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Yu Z, Coorens THH, Uddin MM, Ardlie KG, Lennon N, Natarajan P. Genetic variation across and within individuals. Nat Rev Genet 2024:10.1038/s41576-024-00709-x. [PMID: 38548833 DOI: 10.1038/s41576-024-00709-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] [Accepted: 02/09/2024] [Indexed: 04/12/2024]
Abstract
Germline variation and somatic mutation are intricately connected and together shape human traits and disease risks. Germline variants are present from conception, but they vary between individuals and accumulate over generations. By contrast, somatic mutations accumulate throughout life in a mosaic manner within an individual due to intrinsic and extrinsic sources of mutations and selection pressures acting on cells. Recent advancements, such as improved detection methods and increased resources for association studies, have drastically expanded our ability to investigate germline and somatic genetic variation and compare underlying mutational processes. A better understanding of the similarities and differences in the types, rates and patterns of germline and somatic variants, as well as their interplay, will help elucidate the mechanisms underlying their distinct yet interlinked roles in human health and biology.
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Affiliation(s)
- Zhi Yu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Md Mesbah Uddin
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pradeep Natarajan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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2
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Coorens THH, Spencer Chapman M, Williams N, Martincorena I, Stratton MR, Nangalia J, Campbell PJ. Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples. Nat Protoc 2024:10.1038/s41596-024-00962-8. [PMID: 38396041 DOI: 10.1038/s41596-024-00962-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/13/2023] [Indexed: 02/25/2024]
Abstract
Phylogenetic trees are a powerful means to display the evolutionary history of species, pathogens and, more recently, individual cells of the human body. Whole-genome sequencing of laser capture microdissections or expanded stem cells has allowed the discovery of somatic mutations in clones, which can be used as natural barcodes to reconstruct the developmental history of individual cells. Here we describe Sequoia, our pipeline to reconstruct lineage trees from clones of normal cells. Candidate somatic mutations are called against the human reference genome and filtered to exclude germline mutations and artifactual variants. These filtered somatic mutations form the basis for phylogeny reconstruction using a maximum parsimony framework. Lastly, we use a maximum likelihood framework to explicitly map mutations to branches in the phylogenetic tree. The resulting phylogenies can then serve as a basis for many subsequent analyses, including investigating embryonic development, tissue dynamics in health and disease, and mutational signatures. Sequoia can be readily applied to any clonal somatic mutation dataset, including single-cell DNA sequencing datasets, using the commands and scripts provided. Moreover, Sequoia is highly flexible and can be easily customized. Typically, the runtime of the core script ranges from minutes to an hour for datasets with a moderate number (50,000-150,000) of variants. Competent bioinformatic skills, including in-depth knowledge of the R programming language, are required. A high-performance computing cluster (one that is capable of running mutation-calling algorithms and other aspects of the analysis at scale) is also required, especially if handling large datasets.
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Affiliation(s)
- Tim H H Coorens
- Wellcome Sanger Institute, Hinxton, UK.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Haematology, Barts Health NHS Trust, London, UK.
- Department of Haemato-oncology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | | | | | | | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
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3
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Ijaz J, Harry E, Raine K, Menzies A, Beal K, Quail MA, Zumalave S, Jung H, Coorens THH, Lawson ARJ, Leongamornlert D, Francies HE, Garnett MJ, Ning Z, Campbell PJ. Haplotype-specific assembly of shattered chromosomes in esophageal adenocarcinomas. Cell Genom 2024; 4:100484. [PMID: 38232733 PMCID: PMC10879010 DOI: 10.1016/j.xgen.2023.100484] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/13/2023] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
The epigenetic landscape of cancer is regulated by many factors, but primarily it derives from the underlying genome sequence. Chromothripsis is a catastrophic localized genome shattering event that drives, and often initiates, cancer evolution. We characterized five esophageal adenocarcinoma organoids with chromothripsis using long-read sequencing and transcriptome and epigenome profiling. Complex structural variation and subclonal variants meant that haplotype-aware de novo methods were required to generate contiguous cancer genome assemblies. Chromosomes were assembled separately and scaffolded using haplotype-resolved Hi-C reads, producing accurate assemblies even with up to 900 structural rearrangements. There were widespread differences between the chromothriptic and wild-type copies of chromosomes in topologically associated domains, chromatin accessibility, histone modifications, and gene expression. Differential epigenome peaks were most enriched within 10 kb of chromothriptic structural variants. Alterations in transcriptome and higher-order chromosome organization frequently occurred near differential epigenetic marks. Overall, chromothripsis reshapes gene regulation, causing coordinated changes in epigenetic landscape, transcription, and chromosome conformation.
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Affiliation(s)
- Jannat Ijaz
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
| | | | - Keiran Raine
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Health Innovation East, Unit C, Magog Court, Shelford Bottom, Cambridge CB22 3AD, UK
| | | | | | | | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | - Hayley E Francies
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK; GSK, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | | | - Zemin Ning
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
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4
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Treger TD, Lawrence JEG, Anderson ND, Coorens THH, Letunovska A, Abby E, Lee-Six H, Oliver TRW, Al-Saadi R, Tullus K, Morcrette G, Hutchinson JC, Rampling D, Sebire N, Pritchard-Jones K, Young MD, Mitchell TJ, Jones PH, Tran M, Behjati S, Chowdhury T. Targetable NOTCH1 rearrangements in reninoma. Nat Commun 2023; 14:5826. [PMID: 37749094 PMCID: PMC10519988 DOI: 10.1038/s41467-023-41118-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 08/23/2023] [Indexed: 09/27/2023] Open
Abstract
Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assess somatic changes in reninoma and find structural variants that generate canonical activating rearrangements of, NOTCH1 whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observe excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.
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Affiliation(s)
- Taryn D Treger
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - John E G Lawrence
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | | | - Tim H H Coorens
- Broad Institute of MIT and Harvard, Cambridge, 02142 MA, USA
| | - Aleksandra Letunovska
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Emilie Abby
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Henry Lee-Six
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Reem Al-Saadi
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Kjell Tullus
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Guillaume Morcrette
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - J Ciaran Hutchinson
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Dyanne Rampling
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | - Neil Sebire
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK
| | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Early Cancer Institute, University of Cambridge, Cambridge, CB2 0XZ, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Oncology, University of Cambridge, Cambridge, CB2 OXZ, UK
| | - Maxine Tran
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, NW3 2QG, UK.
- Faculty of Medical Sciences, Division of Surgery and Interventional Science, University College London, London, NW3 2PS, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
| | - Tanzina Chowdhury
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, London, WC1N 3JH, UK.
