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - William Cross
- Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Daniel Chubb
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Anna Frangou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Andreas J Gruber
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
| | - Ben Kinnersley
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Boris Noyvert
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - David Church
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Trevor Graham
- Barts Cancer Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Richard Houlston
- Institute of Cancer Research, Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Sottoriva
- Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - David Wedge
- Manchester Interdisciplinary Biocentre, University of Manchester, Manchester M1 7DN, UK
| | - Mark A Jenkins
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Roland P Kuiper
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Princess Máxima Center for Pediatric Oncology, 3584 Utrecht, the Netherlands
| | - Andrew W Roberts
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Molecular Genetics Laboratory, South East Scotland Genetic Service, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia; University of Melbourne, Department of Medical Biology, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - Jeremy P Cheadle
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK
| | - Marjolijn J L Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands; Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Viktor H Koelzer
- Department of Pathology and Molecular Pathology, University Hospital Zurich, University of Zurich, Zürich, Switzerland
| | - Andres Dacal Rivas
- Servicio de Digestivo, Hospital Lucus Augusti, Instituto de Investigación Sanitaria de Santiago, Lugo, Galicia, Spain
| | - Ingrid M Winship
- Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia; Department of Medicine, Melbourne Medical School, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Clara Ruiz Ponte
- Fundación Pública Galega de Medicina Xenómica SERGAS, Grupo de Medicina Xenómica-USC, Instituto de Investigación Sanitaria de Santiago, Centro de Investigación Biomédica en Red de Enfermedades Raras, Santiago de Compostela, Galicia, Spain
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, VIC, Australia; Genomic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Derek G Power
- Department of Medical Oncology, Cork University Hospital, Cork, Ireland
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland; School of Medicine University College, Dublin, Ireland
| | - Ian P M Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK.
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University, School of Medicine, Cardiff, UK.
| | - Ian J Majewski
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
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13
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Gatenbee CD, Baker AM, Schenck RO, Strobl M, West J, Neves MP, Hasan SY, Lakatos E, Martinez P, Cross WCH, Jansen M, Rodriguez-Justo M, Whelan CJ, Sottoriva A, Leedham S, Robertson-Tessi M, Graham TA, Anderson ARA. Immunosuppressive niche engineering at the onset of human colorectal cancer. Nat Commun 2022; 13:1798. [PMID: 35379804 PMCID: PMC8979971 DOI: 10.1038/s41467-022-29027-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022] Open
Abstract
The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique opportunity to study the transition to malignancy as pre-cancers (adenomas) and early-stage cancers are frequently resected. Here, we examine tumor-immune eco-evolutionary dynamics from pre-cancer to carcinoma using a computational model, ecological analysis of digital pathology data, and neoantigen prediction in 62 patient samples. Modeling predicted recruitment of immunosuppressive cells would be the most common driver of transformation. As predicted, ecological analysis reveals that progressed adenomas co-localized with immunosuppressive cells and cytokines, while benign adenomas co-localized with a mixed immune response. Carcinomas converge to a common immune "cold" ecology, relaxing selection against immunogenicity and high neoantigen burdens, with little evidence for PD-L1 overexpression driving tumor initiation. These findings suggest re-engineering the immunosuppressive niche may prove an effective immunotherapy in CRC.
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Affiliation(s)
- Chandler D Gatenbee
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Ryan O Schenck
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Maximilian Strobl
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Jeffrey West
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Margarida P Neves
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Sara Yakub Hasan
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
- Lyon Cancer Institute, Lyon, France
| | - William C H Cross
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Marnix Jansen
- Department of Pathology, University College London Hospital, London, UK
| | | | - Christopher J Whelan
- Cancer Physiology, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
- Department of Biological Sciences, University of Illinois at Chicago, 845 West Taylor Street, Chicago, IL, 60607, USA
| | - Andrea Sottoriva
- Center for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Simon Leedham
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, OX37BN, UK
| | - Mark Robertson-Tessi
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, SRB 4, Tampa, FL, 336122, USA.
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14
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Stankunaite R, George SL, Gallagher L, Jamal S, Shaikh R, Yuan L, Hughes D, Proszek PZ, Carter P, Pietka G, Heide T, James C, Tari H, Lynn C, Jain N, Portela LR, Rogers T, Vaidya SJ, Chisholm JC, Carceller F, Szychot E, Mandeville H, Angelini P, Jesudason AB, Jackson M, Marshall LV, Gatz SA, Anderson J, Sottoriva A, Chesler L, Hubank M. Circulating tumour DNA sequencing to determine therapeutic response and identify tumour heterogeneity in patients with paediatric solid tumours. Eur J Cancer 2022; 162:209-220. [PMID: 34933802 DOI: 10.1016/j.ejca.2021.09.042] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/13/2021] [Accepted: 09/28/2021] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Clinical diagnostic sequencing of circulating tumour DNA (ctDNA) is well advanced for adult patients, but application to paediatric cancer patients lags behind. METHODS To address this, we have developed a clinically relevant (67 gene) NGS capture panel and accompanying workflow that enables sensitive and reliable detection of low-frequency genetic variants in cell-free DNA (cfDNA) from children with solid tumours. We combined gene panel sequencing with low pass whole-genome sequencing of the same library to inform on genome-wide copy number changes in the blood. RESULTS Analytical validity was evaluated using control materials, and the method was found to be highly sensitive (0.96 for SNVs and 0.97 for INDEL), specific (0.82 for SNVs and 0.978 for INDEL), repeatable (>0.93 [95% CI: 0.89-0.95]) and reproducible (>0.87 [95% CI: 0.87-0.95]). Potential for clinical application was demonstrated in 39 childhood cancer patients with a spectrum of solid tumours in which the single nucleotide variants expected from tumour sequencing were detected in cfDNA in 94.4% (17/18) of cases with active extracranial disease. In 13 patients, where serial samples were available, we show a close correlation between events detected in cfDNA and treatment response, demonstrate that cfDNA analysis could be a useful tool to monitor disease progression, and show cfDNA sequencing has the potential to identify targetable variants that were not detected in tumour samples. CONCLUSIONS This is the first pan-cancer DNA sequencing panel that we know to be optimised for cfDNA in children for blood-based molecular diagnostics in paediatric solid tumours.
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Affiliation(s)
- Reda Stankunaite
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Sally L George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Lewis Gallagher
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Sabri Jamal
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Ridwan Shaikh
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Lina Yuan
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Debbie Hughes
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Paula Z Proszek
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Paul Carter
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Grzegorz Pietka
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Chela James
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Haider Tari
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Glioma Lab, The Institute of Cancer Research, London, UK.
| | - Claire Lynn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Neha Jain
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Laura Rey Portela
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Tony Rogers
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK.
| | - Sucheta J Vaidya
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Julia C Chisholm
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Elwira Szychot
- Oak Centre for Children and Young People, Royal Marsden NHS Foundation Trust Hospital, Sutton, UK; Department of Paediatrics, Paediatric Oncology and Immunology, Pomeranian Medical University, Szczecin, Poland.
| | - Henry Mandeville
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Paola Angelini
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Angela B Jesudason
- Department of Paediatric Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh, UK
| | - Michael Jackson
- Department of Paediatric Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh, UK
| | - Lynley V Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Susanne A Gatz
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK.
| | - John Anderson
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Michael Hubank
- Molecular Pathology Section, The Institute of Cancer Research, London, UK; Clinical Genomics, The Royal Marsden NHS Foundation, London, UK.
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15
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Smyth EC, Vlachogiannis G, Hedayat S, Harbery A, Hulkki-Wilson S, Salati M, Kouvelakis K, Fernandez-Mateos J, Cresswell GD, Fontana E, Seidlitz T, Peckitt C, Hahne JC, Lampis A, Begum R, Watkins D, Rao S, Starling N, Waddell T, Okines A, Crosby T, Mansoor W, Wadsley J, Middleton G, Fassan M, Wotherspoon A, Braconi C, Chau I, Vivanco I, Sottoriva A, Stange DE, Cunningham D, Valeri N. EGFR amplification and outcome in a randomised phase III trial of chemotherapy alone or chemotherapy plus panitumumab for advanced gastro-oesophageal cancers. Gut 2021; 70:1632-1641. [PMID: 33199443 PMCID: PMC8355876 DOI: 10.1136/gutjnl-2020-322658] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 01/17/2023]
Abstract
OBJECTIVE Epidermal growth factor receptor (EGFR) inhibition may be effective in biomarker-selected populations of advanced gastro-oesophageal adenocarcinoma (aGEA) patients. Here, we tested the association between outcome and EGFR copy number (CN) in pretreatment tissue and plasma cell-free DNA (cfDNA) of patients enrolled in a randomised first-line phase III clinical trial of chemotherapy or chemotherapy plus the anti-EGFR monoclonal antibody panitumumab in aGEA (NCT00824785). DESIGN EGFR CN by either fluorescence in situ hybridisation (n=114) or digital-droplet PCR in tissues (n=250) and plasma cfDNAs (n=354) was available for 474 (86%) patients in the intention-to-treat (ITT) population. Tissue and plasma low-pass whole-genome sequencing was used to screen for coamplifications in receptor tyrosine kinases. Interaction between chemotherapy and EGFR inhibitors was modelled in patient-derived organoids (PDOs) from aGEA patients. RESULTS EGFR amplification in cfDNA correlated with poor survival in the ITT population and similar trends were observed when the analysis was conducted in tissue and plasma by treatment arm. EGFR inhibition in combination with chemotherapy did not correlate with improved survival, even in patients with significant EGFR CN gains. Addition of anti-EGFR inhibitors to the chemotherapy agent epirubicin in PDOs, resulted in a paradoxical increase in viability and accelerated progression through the cell cycle, associated with p21 and cyclin B1 downregulation and cyclin E1 upregulation, selectively in organoids from EGFR-amplified aGEA. CONCLUSION EGFR CN can be accurately measured in tissue and liquid biopsies and may be used for the selection of aGEA patients. EGFR inhibitors may antagonise the antitumour effect of anthracyclines with important implications for the design of future combinatorial trials.