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5
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Coorens THH, Collord G, Treger TD, Adams S, Mitchell E, Newman B, Getz G, Godfrey AL, Bartram J, Behjati S. Clonal origin of KMT2A wild-type lineage-switch leukemia following CAR-T cell and blinatumomab therapy. Nat Cancer 2023; 4:1095-1101. [PMID: 37474833 PMCID: PMC10447231 DOI: 10.1038/s43018-023-00604-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/22/2023] [Indexed: 07/22/2023]
Abstract
Children with acute lymphoblastic leukemia (ALL) undergoing anti-CD19 therapy occasionally develop acute myeloid leukemia (AML). The clonal origin of such lineage-switch leukemias1-4 remains unresolved. Here, we reconstructed the phylogeny of multiple leukemias in a girl who, following multiply relapsed ALL, received anti-CD19 cellular and antibody treatment and subsequently developed AML. Whole genome sequencing unambiguously revealed the AML derived from the initial ALL, with distinct driver mutations that were detectable before emergence. Extensive prior diversification and subsequent clonal selection underpins this fatal lineage switch. Genomic monitoring of primary leukemias and recurrences may predict therapy resistance, especially regarding anti-CD19 treatment.
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Affiliation(s)
| | - Grace Collord
- Great Ormond Street Hospital for Children, London, UK
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Stuart Adams
- Great Ormond Street Hospital for Children, London, UK
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Barbara Newman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gad Getz
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Anna L Godfrey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jack Bartram
- Great Ormond Street Hospital for Children, London, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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6
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Ellis P, Moore L, Sanders MA, Butler TM, Brunner SF, Lee-Six H, Osborne R, Farr B, Coorens THH, Lawson ARJ, Cagan A, Stratton MR, Martincorena I, Campbell PJ. Author Correction: Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat Protoc 2023:10.1038/s41596-023-00816-9. [PMID: 36849600 DOI: 10.1038/s41596-023-00816-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Affiliation(s)
- Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.,Inivata Limited, The Glenn Berge Building, Babraham Research Campus, Babraham, UK
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.,Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Simon F Brunner
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Robert Osborne
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.,Inivata Limited, The Glenn Berge Building, Babraham Research Campus, Babraham, UK
| | - Ben Farr
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Andrew R J Lawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mike R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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7
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Wang Y, Robinson PS, Coorens THH, Moore L, Lee-Six H, Noorani A, Sanders MA, Jung H, Katainen R, Heuschkel R, Brunton-Sim R, Weston R, Read D, Nobbs B, Fitzgerald RC, Saeb-Parsy K, Martincorena I, Campbell PJ, Rushbrook S, Zilbauer M, Buczacki SJA, Stratton MR. APOBEC mutagenesis is a common process in normal human small intestine. Nat Genet 2023; 55:246-254. [PMID: 36702998 PMCID: PMC9925384 DOI: 10.1038/s41588-022-01296-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 12/16/2022] [Indexed: 01/27/2023]
Abstract
APOBEC mutational signatures SBS2 and SBS13 are common in many human cancer types. However, there is an incomplete understanding of its stimulus, when it occurs in the progression from normal to cancer cell and the APOBEC enzymes responsible. Here we whole-genome sequenced 342 microdissected normal epithelial crypts from the small intestines of 39 individuals and found that SBS2/SBS13 mutations were present in 17% of crypts, more frequent than most other normal tissues. Crypts with SBS2/SBS13 often had immediate crypt neighbors without SBS2/SBS13, suggesting that the underlying cause of SBS2/SBS13 is cell-intrinsic. APOBEC mutagenesis occurred in an episodic manner throughout the human lifespan, including in young children. APOBEC1 mRNA levels were very high in the small intestine epithelium, but low in the large intestine epithelium and other tissues. The results suggest that the high levels of SBS2/SBS13 in the small intestine are collateral damage from APOBEC1 fulfilling its physiological function of editing APOB mRNA.
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Affiliation(s)
- Yichen Wang
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Philip S Robinson
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Ayesha Noorani
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Hyunchul Jung
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robert Heuschkel
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
| | | | - Robyn Weston
- NIHR Clinical Research Network-East of England, Addenbrooke's Hospital, Cambridge, UK
| | - Debbie Read
- NIHR Clinical Research Network-East of England, Addenbrooke's Hospital, Cambridge, UK
| | - Beverley Nobbs
- NIHR Clinical Research Network-East of England, Addenbrooke's Hospital, Cambridge, UK
| | - Rebecca C Fitzgerald
- The Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK
| | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, UK.
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8
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Oliver TRW, Chappell L, Sanghvi R, Deighton L, Ansari-Pour N, Dentro SC, Young MD, Coorens THH, Jung H, Butler T, Neville MDC, Leongamornlert D, Sanders MA, Hooks Y, Cagan A, Mitchell TJ, Cortes-Ciriano I, Warren AY, Wedge DC, Heer R, Coleman N, Murray MJ, Campbell PJ, Rahbari R, Behjati S. Clonal diversification and histogenesis of malignant germ cell tumours. Nat Commun 2022; 13:4272. [PMID: 35953478 PMCID: PMC9372159 DOI: 10.1038/s41467-022-31375-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/26/2022] [Accepted: 06/13/2022] [Indexed: 12/21/2022] Open
Abstract
Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.
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Affiliation(s)
- Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | | | | | | | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Isidro Cortes-Ciriano
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Matthew J Murray
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | | | | | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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9
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Robinson PS, Thomas LE, Abascal F, Jung H, Harvey LMR, West HD, Olafsson S, Lee BCH, Coorens THH, Lee-Six H, Butlin L, Lander N, Truscott R, Sanders MA, Lensing SV, Buczacki SJA, Ten Hoopen R, Coleman N, Brunton-Sim R, Rushbrook S, Saeb-Parsy K, Lalloo F, Campbell PJ, Martincorena I, Sampson JR, Stratton MR. Inherited MUTYH mutations cause elevated somatic mutation rates and distinctive mutational signatures in normal human cells. Nat Commun 2022; 13:3949. [PMID: 35803914 PMCID: PMC9270427 DOI: 10.1038/s41467-022-31341-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 10/12/2021] [Accepted: 06/14/2022] [Indexed: 12/21/2022] Open
Abstract
Cellular DNA damage caused by reactive oxygen species is repaired by the base excision repair (BER) pathway which includes the DNA glycosylase MUTYH. Inherited biallelic MUTYH mutations cause predisposition to colorectal adenomas and carcinoma. However, the mechanistic progression from germline MUTYH mutations to MUTYH-Associated Polyposis (MAP) is incompletely understood. Here, we sequence normal tissue DNAs from 10 individuals with MAP. Somatic base substitution mutation rates in intestinal epithelial cells were elevated 2 to 4-fold in all individuals, except for one showing a 31-fold increase, and were also increased in other tissues. The increased mutation burdens were of multiple mutational signatures characterised by C > A changes. Different mutation rates and signatures between individuals are likely due to different MUTYH mutations or additional inherited mutations in other BER pathway genes. The elevated base substitution rate in normal cells likely accounts for the predisposition to neoplasia in MAP. Despite ubiquitously elevated mutation rates, individuals with MAP do not display overt evidence of premature ageing. Thus, accumulation of somatic mutations may not be sufficient to cause the global organismal functional decline of ageing.
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Affiliation(s)
- Philip S Robinson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Laura E Thomas
- Institute of Life Science, Swansea University, Swansea, SA28PP, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hyunchul Jung
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Hannah D West
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Sigurgeir Olafsson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Bernard C H Lee
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Laura Butlin
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, 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
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Haematology, Erasmus University Medical Centre, 3015 CN, Rotterdam, The Netherlands
| | - Stefanie V Lensing
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences, Medical Sciences Division, University of Oxford, Oxford, UK
| | | | - Nicholas Coleman
- Department of Pathology, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Simon Rushbrook
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital, Oxford Road, Manchester, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, CB10 1SA, UK.
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10
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Mitchell E, Spencer Chapman M, Williams N, Dawson KJ, Mende N, Calderbank EF, Jung H, Mitchell T, Coorens THH, Spencer DH, Machado H, Lee-Six H, Davies M, Hayler D, Fabre MA, Mahbubani K, Abascal F, Cagan A, Vassiliou GS, Baxter J, Martincorena I, Stratton MR, Kent DG, Chatterjee K, Parsy KS, Green AR, Nangalia J, Laurenti E, Campbell PJ. Clonal dynamics of haematopoiesis across the human lifespan. Nature 2022; 606:343-350. [PMID: 35650442 PMCID: PMC9177428 DOI: 10.1038/s41586-022-04786-y] [Citation(s) in RCA: 128] [Impact Index Per Article: 64.0] [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: 08/16/2021] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Age-related change in human haematopoiesis causes reduced regenerative capacity1, cytopenias2, immune dysfunction3 and increased risk of blood cancer4-6, but the reason for such abrupt functional decline after 70 years of age remains unclear. Here we sequenced 3,579 genomes from single cell-derived colonies of haematopoietic cells across 10 human subjects from 0 to 81 years of age. Haematopoietic stem cells or multipotent progenitors (HSC/MPPs) accumulated a mean of 17 mutations per year after birth and lost 30 base pairs per year of telomere length. Haematopoiesis in adults less than 65 years of age was massively polyclonal, with high clonal diversity and a stable population of 20,000-200,000 HSC/MPPs contributing evenly to blood production. By contrast, haematopoiesis in individuals aged over 75 showed profoundly decreased clonal diversity. In each of the older subjects, 30-60% of haematopoiesis was accounted for by 12-18 independent clones, each contributing 1-34% of blood production. Most clones had begun their expansion before the subject was 40 years old, but only 22% had known driver mutations. Genome-wide selection analysis estimated that between 1 in 34 and 1 in 12 non-synonymous mutations were drivers, accruing at constant rates throughout life, affecting more genes than identified in blood cancers. Loss of the Y chromosome conferred selective benefits in males. Simulations of haematopoiesis, with constant stem cell population size and constant acquisition of driver mutations conferring moderate fitness benefits, entirely explained the abrupt change in clonal structure in the elderly. Rapidly decreasing clonal diversity is a universal feature of haematopoiesis in aged humans, underpinned by pervasive positive selection acting on many more genes than currently identified.
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Affiliation(s)
- Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | | | - Nicole Mende
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Emily F Calderbank
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | | | | | | | - David H Spencer
- Department of Medicine, McDonnell Genome Institute, Washington University, St Louis, MO, USA
| | | | | | - Megan Davies
- Cambridge Molecular Diagnostics, Milton Road, Cambridge, UK
| | - Daniel Hayler
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Margarete A Fabre
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Krishnaa Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | | | - George S Vassiliou
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joanna Baxter
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - David G Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Krishna Chatterjee
- Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Anthony R Green
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Elisa Laurenti
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.
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11
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Lee BCH, Robinson PS, Coorens THH, Yan HHN, Olafsson S, Lee-Six H, Sanders MA, Siu HC, Hewinson J, Yue SSK, Tsui WY, Chan ASY, Chan AKW, Ho SL, Campbell PJ, Martincorena I, Buczacki SJA, Yuen ST, Leung SY, Stratton MR. Mutational landscape of normal epithelial cells in Lynch Syndrome patients. Nat Commun 2022; 13:2710. [PMID: 35581206 PMCID: PMC9114395 DOI: 10.1038/s41467-022-29920-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 10/13/2021] [Accepted: 04/07/2022] [Indexed: 01/01/2023] Open
Abstract
Lynch Syndrome (LS) is an autosomal dominant disease conferring a high risk of colorectal cancer due to germline heterozygous mutations in a DNA mismatch repair (MMR) gene. Although cancers in LS patients show elevated somatic mutation burdens, information on mutation rates in normal tissues and understanding of the trajectory from normal to cancer cell is limited. Here we whole genome sequence 152 crypts from normal and neoplastic epithelial tissues from 10 LS patients. In normal tissues the repertoire of mutational processes and mutation rates is similar to that found in wild type individuals. A morphologically normal colonic crypt with an increased mutation burden and MMR deficiency-associated mutational signatures is identified, which may represent a very early stage of LS pathogenesis. Phylogenetic trees of tumour crypts indicate that the most recent ancestor cell of each tumour is already MMR deficient and has experienced multiple cycles of clonal evolution. This study demonstrates the genomic stability of epithelial cells with heterozygous germline MMR gene mutations and highlights important differences in the pathogenesis of LS from other colorectal cancer predisposition syndromes.
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Affiliation(s)
- Bernard C H Lee
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Philip S Robinson
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | | | - Helen H N Yan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | | | - Hoi Cheong Siu
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | - Sarah S K Yue
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Yin Tsui
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Annie S Y Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Anthony K W Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Siu Lun Ho
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Siu Tsan Yuen
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong.
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong.
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12
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Khabirova E, Jardine L, Coorens THH, Webb S, Treger TD, Engelbert J, Porter T, Prigmore E, Collord G, Piapi A, Teichmann SA, Inglott S, Williams O, Heidenreich O, Young MD, Straathof K, Bomken S, Bartram J, Haniffa M, Behjati S. Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia. Nat Med 2022; 28:743-751. [PMID: 35288693 PMCID: PMC9018413 DOI: 10.1038/s41591-022-01720-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [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: 08/03/2021] [Accepted: 01/27/2022] [Indexed: 12/23/2022]
Abstract
KMT2A-rearranged infant ALL is an aggressive childhood leukemia with poor prognosis. Here, we investigated the developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia (B-ALL) using bulk messenger RNA (mRNA) meta-analysis and examination of single lymphoblast transcriptomes against a developing bone marrow reference. KMT2A-rearranged infant B-ALL was uniquely dominated by an early lymphocyte precursor (ELP) state, whereas less adverse NUTM1-rearranged infant ALL demonstrated signals of later developing B cells, in line with most other childhood B-ALLs. We compared infant lymphoblasts with ELP cells and revealed that the cancer harbored hybrid myeloid-lymphoid features, including nonphysiological antigen combinations potentially targetable to achieve cancer specificity. We validated surface coexpression of exemplar combinations by flow cytometry. Through analysis of shared mutations in separate leukemias from a child with infant KMT2A-rearranged B-ALL relapsing as AML, we established that KMT2A rearrangement occurred in very early development, before hematopoietic specification, emphasizing that cell of origin cannot be inferred from the transcriptional state.