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Affiliation(s)
- Elizabeth C Smyth
- Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Georgios Vlachogiannis
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Somaieh Hedayat
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Alice Harbery
- Cancer Therapeutics, The Institute of Cancer Research, Sutton, UK
| | | | - Massimiliano Salati
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Kyriakos Kouvelakis
- Clinical Research & Development, Royal Marsden Hospital NHS Trust, London, UK
| | | | - George D Cresswell
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Elisa Fontana
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
| | - Therese Seidlitz
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Dresden, Germany
| | - Clare Peckitt
- Clinical Research & Development, Royal Marsden Hospital NHS Trust, London, UK
| | - Jens C Hahne
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Andrea Lampis
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Ruwaida Begum
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - David Watkins
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Sheela Rao
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Naureen Starling
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Tom Waddell
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
- Department of Medical Oncology, Christie Hospital, Manchester, UK
| | - Alicia Okines
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Tom Crosby
- Department of Clinical Oncology, Velindre Cancer Centre, Cardiff, UK
| | - Was Mansoor
- Department of Medical Oncology, Christie Hospital, Manchester, UK
| | - Jonathan Wadsley
- Cancer Clinical Trials Centre, Weston Park Cancer Centre, Sheffield, UK
| | - Gary Middleton
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, Padova, Italy
| | | | - Chiara Braconi
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
- Cancer Therapeutics, The Institute of Cancer Research, Sutton, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ian Chau
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Igor Vivanco
- Cancer Therapeutics, The Institute of Cancer Research, Sutton, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
| | - Daniel E Stange
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital Carl Gustav Carus, Dresden, Germany
- German Cancer Consortium (DKTK), Partner Site Dresden, Heidelberg, Germany
- National Center for Tumor Diseases, Partner Site Dresden, Heidelberg, Germany
| | - David Cunningham
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
| | - Nicola Valeri
- Department of Medicine, Royal Marsden Hospital NHS Trust, London, UK
- Molecular Pathology, The Institute of Cancer Research, Sutton, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, Sutton, UK
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16
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Bollen Y, Stelloo E, van Leenen P, van den Bos M, Ponsioen B, Lu B, van Roosmalen MJ, Bolhaqueiro ACF, Kimberley C, Mossner M, Cross WCH, Besselink NJM, van der Roest B, Boymans S, Oost KC, de Vries SG, Rehmann H, Cuppen E, Lens SMA, Kops GJPL, Kloosterman WP, Terstappen LWMM, Barnes CP, Sottoriva A, Graham TA, Snippert HJG. Reconstructing single-cell karyotype alterations in colorectal cancer identifies punctuated and gradual diversification patterns. Nat Genet 2021; 53:1187-1195. [PMID: 34211178 PMCID: PMC8346364 DOI: 10.1038/s41588-021-00891-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/24/2021] [Indexed: 01/17/2023]
Abstract
Central to tumor evolution is the generation of genetic diversity. However, the extent and patterns by which de novo karyotype alterations emerge and propagate within human tumors are not well understood, especially at single-cell resolution. Here, we present 3D Live-Seq-a protocol that integrates live-cell imaging of tumor organoid outgrowth and whole-genome sequencing of each imaged cell to reconstruct evolving tumor cell karyotypes across consecutive cell generations. Using patient-derived colorectal cancer organoids and fresh tumor biopsies, we demonstrate that karyotype alterations of varying complexity are prevalent and can arise within a few cell generations. Sub-chromosomal acentric fragments were prone to replication and collective missegregation across consecutive cell divisions. In contrast, gross genome-wide karyotype alterations were generated in a single erroneous cell division, providing support that aneuploid tumor genomes can evolve via punctuated evolution. Mapping the temporal dynamics and patterns of karyotype diversification in cancer enables reconstructions of evolutionary paths to malignant fitness.
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Affiliation(s)
- Yannik Bollen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
- Medical Cell Biophysics, TechMed Centre, University of Twente, Enschede, the Netherlands
| | - Ellen Stelloo
- Oncode Institute, Utrecht, the Netherlands
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Petra van Leenen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Myrna van den Bos
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Bas Ponsioen
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Bingxin Lu
- Department of Cell and Developmental Biology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Markus J van Roosmalen
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ana C F Bolhaqueiro
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Christopher Kimberley
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Maximilian Mossner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - William C H Cross
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- UCL Cancer Institute, UCL, London, UK
| | - Nicolle J M Besselink
- Oncode Institute, Utrecht, the Netherlands
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Bastiaan van der Roest
- Oncode Institute, Utrecht, the Netherlands
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Sander Boymans
- Oncode Institute, Utrecht, the Netherlands
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Koen C Oost
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Sippe G de Vries
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Holger Rehmann
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Edwin Cuppen
- Oncode Institute, Utrecht, the Netherlands
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Hartwig Medical Foundation, Amsterdam, the Netherlands
| | - Susanne M A Lens
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Geert J P L Kops
- Oncode Institute, Utrecht, the Netherlands
- Hubrecht Institute, KNAW, Utrecht, the Netherlands
- University Medical Center Utrecht, Utrecht, the Netherlands
| | - Wigard P Kloosterman
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Leon W M M Terstappen
- Medical Cell Biophysics, TechMed Centre, University of Twente, Enschede, the Netherlands
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Trevor A Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Hugo J G Snippert
- Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
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17
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Kessler K, Mackay A, Molinari V, Tari H, Burford A, Sottoriva A, Vinci M, Jones C. DIPG-63. LOSS OF THE H4 LYSINE METHYLTRANSFERASE KMT5B DRIVES INVASION / MIGRATION BY DEPLETING H3K27me3 AT LOCI OTHERWISE RETAINED IN H3K27M MUTANT DIPG CELLS. Neuro Oncol 2020. [PMCID: PMC7715350 DOI: 10.1093/neuonc/noaa222.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Diffuse intrinsic pontine glioma (DIPG) and other diffuse midline glioma (DMG) are characterised by K27M mutations in histone H3 variants. The major functional consequence is a global loss of the repressive mark H3K27me3, causing a raft of transcriptional changes promoting tumorigenesis, although certain key loci retain trimethylation, such as CDKN2A/B. We recently identified subclonal loss-of-function mutations in the H4 lysine methyltransferase KMT5B to be associated with an enhanced invasion/migration, but the mechanism by which this occurred was unclear. Here we show by ChIP-seq using patient-derived subclonal DIPG models and CRISPR-Cas9 depletion that loss of KMT5B (or KMT5C) causes a paradoxical increase in global levels of H4K20me3 in promoters and regulatory regions, only ablated by knocking out both enzymes. Loss of KMT5B alone further causes loss of the majority of otherwise retained H3K27me3 loci in DIPG cells, although CDKN2A/B itself was spared. De-repression occurred at bivalent loci marked by H3K4me3 and had elevated gene expression by RNAseq; these were significantly enriched for genes involved in chromatin remodelling and invasion/migration, the latter including MMP9/MMP24. Phenotypic assessment of the models in vitro by high-throughput imaging demonstrated significantly increased invasion and migration in association with either KMT5B or KMT5C loss, but not both. Quantitative proteomic assessment of the secretome identified factors by which a minority of KMT5B-deficient cells may signal to promote motility of the neighbouring populations. These data suggest a previously unrecognised trans-histone (H4/H3) interaction in DIPG cells with a potentially profound effect on their diffusely infiltrating phenotype.
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Affiliation(s)
- Ketty Kessler
- The Institute of Cancer Research, London, United Kingdom
| | - Alan Mackay
- The Institute of Cancer Research, London, United Kingdom
| | | | - Haider Tari
- The Institute of Cancer Research, London, United Kingdom
| | - Anna Burford
- The Institute of Cancer Research, London, United Kingdom
| | | | - Maria Vinci
- Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Chris Jones
- The Institute of Cancer Research, London, United Kingdom
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18
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Caravagna G, Sanguinetti G, Graham TA, Sottoriva A. The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. BMC Bioinformatics 2020; 21:531. [PMID: 33203356 PMCID: PMC7672894 DOI: 10.1186/s12859-020-03863-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 11/04/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution methods are used to determine the composition of cancer subpopulations in the biopsy sample, a fundamental step to determine clonal expansions and their evolutionary trajectories. RESULTS In a recent work we have developed a new model-based approach to carry out subclonal deconvolution from the site frequency spectrum of somatic mutations. This new method integrates, for the first time, an explicit model for neutral evolutionary forces that participate in clonal expansions; in that work we have also shown that our method improves largely over competing data-driven methods. In this Software paper we present mobster, an open source R package built around our new deconvolution approach, which provides several functions to plot data and fit models, assess their confidence and compute further evolutionary analyses that relate to subclonal deconvolution. CONCLUSIONS We present the mobster package for tumour subclonal deconvolution from bulk sequencing, the first approach to integrate Machine Learning and Population Genetics which can explicitly model co-existing neutral and positive selection in cancer. We showcase the analysis of two datasets, one simulated and one from a breast cancer patient, and overview all package functionalities.