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Affiliation(s)
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Haematology Department, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Grace Collord
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University College London Hospital, London, UK
- Department of Haematology, University College London Cancer Institute, London, UK
| | - Alice Piapi
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | | | - Sarah Inglott
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
| | - Owen Williams
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Olaf Heidenreich
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Karin Straathof
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Bomken
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.
- The Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Jack Bartram
- Great Ormond Street Hospital for Children NHS Foundation Trust and NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK.
- UCL Great Ormond Street Institute of Child Health, London, UK.
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK.
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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13
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Cagan A, Baez-Ortega A, Brzozowska N, Abascal F, Coorens THH, Sanders MA, Lawson ARJ, Harvey LMR, Bhosle S, Jones D, Alcantara RE, Butler TM, Hooks Y, Roberts K, Anderson E, Lunn S, Flach E, Spiro S, Januszczak I, Wrigglesworth E, Jenkins H, Dallas T, Masters N, Perkins MW, Deaville R, Druce M, Bogeska R, Milsom MD, Neumann B, Gorman F, Constantino-Casas F, Peachey L, Bochynska D, Smith ESJ, Gerstung M, Campbell PJ, Murchison EP, Stratton MR, Martincorena I. Somatic mutation rates scale with lifespan across mammals. Nature 2022; 604:517-524. [PMID: 35418684 PMCID: PMC9021023 DOI: 10.1038/s41586-022-04618-z] [Citation(s) in RCA: 160] [Impact Index Per Article: 80.0] [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: 08/17/2021] [Accepted: 03/07/2022] [Indexed: 12/22/2022]
Abstract
The rates and patterns of somatic mutation in normal tissues are largely unknown outside of humans1-7. Comparative analyses can shed light on the diversity of mutagenesis across species, and on long-standing hypotheses about the evolution of somatic mutation rates and their role in cancer and ageing. Here we performed whole-genome sequencing of 208 intestinal crypts from 56 individuals to study the landscape of somatic mutation across 16 mammalian species. We found that somatic mutagenesis was dominated by seemingly endogenous mutational processes in all species, including 5-methylcytosine deamination and oxidative damage. With some differences, mutational signatures in other species resembled those described in humans8, although the relative contribution of each signature varied across species. Notably, the somatic mutation rate per year varied greatly across species and exhibited a strong inverse relationship with species lifespan, with no other life-history trait studied showing a comparable association. Despite widely different life histories among the species we examined-including variation of around 30-fold in lifespan and around 40,000-fold in body mass-the somatic mutation burden at the end of lifespan varied only by a factor of around 3. These data unveil common mutational processes across mammals, and suggest that somatic mutation rates are evolutionarily constrained and may be a contributing factor in ageing.
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Affiliation(s)
- Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
| | - Adrian Baez-Ortega
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Natalia Brzozowska
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Andrew R J Lawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Shriram Bhosle
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - David Jones
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Raul E Alcantara
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Kirsty Roberts
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Elizabeth Anderson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Sharna Lunn
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Edmund Flach
- Wildlife Health Services, Zoological Society of London, London, UK
| | - Simon Spiro
- Wildlife Health Services, Zoological Society of London, London, UK
| | - Inez Januszczak
- Wildlife Health Services, Zoological Society of London, London, UK
- The Natural History Museum, London, UK
| | | | - Hannah Jenkins
- Wildlife Health Services, Zoological Society of London, London, UK
| | - Tilly Dallas
- Wildlife Health Services, Zoological Society of London, London, UK
| | - Nic Masters
- Wildlife Health Services, Zoological Society of London, London, UK
| | | | - Robert Deaville
- Institute of Zoology, Zoological Society of London, London, UK
| | - Megan Druce
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH (HI-STEM), Heidelberg, Germany
| | - Ruzhica Bogeska
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH (HI-STEM), Heidelberg, Germany
| | - Michael D Milsom
- Division of Experimental Hematology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine GmbH (HI-STEM), Heidelberg, Germany
| | - Björn Neumann
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Frank Gorman
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Laura Peachey
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Bristol Veterinary School, Faculty of Health Sciences, University of Bristol, Langford, UK
| | - Diana Bochynska
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Department of Pathology, Faculty of Veterinary Medicine, Universitatea de Stiinte Agricole si Medicina Veterinara, Cluj-Napoca, Romania
| | | | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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14
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Coorens THH, Oliver TRW, Sanghvi R, Sovio U, Cook E, Vento-Tormo R, Haniffa M, Young MD, Rahbari R, Sebire N, Campbell PJ, Charnock-Jones DS, Smith GCS, Behjati S. Author Correction: Inherent mosaicism and extensive mutation of human placentas. Nature 2022; 603:E17. [PMID: 35228729 DOI: 10.1038/s41586-021-04347-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Gordon C S Smith
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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15
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Thorbinson C, Penn A, Nicola P, Hardcastle C, Waller S, Ramsden S, Coorens THH, Tang V, Cheesman E, Douzgou S, Meyer S. Embryonal sarcoma of the liver in a girl with Cockayne syndrome. Clin Genet 2021; 101:375-376. [PMID: 34878179 DOI: 10.1111/cge.14094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/29/2022]
Abstract
The first reported malignancy associated with Cockayne syndrome.
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Affiliation(s)
- Colin Thorbinson
- Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital, Manchester NHS Foundation Trust Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Anthony Penn
- Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital, Manchester NHS Foundation Trust Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK
| | - Pantelis Nicola
- Manchester Academic Health Science Centre, Manchester, UK.,The Christie NHS Foundation Trust, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester, UK.,Division of Cancer Sciences, University of Manchester, Manchester, UK
| | - Claire Hardcastle
- Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester, UK
| | - Sarah Waller
- Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester, UK
| | - Simon Ramsden
- Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester, UK
| | | | - Vivian Tang
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Radiology, Royal Manchester Children's Hospital, Manchester, UK
| | - Edmund Cheesman
- Manchester Academic Health Science Centre, Manchester, UK.,Department of Paediatric Pathology, Royal Manchester Children's Hospital, Manchester, UK
| | - Sofia Douzgou
- Manchester Academic Health Science Centre, Manchester, UK.,Manchester Centre for Genomic Medicine, Manchester, UK.,Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Manchester, UK.,Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Stefan Meyer
- Department of Paediatric Haematology and Oncology, Royal Manchester Children's Hospital, Manchester NHS Foundation Trust Manchester, Manchester, UK.,Manchester Academic Health Science Centre, Manchester, UK.,The Christie NHS Foundation Trust, Manchester, UK.,Division of Cancer Sciences, University of Manchester, Manchester, UK
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16
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Ng SWK, Rouhani FJ, Brunner SF, Brzozowska N, Aitken SJ, Yang M, Abascal F, Moore L, Nikitopoulou E, Chappell L, Leongamornlert D, Ivovic A, Robinson P, Butler T, Sanders MA, Williams N, Coorens THH, Teague J, Raine K, Butler AP, Hooks Y, Wilson B, Birtchnell N, Naylor H, Davies SE, Stratton MR, Martincorena I, Rahbari R, Frezza C, Hoare M, Campbell PJ. Convergent somatic mutations in metabolism genes in chronic liver disease. Nature 2021; 598:473-478. [PMID: 34646017 DOI: 10.1038/s41586-021-03974-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/31/2021] [Indexed: 02/08/2023]
Abstract
The progression of chronic liver disease to hepatocellular carcinoma is caused by the acquisition of somatic mutations that affect 20-30 cancer genes1-8. Burdens of somatic mutations are higher and clonal expansions larger in chronic liver disease9-13 than in normal liver13-16, which enables positive selection to shape the genomic landscape9-13. Here we analysed somatic mutations from 1,590 genomes across 34 liver samples, including healthy controls, alcohol-related liver disease and non-alcoholic fatty liver disease. Seven of the 29 patients with liver disease had mutations in FOXO1, the major transcription factor in insulin signalling. These mutations affected a single hotspot within the gene, impairing the insulin-mediated nuclear export of FOXO1. Notably, six of the seven patients with FOXO1S22W hotspot mutations showed convergent evolution, with variants acquired independently by up to nine distinct hepatocyte clones per patient. CIDEB, which regulates lipid droplet metabolism in hepatocytes17-19, and GPAM, which produces storage triacylglycerol from free fatty acids20,21, also had a significant excess of mutations. We again observed frequent convergent evolution: up to fourteen independent clones per patient with CIDEB mutations and up to seven clones per patient with GPAM mutations. Mutations in metabolism genes were distributed across multiple anatomical segments of the liver, increased clone size and were seen in both alcohol-related liver disease and non-alcoholic fatty liver disease, but rarely in hepatocellular carcinoma. Master regulators of metabolic pathways are a frequent target of convergent somatic mutation in alcohol-related and non-alcoholic fatty liver disease.
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Affiliation(s)
- Stanley W K Ng
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Foad J Rouhani
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
- Department of Surgery, Addenbrooke's Hospital, Cambridge, UK
| | - Simon F Brunner
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Sarah J Aitken
- CRUK Cambridge Institute, Cambridge, UK
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Ming Yang
- MRC Cancer Unit, University of Cambridge, Cambridge, UK
| | | | - Luiza Moore
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Lia Chappell
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | | | - Philip Robinson
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Timothy Butler
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Tim H H Coorens
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Jon Teague
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Keiran Raine
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Adam P Butler
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | - Beverley Wilson
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Huw Naylor
- Department of Surgery, Addenbrooke's Hospital, Cambridge, UK
| | - Susan E Davies
- Department of Pathology, Addenbrooke's Hospital, Cambridge, UK
| | | | | | - Raheleh Rahbari
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK
| | | | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK.
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Sanger Institute, Hinxton, UK.
- Stem Cell Institute, University of Cambridge, Cambridge, UK.
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17
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Robinson PS, Coorens THH, Palles C, Mitchell E, Abascal F, Olafsson S, Lee BCH, Lawson ARJ, Lee-Six H, Moore L, Sanders MA, Hewinson J, Martin L, Pinna CMA, Galavotti S, Rahbari R, Campbell PJ, Martincorena I, Tomlinson I, Stratton MR. Increased somatic mutation burdens in normal human cells due to defective DNA polymerases. Nat Genet 2021; 53:1434-1442. [PMID: 34594041 PMCID: PMC8492474 DOI: 10.1038/s41588-021-00930-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [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: 02/17/2021] [Accepted: 07/28/2021] [Indexed: 02/08/2023]
Abstract
Mutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE/POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/POLD1 mutations cause familial cancer predisposition. Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens. Except for increased cancer risk, individuals with germline POLE/POLD1 mutations do not exhibit overt features of premature aging. These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.
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Affiliation(s)
- Philip S Robinson
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | | | - Bernard C H Lee
- Wellcome Sanger Institute, Hinxton, UK
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | | | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Claudia M A Pinna
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Sara Galavotti
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | | | | | | | - Ian Tomlinson
- Edinburgh Cancer Research Centre, IGMM, University of Edinburgh, Edinburgh, UK.
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18
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Moore L, Cagan A, Coorens THH, Neville MDC, Sanghvi R, Sanders MA, Oliver TRW, Leongamornlert D, Ellis P, Noorani A, Mitchell TJ, Butler TM, Hooks Y, Warren AY, Jorgensen M, Dawson KJ, Menzies A, O'Neill L, Latimer C, Teng M, van Boxtel R, Iacobuzio-Donahue CA, Martincorena I, Heer R, Campbell PJ, Fitzgerald RC, Stratton MR, Rahbari R. The mutational landscape of human somatic and germline cells. Nature 2021; 597:381-386. [PMID: 34433962 DOI: 10.1038/s41586-021-03822-7] [Citation(s) in RCA: 134] [Impact Index Per Article: 44.7] [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: 11/23/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022]
Abstract
Over the course of an individual's lifetime, normal human cells accumulate mutations1. Here we compare the mutational landscape in 29 cell types from the soma and germline using multiple samples from the same individuals. Two ubiquitous mutational signatures, SBS1 and SBS5/40, accounted for the majority of acquired mutations in most cell types, but their absolute and relative contributions varied substantially. SBS18, which potentially reflects oxidative damage2, and several additional signatures attributed to exogenous and endogenous exposures contributed mutations to subsets of cell types. The rate of mutation was lowest in spermatogonia, the stem cells from which sperm are generated and from which most genetic variation in the human population is thought to originate. This was due to low rates of ubiquitous mutational processes and may be partially attributable to a low rate of cell division in basal spermatogonia. These results highlight similarities and differences in the maintenance of the germline and soma.