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Affiliation(s)
- Giulio Caravagna
- University of Trieste, Trieste, Italy.
- The Institute of Cancer Research, London, UK.
| | | | - Trevor A Graham
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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19
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Kessler K, Mackay A, Molinari V, Tari H, Burford A, Sottoriva A, Vinci M, Jones C. EPCO-05. LOSS OF THE H4 LYSINE METHYLTRANSFERASE KMT5B DRIVES INVASION / MIGRATION BY DEPLETING H3K27me3 AT LOCI OTHERWISE RETAINED IN H3K27M MUTANT DIPG CELLS. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Diffuse intrinsic pontine glioma (DIPG) and other diffuse midline glioma (DMG) are characterised by K27M mutations in histone H3 variants. The major functional consequence is a global loss of the repressive mark H3K27me3, causing a raft of transcriptional changes promoting tumorigenesis, although certain key loci retain trimethylation, such as CDKN2A/B. We recently identified subclonal loss-of-function mutations in the H4 lysine methyltransferase KMT5B to be associated with an enhanced invasion/migration, but the mechanism by which this occurred was unclear. Here we show by ChIP-seq using patient-derived subclonal DIPG models and CRISPR-Cas9 depletion that loss of KMT5B (or KMT5C) causes a paradoxical increase in global levels of H4K20me3 in promoters and regulatory regions, only ablated by knocking out both enzymes. Loss of KMT5B alone further causes loss of the majority of otherwise retained H3K27me3 loci in DIPG cells, although CDKN2A/B itself was spared. De-repression occurred at bivalent loci marked by H3K4me3 and had elevated gene expression by RNAseq; these were significantly enriched for genes involved in chromatin remodelling and invasion/migration, the latter including MMP9/MMP24. Phenotypic assessment of the models in vitro by high-throughput imaging demonstrated significantly increased invasion and migration in association with either KMT5B or KMT5C loss, but not both. Quantitative proteomic assessment of the secretome identified factors by which a minority of KMT5B-deficient cells may signal to promote motility of the neighbouring populations. These data suggest a previously unrecognised trans-histone (H4/H3) interaction in DIPG cells with a potentially profound effect on their diffusely infiltrating phenotype.
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Affiliation(s)
- Ketty Kessler
- Institute of Cancer Research, London, United Kingdom
| | - Alan Mackay
- Institute of Cancer Research, London, United Kingdom
| | | | - Haider Tari
- Institute of Cancer Research, London, United Kingdom
| | - Anna Burford
- Institute of Cancer Research, London, United Kingdom
| | | | - Maria Vinci
- Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Chris Jones
- Institute of Cancer Research, London, United Kingdom
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20
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Lakatos E, Williams MJ, Schenck RO, Cross WCH, Househam J, Zapata L, Werner B, Gatenbee C, Robertson-Tessi M, Barnes CP, Anderson ARA, Sottoriva A, Graham TA. Evolutionary dynamics of neoantigens in growing tumors. Nat Genet 2020; 52:1057-1066. [PMID: 32929288 PMCID: PMC7610467 DOI: 10.1038/s41588-020-0687-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/06/2020] [Indexed: 02/08/2023]
Abstract
Cancers accumulate mutations that lead to neoantigens, novel peptides that elicit an immune response, and consequently undergo evolutionary selection. Here we establish how negative selection shapes the clonality of neoantigens in a growing cancer by constructing a mathematical model of neoantigen evolution. The model predicts that, without immune escape, tumor neoantigens are either clonal or at low frequency; hypermutated tumors can only establish after the evolution of immune escape. Moreover, the site frequency spectrum of somatic variants under negative selection appears more neutral as the strength of negative selection increases, which is consistent with classical neutral theory. These predictions are corroborated by the analysis of neoantigen frequencies and immune escape in exome and RNA sequencing data from 879 colon, stomach and endometrial cancers.
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Affiliation(s)
- Eszter Lakatos
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Marc J Williams
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ryan O Schenck
- Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - William C H Cross
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Jacob Househam
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Evolutionary Dynamics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Chandler Gatenbee
- Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
| | | | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Genomics and Computational Biology, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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21
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Caravagna G, Heide T, Williams MJ, Zapata L, Nichol D, Chkhaidze K, Cross W, Cresswell GD, Werner B, Acar A, Chesler L, Barnes CP, Sanguinetti G, Graham TA, Sottoriva A. Subclonal reconstruction of tumors by using machine learning and population genetics. Nat Genet 2020; 52:898-907. [PMID: 32879509 PMCID: PMC7610388 DOI: 10.1038/s41588-020-0675-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Most cancer genomic data are generated from bulk samples composed of mixtures of cancer subpopulations, as well as normal cells. Subclonal reconstruction methods based on machine learning aim to separate those subpopulations in a sample and infer their evolutionary history. However, current approaches are entirely data driven and agnostic to evolutionary theory. We demonstrate that systematic errors occur in the analysis if evolution is not accounted for, and this is exacerbated with multi-sampling of the same tumor. We present a novel approach for model-based tumor subclonal reconstruction, called MOBSTER, which combines machine learning with theoretical population genetics. Using public whole-genome sequencing data from 2,606 samples from different cohorts, new data and synthetic validation, we show that this method is more robust and accurate than current techniques in single-sample, multiregion and longitudinal data. This approach minimizes the confounding factors of nonevolutionary methods, thus leading to more accurate recovery of the evolutionary history of human cancers.
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Affiliation(s)
- Giulio Caravagna
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Marc J Williams
- Evolution and Cancer Lab, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ketevan Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - William Cross
- Evolution and Cancer Lab, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology and UCL Genetics Institute, University College London, London, UK
| | - Guido Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh, UK
- International School for Advanced Studies, Trieste, Italy
| | - Trevor A Graham
- Evolution and Cancer Lab, Barts Cancer Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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22
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Lupo B, Sassi F, Pinnelli M, Galimi F, Zanella ER, Vurchio V, Migliardi G, Gagliardi PA, Puliafito A, Manganaro D, Luraghi P, Kragh M, Pedersen MW, Horak ID, Boccaccio C, Medico E, Primo L, Nichol D, Spiteri I, Heide T, Vatsiou A, Graham TA, Élez E, Argiles G, Nuciforo P, Sottoriva A, Dienstmann R, Pasini D, Grassi E, Isella C, Bertotti A, Trusolino L. Colorectal cancer residual disease at maximal response to EGFR blockade displays a druggable Paneth cell-like phenotype. Sci Transl Med 2020; 12:eaax8313. [PMID: 32759276 DOI: 10.1126/scitranslmed.aax8313] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 12/19/2019] [Accepted: 05/22/2020] [Indexed: 12/11/2022]
Abstract
Blockade of epidermal growth factor receptor (EGFR) causes tumor regression in some patients with metastatic colorectal cancer (mCRC). However, residual disease reservoirs typically remain even after maximal response to therapy, leading to relapse. Using patient-derived xenografts (PDXs), we observed that mCRC cells surviving EGFR inhibition exhibited gene expression patterns similar to those of a quiescent subpopulation of normal intestinal secretory precursors with Paneth cell characteristics. Compared with untreated tumors, these pseudodifferentiated tumor remnants had reduced expression of genes encoding EGFR-activating ligands, enhanced activity of human epidermal growth factor receptor 2 (HER2) and HER3, and persistent signaling along the phosphatidylinositol 3-kinase (PI3K) pathway. Clinically, properties of residual disease cells from the PDX models were detected in lingering tumors of responsive patients and in tumors of individuals who had experienced early recurrence. Mechanistically, residual tumor reprogramming after EGFR neutralization was mediated by inactivation of Yes-associated protein (YAP), a master regulator of intestinal epithelium recovery from injury. In preclinical trials, Pan-HER antibodies minimized residual disease, blunted PI3K signaling, and induced long-term tumor control after treatment discontinuation. We found that tolerance to EGFR inhibition is characterized by inactivation of an intrinsic lineage program that drives both regenerative signaling during intestinal repair and EGFR-dependent tumorigenesis. Thus, our results shed light on CRC lineage plasticity as an adaptive escape mechanism from EGFR-targeted therapy and suggest opportunities to preemptively target residual disease.
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Affiliation(s)
- Barbara Lupo
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Francesco Sassi
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Marika Pinnelli
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Francesco Galimi
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | | | - Valentina Vurchio
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Giorgia Migliardi
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Paolo Armando Gagliardi
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Alberto Puliafito
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Daria Manganaro
- IEO, European Institute of Oncology IRCCS, 20139 Milano, Italy
| | - Paolo Luraghi
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | | | | | | | - Carla Boccaccio
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Enzo Medico
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Luca Primo
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Daniel Nichol
- The Institute of Cancer Research, London SW7 3RP, UK
| | | | - Timon Heide
- The Institute of Cancer Research, London SW7 3RP, UK
| | | | - Trevor A Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Elena Élez
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Guillem Argiles
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Paolo Nuciforo
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | | | | | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, 20139 Milano, Italy
- Department of Health Sciences, University of Milano, 20142 Milano, Italy
| | - Elena Grassi
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Claudio Isella
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Andrea Bertotti
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy.