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Affiliation(s)
- Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Matthew D C Neville
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rashesh Sanghvi
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Thomas R W Oliver
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Inivata, Cambridge, UK
| | - Ayesha Noorani
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Anne Y Warren
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mabel Teng
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology and Oncode Institute, Utrecht, Netherlands
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Rakesh Heer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Newcastle Urology, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | | | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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19
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Coorens THH, Moore L, Robinson PS, Sanghvi R, Christopher J, Hewinson J, Przybilla MJ, Lawson ARJ, Spencer Chapman M, Cagan A, Oliver TRW, Neville MDC, Hooks Y, Noorani A, Mitchell TJ, Fitzgerald RC, Campbell PJ, Martincorena I, Rahbari R, Stratton MR. Extensive phylogenies of human development inferred from somatic mutations. Nature 2021; 597:387-392. [PMID: 34433963 DOI: 10.1038/s41586-021-03790-y] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [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: 11/25/2020] [Accepted: 07/01/2021] [Indexed: 01/01/2023]
Abstract
Starting from the zygote, all cells in the human body continuously acquire mutations. Mutations shared between different cells imply a common progenitor and are thus naturally occurring markers for lineage tracing1,2. Here we reconstruct extensive phylogenies of normal tissues from three adult individuals using whole-genome sequencing of 511 laser capture microdissections. Reconstructed embryonic progenitors in the same generation of a phylogeny often contribute to different extents to the adult body. The degree of this asymmetry varies between individuals, with ratios between the two reconstructed daughter cells of the zygote ranging from 60:40 to 93:7. Asymmetries pervade subsequent generations and can differ between tissues in the same individual. The phylogenies resolve the spatial embryonic patterning of tissues, revealing contiguous patches of, on average, 301 crypts in the adult colonic epithelium derived from a most recent embryonic cell and also a spatial effect in brain development. Using data from ten additional men, we investigated the developmental split between soma and germline, with results suggesting an extraembryonic contribution to primordial germ cells. This research demonstrates that, despite reaching the same ultimate tissue patterns, early bottlenecks and lineage commitments lead to substantial variation in embryonic patterns both within and between individuals.
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Affiliation(s)
| | - Luiza Moore
- Wellcome Sanger Institute, Hinxton, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Philip S Robinson
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Joseph Christopher
- Wellcome Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Michael Spencer Chapman
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | | | | | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
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20
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Spencer Chapman M, Ranzoni AM, Myers B, Williams N, Coorens THH, Mitchell E, Butler T, Dawson KJ, Hooks Y, Moore L, Nangalia J, Robinson PS, Yoshida K, Hook E, Campbell PJ, Cvejic A. Lineage tracing of human development through somatic mutations. Nature 2021; 595:85-90. [PMID: 33981037 DOI: 10.1038/s41586-021-03548-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [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: 05/29/2020] [Accepted: 04/13/2021] [Indexed: 12/21/2022]
Abstract
The ontogeny of the human haematopoietic system during fetal development has previously been characterized mainly through careful microscopic observations1. Here we reconstruct a phylogenetic tree of blood development using whole-genome sequencing of 511 single-cell-derived haematopoietic colonies from healthy human fetuses at 8 and 18 weeks after conception, coupled with deep targeted sequencing of tissues of known embryonic origin. We found that, in healthy fetuses, individual haematopoietic progenitors acquire tens of somatic mutations by 18 weeks after conception. We used these mutations as barcodes and timed the divergence of embryonic and extra-embryonic tissues during development, and estimated the number of blood antecedents at different stages of embryonic development. Our data support a hypoblast origin of the extra-embryonic mesoderm and primitive blood in humans.
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Affiliation(s)
- Michael Spencer Chapman
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, Hammersmith Hospital, Imperial College Healthcare NHS Trust, London, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Anna Maria Ranzoni
- Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Brynelle Myers
- Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - Emily Mitchell
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
| | | | | | | | - Luiza Moore
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jyoti Nangalia
- Wellcome Trust Sanger Institute, Hinxton, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Philip S Robinson
- Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | | | - Elizabeth Hook
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Peter J Campbell
- Wellcome Trust Sanger Institute, Hinxton, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Hinxton, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
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21
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Young MD, Mitchell TJ, Custers L, Margaritis T, Morales-Rodriguez F, Kwakwa K, Khabirova E, Kildisiute G, Oliver TRW, de Krijger RR, van den Heuvel-Eibrink MM, Comitani F, Piapi A, Bugallo-Blanco E, Thevanesan C, Burke C, Prigmore E, Ambridge K, Roberts K, Braga FAV, Coorens THH, Del Valle I, Wilbrey-Clark A, Mamanova L, Stewart GD, Gnanapragasam VJ, Rampling D, Sebire N, Coleman N, Hook L, Warren A, Haniffa M, Kool M, Pfister SM, Achermann JC, He X, Barker RA, Shlien A, Bayraktar OA, Teichmann SA, Holstege FC, Meyer KB, Drost J, Straathof K, Behjati S. Single cell derived mRNA signals across human kidney tumors. Nat Commun 2021; 12:3896. [PMID: 34162837 PMCID: PMC8222373 DOI: 10.1038/s41467-021-23949-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 11/06/2020] [Accepted: 05/25/2021] [Indexed: 01/16/2023] Open
Abstract
Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference "cellular signals" in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of "fetalness" with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer.
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Affiliation(s)
- Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Lars Custers
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | | | - Francisco Morales-Rodriguez
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Eleonora Khabirova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gerda Kildisiute
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Alice Piapi
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | | | | | - Christina Burke
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kirsty Ambridge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kenny Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ignacio Del Valle
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Vincent J Gnanapragasam
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Urology Translational Research and Clinical Trials office, Cambridge Biomedical Campus Cambridge CB2 0QQ University of Cambridge, Cambridge, UK
| | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Neil Sebire
- NIHR Great Ormond Street Hospital BRC and Institute of Child Health, London, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Anne Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
- Intitute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
| | - Stefan M Pfister
- Hopp Children´s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Division of Pediatric Neurooncology, Heidelberg, Germany
- Heidelberg University Hospital, Department of Pediatric Hematology and Oncology, Heidelberg, Germany
| | - John C Achermann
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK
| | - Xiaoling He
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Roger A Barker
- MRC-WT Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Omer A Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Frank C Holstege
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health, London, UK.