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, 10060 Candiolo, Torino, Italy.
- Candiolo Cancer Institute-FPO IRCCS, 10060 Candiolo, Torino, Italy
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23
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Loupakis F, Depetris I, Biason P, Intini R, Prete AA, Leone F, Lombardi P, Filippi R, Spallanzani A, Cascinu S, Bonetti LR, Maddalena G, Valeri N, Sottoriva A, Zapata L, Salmaso R, Munari G, Rugge M, Dei Tos AP, Golovato J, Sanborn JZ, Nguyen A, Schirripa M, Zagonel V, Lonardi S, Fassan M. Prediction of Benefit from Checkpoint Inhibitors in Mismatch Repair Deficient Metastatic Colorectal Cancer: Role of Tumor Infiltrating Lymphocytes. Oncologist 2020; 25:481-487. [PMID: 31967692 PMCID: PMC7288636 DOI: 10.1634/theoncologist.2019-0611] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/27/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Immunotherapy with immune checkpoint inhibitors (ICIs) is highly effective in microsatellite instability-high (MSI-H) metastatic colorectal cancer (mCRC); however, specific predictive biomarkers are lacking. PATIENTS AND METHODS Data and samples from 85 patients with MSI-H mCRC treated with ICIs were gathered. Tumor infiltrating lymphocytes (TILs) and tumor mutational burden (TMB) were analyzed in an exploratory cohort of "super" responders and "clearly" refractory patients; TILs were then evaluated in the whole cohort of patients. Primary objectives were the correlation between the number of TILs and TMB and their role as biomarkers of ICI efficacy. Main endpoints included response rate (RR), progression-free survival (PFS), and overall survival (OS). RESULTS In the exploratory cohort, an increasing number of TILs correlated to higher TMB (Pearson's test, p = .0429). In the whole cohort, median number of TILs was 3.6 in responders compared with 1.8 in nonresponders (Mann-Whitney test, p = .0448). RR was 70.6% in patients with high number of TILs (TILs-H) compared with 42.9% in patients with low number of TILs (odds ratio = 3.20, p = .0291). Survival outcomes differed significantly in favor of TILs-H (PFS: hazard ratio [HR] = 0.42, p = .0278; OS: HR = 0.41, p = .0463). CONCLUSION A significant correlation between higher TMB and increased number of TILs was shown. A significantly higher activity and better PFS and OS with ICI in MSI-H mCRC were reported in cases with high number of TILs, thus supporting further studies of TIL count as predictive biomarker of ICI efficacy. IMPLICATIONS FOR PRACTICE Microsatellite instability is the result of mismatch repair protein deficiency, caused by germline mutations or somatic modifications in mismatch repair genes. In metastatic colorectal cancer (mCRC), immunotherapy (with immune checkpoint inhibitors [ICIs]) demonstrated remarkable clinical benefit in microsatellite instability-high (MSI-H) patients. ICI primary resistance has been observed in approximately 25% of patients with MSI-H mCRC, underlining the need for predictive biomarkers. In this study, tumor mutational burden (TMB) and tumor infiltrating lymphocyte (TIL) analyses were performed in an exploratory cohort of patients with MSI-H mCRC treated with ICIs, demonstrating a significant correlation between higher TMB and increased number of TILs. Results also demonstrated a significant correlation between high number of TILs and clinical responses and survival benefit in a large data set of patients with MSI-H mCRC treated with ICI. TMB and TILs could represent predictive biomarkers of ICI efficacy in MSI-H mCRC and should be incorporated in future trials testing checkpoint inhibitors in colorectal cancer.
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Affiliation(s)
- Fotios Loupakis
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Ilaria Depetris
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Paola Biason
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Rossana Intini
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Alessandra Anna Prete
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Francesco Leone
- Medical Oncology, ASL BiellaBiellaItaly
- Medical Oncology, Candiolo Cancer Institute, Fondazione Piemonte per l'Oncologia, IRCCSCandioloItaly
| | - Pasquale Lombardi
- Medical Oncology, Candiolo Cancer Institute, Fondazione Piemonte per l'Oncologia, IRCCSCandioloItaly
- Department of Oncology, University of TurinTurinItaly
| | - Roberto Filippi
- Medical Oncology, Candiolo Cancer Institute, Fondazione Piemonte per l'Oncologia, IRCCSCandioloItaly
- Department of Oncology, University of TurinTurinItaly
| | - Andrea Spallanzani
- Department of Oncology and Haematology, University Hospital of Modena and Reggio EmiliaModenaItaly
| | - Stefano Cascinu
- Department of Oncology and Haematology, University Hospital of Modena and Reggio EmiliaModenaItaly
| | | | - Giulia Maddalena
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer ResearchLondonUnited Kingdom
- Department of Medicine, The Royal Marsden National Health Service (NHS) TrustLondonUnited Kingdom
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Luis Zapata
- Centre for Evolution and Cancer, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Roberta Salmaso
- Surgical Pathology and Cytopathology Unit, Department of Medicine (DIMED), University of Padua, Padua University HospitalPaduaItaly
| | - Giada Munari
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Massimo Rugge
- Surgical Pathology and Cytopathology Unit, Department of Medicine (DIMED), University of Padua, Padua University HospitalPaduaItaly
| | - Angelo Paolo Dei Tos
- Department of Pathology and Molecular Genetics, Treviso General HospitalTrevisoItaly
| | | | | | | | - Marta Schirripa
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Vittorina Zagonel
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Sara Lonardi
- Department of Clinical and Experimental Oncology, Medical Oncology Unit 1, Veneto Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS)PaduaItaly
| | - Matteo Fassan
- Surgical Pathology and Cytopathology Unit, Department of Medicine (DIMED), University of Padua, Padua University HospitalPaduaItaly
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24
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Acar A, Nichol D, Fernandez-Mateos J, Cresswell GD, Barozzi I, Hong SP, Trahearn N, Spiteri I, Stubbs M, Burke R, Stewart A, Caravagna G, Werner B, Vlachogiannis G, Maley CC, Magnani L, Valeri N, Banerji U, Sottoriva A. Exploiting evolutionary steering to induce collateral drug sensitivity in cancer. Nat Commun 2020; 11:1923. [PMID: 32317663 PMCID: PMC7174377 DOI: 10.1038/s41467-020-15596-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/18/2020] [Indexed: 12/17/2022] Open
Abstract
Drug resistance mediated by clonal evolution is arguably the biggest problem in cancer therapy today. However, evolving resistance to one drug may come at a cost of decreased fecundity or increased sensitivity to another drug. These evolutionary trade-offs can be exploited using 'evolutionary steering' to control the tumour population and delay resistance. However, recapitulating cancer evolutionary dynamics experimentally remains challenging. Here, we present an approach for evolutionary steering based on a combination of single-cell barcoding, large populations of 108-109 cells grown without re-plating, longitudinal non-destructive monitoring of cancer clones, and mathematical modelling of tumour evolution. We demonstrate evolutionary steering in a lung cancer model, showing that it shifts the clonal composition of the tumour in our favour, leading to collateral sensitivity and proliferative costs. Genomic profiling revealed some of the mechanisms that drive evolved sensitivity. This approach allows modelling evolutionary steering strategies that can potentially control treatment resistance.
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Affiliation(s)
- Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Javier Fernandez-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Sung Pil Hong
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Nicholas Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Mark Stubbs
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rosemary Burke
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Adam Stewart
- Clinical Pharmacology-Adaptive Therapy Group, Division of Cancer Therapeutics and Clinical Studies, The Institute of Cancer Research, London, UK
| | - Giulio Caravagna
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Georgios Vlachogiannis
- Gastrointestinal Cancer Biology and Genomics Team, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute, Arizona State University, Tempe, USA
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Nicola Valeri
- Gastrointestinal Cancer Biology and Genomics Team, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Foundation Trust, London, UK
| | - Udai Banerji
- CRUK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
- Clinical Pharmacology-Adaptive Therapy Group, Division of Cancer Therapeutics and Clinical Studies, The Institute of Cancer Research, London, UK.
- Drug Development Unit, The Institute of Cancer Research and The Royal Marsden Hospital NHS Foundation Trust, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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25
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Williams MJ, Zapata L, Werner B, Barnes CP, Sottoriva A, Graham TA. Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios. eLife 2020; 9:e48714. [PMID: 32223898 PMCID: PMC7105384 DOI: 10.7554/elife.48714] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in somatic cells. However the link, in somatic evolution, between dN/dS values and fitness coefficients is missing. Here we present a quantitative model of somatic evolutionary dynamics that determines the selective coefficients of individual driver mutations from dN/dS estimates. We then measure the DFE for somatic mutant clones in ostensibly normal oesophagus and skin. We reveal a broad distribution of fitness effects, with the largest fitness increases found for TP53 and NOTCH1 mutants (proliferative bias 1-5%). This study provides the theoretical link between dN/dS values and selective coefficients in somatic evolution, and measures the DFE of mutations in human tissues.
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Affiliation(s)
- Marc J Williams
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Benjamin Werner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Trevor A Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
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Cresswell GD, Nichol D, Spiteri I, Tari H, Zapata L, Heide T, Maley CC, Magnani L, Schiavon G, Ashworth A, Barry P, Sottoriva A. Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. Nat Commun 2020; 11:1446. [PMID: 32221288 PMCID: PMC7101390 DOI: 10.1038/s41467-020-15047-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
Circulating tumour DNA (ctDNA) allows tracking of the evolution of human cancers at high resolution, overcoming many limitations of tissue biopsies. However, exploiting ctDNA to determine how a patient's cancer is evolving in order to aid clinical decisions remains difficult. This is because ctDNA is a mix of fragmented alleles, and the contribution of different cancer deposits to ctDNA is largely unknown. Profiling ctDNA almost invariably requires prior knowledge of what genomic alterations to track. Here, we leverage on a rapid autopsy programme to demonstrate that unbiased genomic characterisation of several metastatic sites and concomitant ctDNA profiling at whole-genome resolution reveals the extent to which ctDNA is representative of widespread disease. We also present a methylation profiling method that allows tracking evolutionary changes in ctDNA at single-molecule resolution without prior knowledge. These results have critical implications for the use of liquid biopsies to monitor cancer evolution in humans and guide treatment.
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Affiliation(s)
- George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Haider Tari
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- Glioma Lab, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Carlo C Maley
- Arizona Cancer Evolution Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luca Magnani
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Gaia Schiavon
- Breast Unit, Royal Marsden Hospital, London, UK
- AstraZeneca, Oncology R&D, Cambridge, UK
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Center, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Peter Barry
- Breast Unit, Royal Marsden Hospital, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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27
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Werner B, Case J, Williams MJ, Chkhaidze K, Temko D, Fernández-Mateos J, Cresswell GD, Nichol D, Cross W, Spiteri I, Huang W, Tomlinson IPM, Barnes CP, Graham TA, Sottoriva A. Measuring single cell divisions in human tissues from multi-region sequencing data. Nat Commun 2020; 11:1035. [PMID: 32098957 PMCID: PMC7042311 DOI: 10.1038/s41467-020-14844-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/29/2020] [Indexed: 01/06/2023] Open
Abstract
Both normal tissue development and cancer growth are driven by a branching process of cell division and mutation accumulation that leads to intra-tissue genetic heterogeneity. However, quantifying somatic evolution in humans remains challenging. Here, we show that multi-sample genomic data from a single time point of normal and cancer tissues contains information on single-cell divisions. We present a new theoretical framework that, applied to whole-genome sequencing data of healthy tissue and cancer, allows inferring the mutation rate and the cell survival/death rate per division. On average, we found that cells accumulate 1.14 mutations per cell division in healthy haematopoiesis and 1.37 mutations per division in brain development. In both tissues, cell survival was maximal during early development. Analysis of 131 biopsies from 16 tumours showed 4 to 100 times increased mutation rates compared to healthy development and substantial inter-patient variation of cell survival/death rates.
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Affiliation(s)
- Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- Evolutionary Dynamics Group, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Jack Case
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
- University of Cambridge, Cambridge, UK
| | - Marc J Williams
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Ketevan Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Temko
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Javier Fernández-Mateos
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - William Cross
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Weini Huang
- Group of Theoretical Biology, The State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen University, 510060, Guangzhou, China
- School of Mathematical Sciences, Queen Mary University London, London, UK
| | - Ian P M Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Centre for Cancer Genomics & Computational Biology, Barts Cancer Institute, Queen Mary University London, London, Charterhouse Square, London, EC1M 6BQ, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Samra Turajlic
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Trevor Graham
- Tumour Biology, Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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Nawaz S, Trahearn NA, Heindl A, Banerjee S, Maley CC, Sottoriva A, Yuan Y. Analysis of tumour ecological balance reveals resource-dependent adaptive strategies of ovarian cancer. EBioMedicine 2019; 48:224-235. [PMID: 31648981 PMCID: PMC6838425 DOI: 10.1016/j.ebiom.2019.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/02/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Despite treatment advances, there remains a significant risk of recurrence in ovarian cancer, at which stage it is usually incurable. Consequently, there is a clear need for improved patient stratification. However, at present clinical prognosticators remain largely unchanged due to the lack of reproducible methods to identify high-risk patients. METHODS In high-grade serous ovarian cancer patients with advanced disease, we spatially define a tumour ecological balance of stromal resource and immune hazard using high-throughput image and spatial analysis of routine histology slides. On this basis an EcoScore is developed to classify tumours by a shift in this balance towards cancer-favouring or inhibiting conditions. FINDINGS The EcoScore provides prognostic value stronger than, and independent of, known risk factors. Crucially, the clinical relevance of mutational burden and genomic instability differ under different stromal resource conditions, suggesting that the selective advantage of these cancer hallmarks is dependent on the context of stromal spatial structure. Under a high resource condition defined by a high level of geographical intermixing of cancer and stromal cells, selection appears to be driven by point mutations; whereas, in low resource tumours featured with high hypoxia and low cancer-immune co-localization, selection is fuelled by aneuploidy. INTERPRETATION Our study offers empirical evidence that cancer fitness depends on tumour spatial constraints, and presents a biological basis for developing better assessments of tumour adaptive strategies in overcoming ecological constraints including immune surveillance and hypoxia.
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Affiliation(s)
- Sidra Nawaz
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK; Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Nicholas A Trahearn
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK; Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Andreas Heindl
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK; Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | | | - Carlo C Maley
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK; Biodesign Center for Personalized Diagnostics, Arizona State University, Tempe, AZ, USA
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK; Division of Molecular Pathology, Institute of Cancer Research, London, UK
| | - Yinyin Yuan
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK; Division of Molecular Pathology, Institute of Cancer Research, London, UK.
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30
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Abstract
To a large extent, cancer conforms to evolutionary rules defined by the rates at which clones mutate, adapt and grow. Next-generation sequencing has provided a snapshot of the genetic landscape of most cancer types, and cancer genomics approaches are driving new insights into cancer evolutionary patterns in time and space. In contrast to species evolution, cancer is a particular case owing to the vast size of tumour cell populations, chromosomal instability and its potential for phenotypic plasticity. Nevertheless, an evolutionary framework is a powerful aid to understand cancer progression and therapy failure. Indeed, such a framework could be applied to predict individual tumour behaviour and support treatment strategies.
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Affiliation(s)
- Samra Turajlic
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK
- Skin and Renal Units, The Royal Marsden NHS Foundation Trust, London, UK
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Laboratory, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Trevor Graham
- Tumour Biology, Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London, UK.
- Department of Medical Oncology, University College London Hospitals, London, UK.
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31
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Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Graham TA, Sottoriva A. Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. PLoS Comput Biol 2019; 15:e1007243. [PMID: 31356595 PMCID: PMC6687187 DOI: 10.1371/journal.pcbi.1007243] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 08/08/2019] [Accepted: 07/05/2019] [Indexed: 12/19/2022] Open
Abstract
Quantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumour growth that accounts for somatic mutations, selection, drift and spatial constraints, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from both bulk and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi-region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumours. We also propose a statistical inference framework that incorporates spatial effects within a growing tumour and so represents a further step forwards in the inference of evolutionary dynamics from genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors remains challenging. However, mechanistic model-based approaches have the potential to capture the sources of noise and better interpret the data.
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Affiliation(s)
- Ketevan Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Marc J. Williams
- Evolution and Cancer Lab, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Weini Huang
- Evolution and Cancer Lab, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Giulio Caravagna
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Trevor A. Graham
- Evolution and Cancer Lab, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
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Chkhaidze K, Heide T, Werner B, Williams MJ, Huang W, Caravagna G, Baker AM, Graham TA, Sottoriva A. Abstract 4232: Spatially constrained tumor growth affects the patterns of clonal selection and neutral drift in cancer genomic data. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Quantification of the effect of spatial tumor sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking. Here we use a spatial stochastic cellular automaton model of tumor growth that accounts for somatic mutations, selection, drift and spatial constrains, to simulate multi-region sequencing data derived from spatial sampling of a neoplasm. We show that the spatial structure of a solid cancer has a major impact on the detection of clonal selection and genetic drift from bulk sequencing data and single-cell sequencing data. Our results indicate that spatial constrains can introduce significant sampling biases when performing multi- region bulk sampling and that such bias becomes a major confounding factor for the measurement of the evolutionary dynamics of human tumors. We present a statistical inference framework that takes into account the spatial effects of a growing tumor and allows inferring the evolutionary dynamics from patient genomic data. Our analysis shows that measuring cancer evolution using next-generation sequencing while accounting for the numerous confounding factors requires a mechanistic model-based approach that captures the sources of noise in the data.
Citation Format: Kate Chkhaidze, Timon Heide, Benjamin Werner, Marc J. Williams, Weini Huang, Giulio Caravagna, Ann-Marie Baker, Trevor A. Graham, Andrea Sottoriva. Spatially constrained tumor growth affects the patterns of clonal selection and neutral drift in cancer genomic data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4232.