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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22
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Molè MA, Coorens THH, Shahbazi MN, Weberling A, Weatherbee BAT, Gantner CW, Sancho-Serra C, Richardson L, Drinkwater A, Syed N, Engley S, Snell P, Christie L, Elder K, Campbell A, Fishel S, Behjati S, Vento-Tormo R, Zernicka-Goetz M. A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre. Nat Commun 2021; 12:3679. [PMID: 34140473 PMCID: PMC8211662 DOI: 10.1038/s41467-021-23758-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 05/11/2021] [Indexed: 01/02/2023] Open
Abstract
Following implantation, the human embryo undergoes major morphogenetic transformations that establish the future body plan. While the molecular events underpinning this process are established in mice, they remain unknown in humans. Here we characterise key events of human embryo morphogenesis, in the period between implantation and gastrulation, using single-cell analyses and functional studies. First, the embryonic epiblast cells transition through different pluripotent states and act as a source of FGF signals that ensure proliferation of both embryonic and extra-embryonic tissues. In a subset of embryos, we identify a group of asymmetrically positioned extra-embryonic hypoblast cells expressing inhibitors of BMP, NODAL and WNT signalling pathways. We suggest that this group of cells can act as the anterior singalling centre to pattern the epiblast. These results provide insights into pluripotency state transitions, the role of FGF signalling and the specification of anterior-posterior axis during human embryo development. Single cell analysis of early human embryos identifies key changes in pluripotency, the requirement of FGF signalling for embryo survival, and defines a putative anterior-like region of hypoblast cells, providing insights into how early human development is regulated.
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Affiliation(s)
- Matteo A Molè
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.,Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Marta N Shahbazi
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Antonia Weberling
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | - Bailey A T Weatherbee
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | - Carlos W Gantner
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK
| | | | - Lucy Richardson
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | - Abbie Drinkwater
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | - Najma Syed
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | - Stephanie Engley
- Herts & Essex Fertility Centre, Bishops College, Cheshunt, Herts, UK
| | | | | | | | | | - Simon Fishel
- CARE Fertility Group, Nottingham, UK.,School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK. .,Cambridge University Hospital, NHS Foundation Trust, Cambridge, UK. .,Department of Paediatrics, University of Cambridge, Cambridge, UK.
| | | | - Magdalena Zernicka-Goetz
- Department of Physiology, Development and Neuroscience, Mammalian Embryo and Stem Cell Group, University of Cambridge, Cambridge, UK. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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23
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Coorens THH, Collord G, Lu W, Mitchell E, Ijaz J, Roberts T, Oliver TRW, Burke GAA, Gattens M, Dickens E, Nangalia J, Tischkowitz M, Anderson J, Shlien A, Godfrey AL, Murray MJ, Behjati S. Clonal hematopoiesis and therapy-related myeloid neoplasms following neuroblastoma treatment. Blood 2021; 137:2992-2997. [PMID: 33598691 PMCID: PMC8160503 DOI: 10.1182/blood.2020010150] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 02/04/2021] [Indexed: 12/21/2022] Open
Affiliation(s)
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Haematology, University College London Hospital, London, United Kingdom
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
| | - Wanhua Lu
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Jannat Ijaz
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Thomas Roberts
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | | | - G A Amos Burke
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Michael Gattens
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Emmy Dickens
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Jyoti Nangalia
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Cambridge Stem Cell Institute, Cambridge, Cambridgeshire, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - John Anderson
- University College London Great Ormond Street Institute of Child Health, London, United Kingdom
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, United Kingdom
| | - Adam Shlien
- The Hospital for Sick Children, Toronto, ON, Canada; and
| | - Anna L Godfrey
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
| | - Matthew J Murray
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
- Department of Pathology and
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, United Kingdom
- Department of Paediatrics, University of Cambridge, Cambridge, United Kingdom
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24
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Abascal F, Harvey LMR, Mitchell E, Lawson ARJ, Lensing SV, Ellis P, Russell AJC, Alcantara RE, Baez-Ortega A, Wang Y, Kwa EJ, Lee-Six H, Cagan A, Coorens THH, Chapman MS, Olafsson S, Leonard S, Jones D, Machado HE, Davies M, Øbro NF, Mahubani KT, Allinson K, Gerstung M, Saeb-Parsy K, Kent DG, Laurenti E, Stratton MR, Rahbari R, Campbell PJ, Osborne RJ, Martincorena I. Somatic mutation landscapes at single-molecule resolution. Nature 2021; 593:405-410. [PMID: 33911282 DOI: 10.1038/s41586-021-03477-4] [Citation(s) in RCA: 187] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Somatic mutations drive the development of cancer and may contribute to ageing and other diseases1,2. Despite their importance, the difficulty of detecting mutations that are only present in single cells or small clones has limited our knowledge of somatic mutagenesis to a minority of tissues. Here, to overcome these limitations, we developed nanorate sequencing (NanoSeq), a duplex sequencing protocol with error rates of less than five errors per billion base pairs in single DNA molecules from cell populations. This rate is two orders of magnitude lower than typical somatic mutation loads, enabling the study of somatic mutations in any tissue independently of clonality. We used this single-molecule sensitivity to study somatic mutations in non-dividing cells across several tissues, comparing stem cells to differentiated cells and studying mutagenesis in the absence of cell division. Differentiated cells in blood and colon displayed remarkably similar mutation loads and signatures to their corresponding stem cells, despite mature blood cells having undergone considerably more divisions. We then characterized the mutational landscape of post-mitotic neurons and polyclonal smooth muscle, confirming that neurons accumulate somatic mutations at a constant rate throughout life without cell division, with similar rates to mitotically active tissues. Together, our results suggest that mutational processes that are independent of cell division are important contributors to somatic mutagenesis. We anticipate that the ability to reliably detect mutations in single DNA molecules could transform our understanding of somatic mutagenesis and enable non-invasive studies on large-scale cohorts.
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Affiliation(s)
| | | | - Emily Mitchell
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | | | | | - Peter Ellis
- Wellcome Sanger Institute, Hinxton, UK
- Inivata, Babraham Research Campus, Cambridge, UK
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Megan Davies
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
| | - Nina F Øbro
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Krishnaa T Mahubani
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Kieren Allinson
- Cambridge Brain Bank, Division of the Human Research Tissue Bank, Addenbrooke's Hospital, Cambridge, UK
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - David G Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - Elisa Laurenti
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | | | | | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Robert J Osborne
- Wellcome Sanger Institute, Hinxton, UK.
- Biofidelity, Cambridge Science Park, Cambridge, UK.
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25
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Coorens THH, Oliver TRW, Sanghvi R, Sovio U, Cook E, Vento-Tormo R, Haniffa M, Young MD, Rahbari R, Sebire N, Campbell PJ, Charnock-Jones DS, Smith GCS, Behjati S. Inherent mosaicism and extensive mutation of human placentas. Nature 2021; 592:80-85. [PMID: 33692543 PMCID: PMC7611644 DOI: 10.1038/s41586-021-03345-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Placentas can exhibit chromosomal aberrations that are absent from the fetus1. The basis of this genetic segregation, which is known as confined placental mosaicism, remains unknown. Here we investigated the phylogeny of human placental cells as reconstructed from somatic mutations, using whole-genome sequencing of 86 bulk placental samples (with a median weight of 28 mg) and of 106 microdissections of placental tissue. We found that every bulk placental sample represents a clonal expansion that is genetically distinct, and exhibits a genomic landscape akin to that of childhood cancer in terms of mutation burden and mutational imprints. To our knowledge, unlike any other healthy human tissue studied so far, the placental genomes often contained changes in copy number. We reconstructed phylogenetic relationships between tissues from the same pregnancy, which revealed that developmental bottlenecks genetically isolate placental tissues by separating trophectodermal lineages from lineages derived from the inner cell mass. Notably, there were some cases with full segregation-within a few cell divisions of the zygote-of placental lineages and lineages derived from the inner cell mass. Such early embryonic bottlenecks may enable the normalization of zygotic aneuploidy. We observed direct evidence for this in a case of mosaic trisomic rescue. Our findings reveal extensive mutagenesis in placental tissues and suggest that mosaicism is a typical feature of placental development.