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Affiliation(s)
| | - Timon Heide
- 1Institute of Cancer Research, London, United Kingdom
| | | | - Marc J. Williams
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Weini Huang
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | | | - Ann-Marie Baker
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
| | - Trevor A. Graham
- 2Barts Cancer Institute, Queen Mary University, London, United Kingdom
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Abstract
Cancers originate from somatic cells in the human body that have accumulated genetic alterations. These mutations modify the phenotype of the cells, allowing them to escape the homeostatic regulation that maintains normal cell number. Viewed through the lens of evolutionary biology, the transformation of normal cells into malignant cells is evolution in action. Evolution continues throughout cancer growth, progression, treatment resistance, and disease relapse, driven by adaptation to changes in the cancer's environment, and intratumor heterogeneity is an inevitable consequence of this evolutionary process. Genomics provides a powerful means to characterize tumor evolution, enabling quantitative measurement of evolving clones across space and time. In this review, we discuss concepts and approaches to quantify and measure this evolutionary process in cancer using genomics.
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Affiliation(s)
- Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom; ,
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London SM2 5NG, United Kingdom
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom; ,
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Spiteri I, Caravagna G, Cresswell GD, Vatsiou A, Nichol D, Acar A, Ermini L, Chkhaidze K, Werner B, Mair R, Brognaro E, Verhaak RGW, Sanguinetti G, Piccirillo SGM, Watts C, Sottoriva A. Evolutionary dynamics of residual disease in human glioblastoma. Ann Oncol 2019; 30:456-463. [PMID: 30452544 PMCID: PMC6442656 DOI: 10.1093/annonc/mdy506] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common and aggressive adult brain malignancy against which conventional surgery and chemoradiation provide limited benefit. Even when a good treatment response is obtained, recurrence inevitably occurs either locally (∼80%) or distally (∼20%), driven by cancer clones that are often genomically distinct from those in the primary tumour. Glioblastoma cells display a characteristic infiltrative phenotype, invading the surrounding tissue and often spreading across the whole brain. Cancer cells responsible for relapse can reside in two compartments of residual disease that are left behind after treatment: the infiltrated normal brain parenchyma and the sub-ventricular zone. However, these two sources of residual disease in glioblastoma are understudied because of the difficulty in sampling these regions during surgery. PATIENT AND METHODS Here, we present the results of whole-exome sequencing of 69 multi-region samples collected using fluorescence-guided resection from 11 patients, including the infiltrating tumour margin and the sub-ventricular zone for each patient, as well as matched blood. We used a phylogenomic approach to dissect the spatio-temporal evolution of each tumour and unveil the relation between residual disease and the main tumour mass. We also analysed two patients with paired primary-recurrence samples with matched residual disease. RESULTS Our results suggest that infiltrative subclones can arise early during tumour growth in a subset of patients. After treatment, the infiltrative subclones may seed the growth of a recurrent tumour, thus representing the 'missing link' between the primary tumour and recurrent disease. CONCLUSIONS These results are consistent with recognised clinical phenotypic behaviour and suggest that more specific therapeutic targeting of cells in the infiltrated brain parenchyma may improve patient's outcome.
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Affiliation(s)
- I Spiteri
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - G Caravagna
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - G D Cresswell
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - A Vatsiou
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - D Nichol
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - A Acar
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - L Ermini
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London; Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - K Chkhaidze
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - B Werner
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London
| | - R Mair
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - E Brognaro
- Department of Neurosurgery, S. Maria Della Misericordia Hospital, Rovigo, Italy
| | - R G W Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, USA
| | - G Sanguinetti
- School of Informatics, University of Edinburgh, Edinburgh, UK
| | - S G M Piccirillo
- Division of Hematology and Oncolog, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, USA.
| | - C Watts
- Institute of Cancer Genome Sciences, University of Birmingham, Birmingham, UK.
| | - A Sottoriva
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London.
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35
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Werner B, Williams MJ, Barnes CP, Graham TA, Sottoriva A. Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'. Nat Genet 2018; 50:1624-1626. [PMID: 30374070 DOI: 10.1038/s41588-018-0235-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Marry University of London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Marry University of London, London, UK
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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36
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Williams MJ, Werner B, Heide T, Barnes CP, Graham TA, Sottoriva A. Reply to 'Revisiting signatures of neutral tumor evolution in the light of complexity of cancer genomic data'. Nat Genet 2018; 50:1628-1630. [PMID: 30250125 DOI: 10.1038/s41588-018-0210-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Marry University of London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, the Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, the Institute of Cancer Research, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Marry University of London, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, the Institute of Cancer Research, London, UK.
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37
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Affiliation(s)
- Timon Heide
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Marry University of London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Benjamin Werner
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Giulio Caravagna
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Marry University of London, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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38
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Cross W, Kovac M, Mustonen V, Temko D, Davis H, Baker AM, Biswas S, Arnold R, Chegwidden L, Gatenbee C, Anderson AR, Koelzer VH, Martinez P, Jiang X, Domingo E, Woodcock DJ, Feng Y, Kovacova M, Maughan T, Jansen M, Rodriguez-Justo M, Ashraf S, Guy R, Cunningham C, East JE, Wedge DC, Wang LM, Palles C, Heinimann K, Sottoriva A, Leedham SJ, Graham TA, Tomlinson IPM. The evolutionary landscape of colorectal tumorigenesis. Nat Ecol Evol 2018; 2:1661-1672. [PMID: 30177804 PMCID: PMC6152905 DOI: 10.1038/s41559-018-0642-z] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/12/2018] [Indexed: 01/19/2023]
Abstract
The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colorectal tumours, we investigate the evolutionary fitness landscape occupied by these neoplasms. Unlike carcinomas, advanced adenomas frequently harbour sub-clonal driver mutations-considered to be functionally important in the carcinogenic process-that have not swept to fixation, and have relatively high genetic heterogeneity. Carcinomas are distinguished from adenomas by widespread aneusomies that are usually clonal and often accrue in a 'punctuated' fashion. We conclude that adenomas evolve across an undulating fitness landscape, whereas carcinomas occupy a sharper fitness peak, probably owing to stabilizing selection.
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Affiliation(s)
- William Cross
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michal Kovac
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Bone Tumour Reference Center at the Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Ville Mustonen
- Organismal and Evolutionary Biology Research Programme, Department of Computer Science, Institute of Biotechnology, Helsinki Institute for Information Technology HIIT, University of Helsinki, Helsinki, Finland
| | - Daniel Temko
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- CoMPLEX, Department of Computer Science, University College London, London, UK
| | - Hayley Davis
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Ann-Marie Baker
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sujata Biswas
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Roland Arnold
- Cancer Bioinfomatics Group, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Chandler Gatenbee
- Integrated Mathematical Oncology Department, Moffitt Comprehensive Cancer Centre, Tampa, FL, USA
| | - Alexander R Anderson
- Integrated Mathematical Oncology Department, Moffitt Comprehensive Cancer Centre, Tampa, FL, USA
| | - Viktor H Koelzer
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Pierre Martinez
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Xiaowei Jiang
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Enric Domingo
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Yun Feng
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Monika Kovacova
- Institute of Mathematics and Physics, Faculty of Mechanical Engineering, Slovak University of Technology in Bratislava, Bratislava, Slovakia
| | - Tim Maughan
- Department of Oncology, University of Oxford, Oxford, UK
| | - Marnix Jansen
- Department of Research Pathology, Cancer Institute, University College London, London, UK
| | - Manuel Rodriguez-Justo
- Department of Research Pathology, Cancer Institute, University College London, London, UK
| | - Shazad Ashraf
- Department of Surgery, University Hospitals Birmingham, Birmingham, UK
| | - Richard Guy
- Department of Colorectal Surgery, Cancer Centre, Churchill Hospital, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - Christopher Cunningham
- Department of Colorectal Surgery, Cancer Centre, Churchill Hospital, Oxford University Hospital NHS Foundation Trust, Oxford, UK
| | - James E East
- Translational Gastroenterology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - David C Wedge
- Big Data Institute, University of Oxford, Oxford, UK
| | - Lai Mun Wang
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Karl Heinimann
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Simon J Leedham
- Gastrointestinal Stem Cell Biology Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Ian P M Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
- Department of Histopathology, University Hospitals Birmingham, Birmingham, UK.
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39
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Barry P, Vatsiou A, Spiteri I, Nichol D, Cresswell GD, Acar A, Trahearn N, Hrebien S, Garcia-Murillas I, Chkhaidze K, Ermini L, Huntingford IS, Cottom H, Zabaglo L, Koelble K, Khalique S, Rusby JE, Muscara F, Dowsett M, Maley CC, Natrajan R, Yuan Y, Schiavon G, Turner N, Sottoriva A. The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer. Clin Cancer Res 2018; 24:4763-4770. [PMID: 29891724 PMCID: PMC6296441 DOI: 10.1158/1078-0432.ccr-17-3374] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/11/2018] [Accepted: 06/05/2018] [Indexed: 01/13/2023]
Abstract
Purpose: The most significant prognostic factor in early breast cancer is lymph node involvement. This stage between localized and systemic disease is key to understanding breast cancer progression; however, our knowledge of the evolution of lymph node malignant invasion remains limited, as most currently available data are derived from primary tumors.Experimental Design: In 11 patients with treatment-naïve node-positive early breast cancer without clinical evidence of distant metastasis, we investigated lymph node evolution using spatial multiregion sequencing (n = 78 samples) of primary and lymph node deposits and genomic profiling of matched longitudinal circulating tumor DNA (ctDNA).Results: Linear evolution from primary to lymph node was rare (1/11), whereas the majority of cases displayed either early divergence between primary and nodes (4/11) or no detectable divergence (6/11), where both primary and nodal cells belonged to a single recent expansion of a metastatic clone. Divergence of metastatic subclones was driven in part by APOBEC. Longitudinal ctDNA samples from 2 of 7 subjects with evaluable plasma taken perioperatively reflected the two major evolutionary patterns and demonstrate that private mutations can be detected even from early metastatic nodal deposits. Moreover, node removal resulted in disappearance of private lymph node mutations in ctDNA.Conclusions: This study sheds new light on a crucial evolutionary step in the natural history of breast cancer, demonstrating early establishment of axillary lymph node metastasis in a substantial proportion of patients. Clin Cancer Res; 24(19); 4763-70. ©2018 AACR.
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Affiliation(s)
- Peter Barry
- Department of Surgery, Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Alexandra Vatsiou
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Inmaculada Spiteri
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Daniel Nichol
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - George D Cresswell
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Ahmet Acar
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas Trahearn
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Sarah Hrebien
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Kate Chkhaidze
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Luca Ermini
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | | | - Hannah Cottom
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Lila Zabaglo
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Konrad Koelble
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Saira Khalique
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Jennifer E Rusby
- Department of Surgery, Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Francesca Muscara
- Department of Surgery, Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Mitch Dowsett
- Ralph Lauren Breast Cancer Research Centre, Royal Marsden Hospital, London, United Kingdom
| | - Carlo C Maley
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
- Biodesign Institute, Arizona State University, Tempe, Arizona
| | - Rachael Natrajan
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Gaia Schiavon
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Nicholas Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.
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40
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Khan KH, Cunningham D, Werner B, Vlachogiannis G, Spiteri I, Heide T, Mateos JF, Vatsiou A, Lampis A, Damavandi MD, Lote H, Huntingford IS, Hedayat S, Chau I, Tunariu N, Mentrasti G, Trevisani F, Rao S, Anandappa G, Watkins D, Starling N, Thomas J, Peckitt C, Khan N, Rugge M, Begum R, Hezelova B, Bryant A, Jones T, Proszek P, Fassan M, Hahne JC, Hubank M, Braconi C, Sottoriva A, Valeri N. Longitudinal Liquid Biopsy and Mathematical Modeling of Clonal Evolution Forecast Time to Treatment Failure in the PROSPECT-C Phase II Colorectal Cancer Clinical Trial. Cancer Discov 2018; 8:1270-1285. [PMID: 30166348 PMCID: PMC6380469 DOI: 10.1158/2159-8290.cd-17-0891] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 05/01/2018] [Accepted: 07/05/2018] [Indexed: 12/14/2022]
Abstract
Sequential profiling of plasma cell-free DNA (cfDNA) holds immense promise for early detection of patient progression. However, how to exploit the predictive power of cfDNA as a liquid biopsy in the clinic remains unclear. RAS pathway aberrations can be tracked in cfDNA to monitor resistance to anti-EGFR monoclonal antibodies in patients with metastatic colorectal cancer. In this prospective phase II clinical trial of single-agent cetuximab in RAS wild-type patients, we combine genomic profiling of serial cfDNA and matched sequential tissue biopsies with imaging and mathematical modeling of cancer evolution. We show that a significant proportion of patients defined as RAS wild-type based on diagnostic tissue analysis harbor aberrations in the RAS pathway in pretreatment cfDNA and, in fact, do not benefit from EGFR inhibition. We demonstrate that primary and acquired resistance to cetuximab are often of polyclonal nature, and these dynamics can be observed in tissue and plasma. Furthermore, evolutionary modeling combined with frequent serial sampling of cfDNA allows prediction of the expected time to treatment failure in individual patients. This study demonstrates how integrating frequently sampled longitudinal liquid biopsies with a mathematical framework of tumor evolution allows individualized quantitative forecasting of progression, providing novel opportunities for adaptive personalized therapies.Significance: Liquid biopsies capture spatial and temporal heterogeneity underpinning resistance to anti-EGFR monoclonal antibodies in colorectal cancer. Dense serial sampling is needed to predict the time to treatment failure and generate a window of opportunity for intervention. Cancer Discov; 8(10); 1270-85. ©2018 AACR. See related commentary by Siravegna and Corcoran, p. 1213 This article is highlighted in the In This Issue feature, p. 1195.
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Affiliation(s)
- Khurum H Khan
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - David Cunningham
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Benjamin Werner
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Georgios Vlachogiannis
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Timon Heide
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Javier Fernandez Mateos
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Alexandra Vatsiou
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Mahnaz Darvish Damavandi
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Hazel Lote
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Ian Said Huntingford
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Somaieh Hedayat
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Ian Chau
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Nina Tunariu
- Department of Radiology, The Royal Marsden NHS Trust, Londonand Sutton, United Kingdom
| | - Giulia Mentrasti
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Francesco Trevisani
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Sheela Rao
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Gayathri Anandappa
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - David Watkins
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Naureen Starling
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Janet Thomas
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Clare Peckitt
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Nasir Khan
- Department of Radiology, The Royal Marsden NHS Trust, Londonand Sutton, United Kingdom
| | - Massimo Rugge
- Department of Medicine and Surgical Pathology, University of Padua, Padua, Italy
| | - Ruwaida Begum
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Blanka Hezelova
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Annette Bryant
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Thomas Jones
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Paula Proszek
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Matteo Fassan
- Department of Medicine and Surgical Pathology, University of Padua, Padua, Italy
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Michael Hubank
- Clinical Genomics, The Centre for Molecular Pathology, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
| | - Chiara Braconi
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom
- Division of Cancer Therapeutics, The Institute of Cancer Research, London and Sutton, United Kingdom
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom.
| | - Nicola Valeri
- Department of Medicine, The Royal Marsden NHS Trust, London and Sutton, United Kingdom.
- Division of Molecular Pathology, The Institute of Cancer Research, London and Sutton, United Kingdom
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41
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Heindl A, Khan AM, Rodrigues DN, Eason K, Sadanandam A, Orbegoso C, Punta M, Sottoriva A, Lise S, Banerjee S, Yuan Y. Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. Nat Commun 2018. [PMID: 30254278 DOI: 10.1038/s41467-018-06130-3] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
How tumor microenvironmental forces shape plasticity of cancer cell morphology is poorly understood. Here, we conduct automated histology image and spatial statistical analyses in 514 high grade serous ovarian samples to define cancer morphological diversification within the spatial context of the microenvironment. Tumor spatial zones, where cancer cell nuclei diversify in shape, are mapped in each tumor. Integration of this spatially explicit analysis with omics and clinical data reveals a relationship between morphological diversification and the dysregulation of DNA repair, loss of nuclear integrity, and increased disease mortality. Within the Immunoreactive subtype, spatial analysis further reveals significantly lower lymphocytic infiltration within diversified zones compared with other tumor zones, suggesting that even immune-hot tumors contain cells capable of immune escape. Our findings support a model whereby a subpopulation of morphologically plastic cancer cells with dysregulated DNA repair promotes ovarian cancer progression through positive selection by immune evasion.
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Affiliation(s)
- Andreas Heindl
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK.,Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Adnan Mujahid Khan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK.,Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Daniel Nava Rodrigues
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Katherine Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK.,Centre for Molecular Pathology, Royal Marsden Hospital, London, SM2 5NG, UK
| | - Cecilia Orbegoso
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Marco Punta
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Stefano Lise
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK.,Division of Clinical Studies, the Institute of Cancer Research, London, UK, SM2 5NG
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK. .,Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK.
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42
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Heindl A, Khan AM, Rodrigues DN, Eason K, Sadanandam A, Orbegoso C, Punta M, Sottoriva A, Lise S, Banerjee S, Yuan Y. Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. Nat Commun 2018; 9:3917. [PMID: 30254278 PMCID: PMC6156340 DOI: 10.1038/s41467-018-06130-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 08/15/2018] [Indexed: 12/22/2022] Open
Abstract
How tumor microenvironmental forces shape plasticity of cancer cell morphology is poorly understood. Here, we conduct automated histology image and spatial statistical analyses in 514 high grade serous ovarian samples to define cancer morphological diversification within the spatial context of the microenvironment. Tumor spatial zones, where cancer cell nuclei diversify in shape, are mapped in each tumor. Integration of this spatially explicit analysis with omics and clinical data reveals a relationship between morphological diversification and the dysregulation of DNA repair, loss of nuclear integrity, and increased disease mortality. Within the Immunoreactive subtype, spatial analysis further reveals significantly lower lymphocytic infiltration within diversified zones compared with other tumor zones, suggesting that even immune-hot tumors contain cells capable of immune escape. Our findings support a model whereby a subpopulation of morphologically plastic cancer cells with dysregulated DNA repair promotes ovarian cancer progression through positive selection by immune evasion.
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Affiliation(s)
- Andreas Heindl
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Adnan Mujahid Khan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Daniel Nava Rodrigues
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Katherine Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK
- Centre for Molecular Pathology, Royal Marsden Hospital, London, SM2 5NG, UK
| | - Cecilia Orbegoso
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Marco Punta
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Stefano Lise
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Susana Banerjee
- Gynaecology Unit, The Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
- Division of Clinical Studies, the Institute of Cancer Research, London, UK, SM2 5NG
| | - Yinyin Yuan
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, SM2 5NG, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SM2 5NG, UK.
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43
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Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA. Author Correction: Quantification of subclonal selection in cancer from bulk sequencing data. Nat Genet 2018; 50:1342. [PMID: 30022114 DOI: 10.1038/s41588-018-0169-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the version of this article originally published, in the "Theoretical framework of subclonal selection" section of the main text, ref. 11 instead of ref. 19 should have been cited at the end of the phrase "Our previously presented frequentist approach to detect subclonal selection from bulk sequencing data involves an R2 test statistic." The error has been corrected in the HTML and PDF versions of the article.
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Affiliation(s)
- Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Benjamin Werner
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK.
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44
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Caravagna G, Giarratano Y, Ramazzotti D, Tomlinson I, Graham TA, Sanguinetti G, Sottoriva A. Detecting repeated cancer evolution from multi-region tumor sequencing data. Nat Methods 2018; 15:707-714. [PMID: 30171232 PMCID: PMC6380470 DOI: 10.1038/s41592-018-0108-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 07/23/2018] [Indexed: 12/13/2022]
Abstract
Recurrent successions of genomic changes, both within and between patients, reflect repeated evolutionary processes that are valuable for the anticipation of cancer progression. Multi-region sequencing allows the temporal order of some genomic changes in a tumor to be inferred, but the robust identification of repeated evolution across patients remains a challenge. We developed a machine-learning method based on transfer learning that allowed us to overcome the stochastic effects of cancer evolution and noise in data and identified hidden evolutionary patterns in cancer cohorts. When applied to multi-region sequencing datasets from lung, breast, renal, and colorectal cancer (768 samples from 178 patients), our method detected repeated evolutionary trajectories in subgroups of patients, which were reproduced in single-sample cohorts (n = 2,935). Our method provides a means of classifying patients on the basis of how their tumor evolved, with implications for the anticipation of disease progression.
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Affiliation(s)
- Giulio Caravagna
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
- School of Informatics, University of Edinburgh, Edinburgh, UK.
| | - Ylenia Giarratano
- School of Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK
| | | | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Trevor A Graham
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | | | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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45
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Zapata L, Quintanilla I, Asensio E, Pellisé M, Cuatrecasas M, Ossowski S, Graham T, Castells A, Sottoriva A, Camps J. PO-334 Distribution of copy number alterations defines clonal populations involved in the evolutionary transition from adenoma-to-carcinoma in colorectal cancer. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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46
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Werner B, Sottoriva A. Variation of mutational burden in healthy human tissues suggests non-random strand segregation and allows measuring somatic mutation rates. PLoS Comput Biol 2018; 14:e1006233. [PMID: 29879111 PMCID: PMC6007938 DOI: 10.1371/journal.pcbi.1006233] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/19/2018] [Accepted: 05/25/2018] [Indexed: 12/03/2022] Open
Abstract
The immortal strand hypothesis poses that stem cells could produce differentiated progeny while conserving the original template strand, thus avoiding accumulating somatic mutations. However, quantitating the extent of non-random DNA strand segregation in human stem cells remains difficult in vivo. Here we show that the change of the mean and variance of the mutational burden with age in healthy human tissues allows estimating strand segregation probabilities and somatic mutation rates. We analysed deep sequencing data from healthy human colon, small intestine, liver, skin and brain. We found highly effective non-random DNA strand segregation in all adult tissues (mean strand segregation probability: 0.98, standard error bounds (0.97,0.99)). In contrast, non-random strand segregation efficiency is reduced to 0.87 (0.78,0.88) in neural tissue during early development, suggesting stem cell pool expansions due to symmetric self-renewal. Healthy somatic mutation rates differed across tissue types, ranging from 3.5 × 10-9/bp/division in small intestine to 1.6 × 10-7/bp/division in skin.
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Affiliation(s)
- Benjamin Werner
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
| | - Andrea Sottoriva
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer Research, London, United Kingdom
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47
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Williams MJ, Werner B, Heide T, Curtis C, Barnes CP, Sottoriva A, Graham TA. Quantification of subclonal selection in cancer from bulk sequencing data. Nat Genet 2018; 50:895-903. [PMID: 29808029 PMCID: PMC6475346 DOI: 10.1038/s41588-018-0128-6] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 03/23/2018] [Indexed: 12/11/2022]
Abstract
Subclonal architectures are prevalent across cancer types. However, the temporal evolutionary dynamics that produce tumor subclones remain unknown. Here we measure clone dynamics in human cancers by using computational modeling of subclonal selection and theoretical population genetics applied to high-throughput sequencing data. Our method determined the detectable subclonal architecture of tumor samples and simultaneously measured the selective advantage and time of appearance of each subclone. We demonstrate the accuracy of our approach and the extent to which evolutionary dynamics are recorded in the genome. Application of our method to high-depth sequencing data from breast, gastric, blood, colon and lung cancer samples, as well as metastatic deposits, showed that detectable subclones under selection, when present, consistently emerged early during tumor growth and had a large fitness advantage (>20%). Our quantitative framework provides new insight into the evolutionary trajectories of human cancers and facilitates predictive measurements in individual tumors from widely available sequencing data.
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Affiliation(s)
- Marc J Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK
- Department of Cell and Developmental Biology, University College London, London, UK
- Centre for Mathematics and Physics in the Life Sciences and Experimental Biology (CoMPLEX), University College London, London, UK
| | - Benjamin Werner
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Timon Heide
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
| | - Christina Curtis
- Departments of Medicine and Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
| | - Andrea Sottoriva
- Evolutionary Genomics & Modelling Lab, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Queen Mary University of London, London, UK.
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48
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Sottoriva A. Divergent adaptation in thyroid cancers. Ann Oncol 2018; 29:1353. [PMID: 29722787 PMCID: PMC6005061 DOI: 10.1093/annonc/mdy170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- A Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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49
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Acar A, Nichol D, Thavasu P, Sagastume I, Mateos J, Stubbs M, Burke R, Maley C, Banerji U, Sottoriva A. PO-498 Quantifying the dynamics of acquired treatment resistance and evolutionary herding for the prediction of collateral sensitivity in cancer model systems. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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50
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Vlachogiannis G, Hedayat S, Vatsiou A, Jamin Y, Fernández-Mateos J, Khan K, Lampis A, Eason K, Huntingford I, Burke R, Rata M, Koh DM, Tunariu N, Collins D, Hulkki-Wilson S, Ragulan C, Spiteri I, Moorcraft SY, Chau I, Rao S, Watkins D, Fotiadis N, Bali M, Darvish-Damavandi M, Lote H, Eltahir Z, Smyth EC, Begum R, Clarke PA, Hahne JC, Dowsett M, de Bono J, Workman P, Sadanandam A, Fassan M, Sansom OJ, Eccles S, Starling N, Braconi C, Sottoriva A, Robinson SP, Cunningham D, Valeri N. Patient-derived organoids model treatment response of metastatic gastrointestinal cancers. Science 2018; 359:920-926. [PMID: 29472484 PMCID: PMC6112415 DOI: 10.1126/science.aao2774] [Citation(s) in RCA: 1041] [Impact Index Per Article: 173.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 10/26/2017] [Accepted: 01/11/2018] [Indexed: 12/20/2022]
Abstract
Patient-derived organoids (PDOs) have recently emerged as robust preclinical models; however, their potential to predict clinical outcomes in patients has remained unclear. We report on a living biobank of PDOs from metastatic, heavily pretreated colorectal and gastroesophageal cancer patients recruited in phase 1/2 clinical trials. Phenotypic and genotypic profiling of PDOs showed a high degree of similarity to the original patient tumors. Molecular profiling of tumor organoids was matched to drug-screening results, suggesting that PDOs could complement existing approaches in defining cancer vulnerabilities and improving treatment responses. We compared responses to anticancer agents ex vivo in organoids and PDO-based orthotopic mouse tumor xenograft models with the responses of the patients in clinical trials. Our data suggest that PDOs can recapitulate patient responses in the clinic and could be implemented in personalized medicine programs.
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Affiliation(s)
| | - Somaieh Hedayat
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Alexandra Vatsiou
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Yann Jamin
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Javier Fernández-Mateos
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Khurum Khan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Andrea Lampis
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Katherine Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Ian Huntingford
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Mihaela Rata
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Dow-Mu Koh
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | - Nina Tunariu
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | - David Collins
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | - Sanna Hulkki-Wilson
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Chanthirika Ragulan
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Inmaculada Spiteri
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | | | - Ian Chau
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Sheela Rao
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - David Watkins
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Nicos Fotiadis
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | - Maria Bali
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
- Department of Radiology, The Royal Marsden NHS Trust, London, UK
| | | | - Hazel Lote
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Zakaria Eltahir
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | | | - Ruwaida Begum
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Jens C Hahne
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Mitchell Dowsett
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital NHS Trust, London, UK
| | - Johann de Bono
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Matteo Fassan
- Department of Medicine, Surgical Pathology and Cytopathology Unit, University of Padua, Padua, Italy
| | | | - Suzanne Eccles
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | | | - Chiara Braconi
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Simon P Robinson
- Cancer Research UK Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden Hospital, London, UK
| | | | - Nicola Valeri
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
- Department of Medicine, The Royal Marsden NHS Trust, London, UK
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