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Affiliation(s)
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Ulla Sovio
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | | | - Muzlifah Haniffa
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | | | | | - Neil Sebire
- Great Ormond Street Hospital for Children NHS Foundation Trust, NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- UCL Great Ormond Street Institute of Child Health, London, UK
| | | | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Gordon C S Smith
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Obstetrics and Gynaecology, University of Cambridge, NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK.
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26
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Custers L, Khabirova E, Coorens THH, Oliver TRW, Calandrini C, Young MD, Vieira Braga FA, Ellis P, Mamanova L, Segers H, Maat A, Kool M, Hoving EW, van den Heuvel-Eibrink MM, Nicholson J, Straathof K, Hook L, de Krijger RR, Trayers C, Allinson K, Behjati S, Drost J. Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours. Nat Commun 2021; 12:1407. [PMID: 33658498 PMCID: PMC7930245 DOI: 10.1038/s41467-021-21675-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [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: 06/01/2020] [Accepted: 02/05/2021] [Indexed: 11/08/2022] Open
Abstract
Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies.
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Affiliation(s)
- Lars Custers
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Oncode Institute, 3584CS, Utrecht, the Netherlands
| | | | - Tim H H Coorens
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Camilla Calandrini
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Oncode Institute, 3584CS, Utrecht, the Netherlands
| | - Matthew D Young
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | | | - Peter Ellis
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK
| | - Heidi Segers
- Department of Pediatric Hemato-Oncology, University Hospital Leuven, Leuven, Belgium
| | - Arie Maat
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany
| | - Eelco W Hoving
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
| | | | - James Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Karin Straathof
- UCL Great Ormond Street Hospital Institute of Child Health Biomedical Research Centre, London, WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3JH, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK
| | - Ronald R de Krijger
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands
- Department of Pathology, University Medical Center Utrecht, 3584CX, Utrecht, the Netherlands
| | - Claire Trayers
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Kieren Allinson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton, Saffron Walden, CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK.
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, the Netherlands.
- Oncode Institute, 3584CS, Utrecht, the Netherlands.
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27
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Ellis P, Moore L, Sanders MA, Butler TM, Brunner SF, Lee-Six H, Osborne R, Farr B, Coorens THH, Lawson ARJ, Cagan A, Stratton MR, Martincorena I, Campbell PJ. Reliable detection of somatic mutations in solid tissues by laser-capture microdissection and low-input DNA sequencing. Nat Protoc 2021; 16:841-871. [PMID: 33318691 DOI: 10.1038/s41596-020-00437-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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: 10/08/2019] [Accepted: 10/08/2020] [Indexed: 01/01/2023]
Abstract
Somatic mutations accumulate in healthy tissues as we age, giving rise to cancer and potentially contributing to ageing. To study somatic mutations in non-neoplastic tissues, we developed a series of protocols to sequence the genomes of small populations of cells isolated from histological sections. Here, we describe a complete workflow that combines laser-capture microdissection (LCM) with low-input genome sequencing, while circumventing the use of whole-genome amplification (WGA). The protocol is subdivided broadly into four steps: tissue processing, LCM, low-input library generation and mutation calling and filtering. The tissue processing and LCM steps are provided as general guidelines that might require tailoring based on the specific requirements of the study at hand. Our protocol for low-input library generation uses enzymatic rather than acoustic fragmentation to generate WGA-free whole-genome libraries. Finally, the mutation calling and filtering strategy has been adapted from previously published protocols to account for artifacts introduced via library creation. To date, we have used this workflow to perform targeted and whole-genome sequencing of small populations of cells (typically 100-1,000 cells) in thousands of microbiopsies from a wide range of human tissues. The low-input DNA protocol is designed to be compatible with liquid handling platforms and make use of equipment and expertise standard to any core sequencing facility. However, obtaining low-input DNA material via LCM requires specialized equipment and expertise. The entire protocol from tissue reception through whole-genome library generation can be accomplished in as little as 1 week, although 2-3 weeks would be a more typical turnaround time.
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Affiliation(s)
- Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Inivata Limited, The Glenn Berge Building, Babraham Research Campus, Babraham, UK
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Simon F Brunner
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Robert Osborne
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
- Inivata Limited, The Glenn Berge Building, Babraham Research Campus, Babraham, UK
| | - Ben Farr
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Andrew R J Lawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Mike R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK.
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28
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Abstract
Childhood tumors that occur synchronously in different anatomical sites usually represent metastatic disease. However, such tumors can be independent neoplasms. We investigated whether cases of bilateral neuroblastoma represented independent tumors in two children with pathogenic germline mutations by genotyping somatic mutations shared between tumors and blood. Our results suggested that in both children, the lineages that had given rise to the tumors had segregated within the first cell divisions of the zygote, without being preceded by a common premalignant clone. In one patient, the tumors had parallel evolution, including distinct second hits in SMARCA4, a putative predisposition gene for neuroblastoma. These findings portray cases of bilateral neuroblastoma as having independent lesions mediated by a germline predisposition. (Funded by Children with Cancer UK and Wellcome.).
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Affiliation(s)
- Tim H H Coorens
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Sarah J Farndon
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Thomas J Mitchell
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Neha Jain
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Sangjin Lee
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Michael Hubank
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Neil Sebire
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - John Anderson
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
| | - Sam Behjati
- From the Wellcome Sanger Institute, Hinxton (T.H.H.C., T.J.M., S.L., S.B.), Cambridge University Hospitals NHS Foundation Trust (S.J.F., T.J.M., S.B.) and the Departments of Surgery (T.J.M.) and Paediatrics (S.B.), University of Cambridge, Cambridge, and UCL Great Ormond Street Institute of Child Health (N.J., N.S., J.A.), Great Ormond Street Hospital for Children NHS Foundation Trust (N.J., N.S., J.A.), and the Royal Marsden NHS Foundation Trust (M.H.), London - all in the United Kingdom
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29
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Lawson ARJ, Abascal F, Coorens THH, Hooks Y, O'Neill L, Latimer C, Raine K, Sanders MA, Warren AY, Mahbubani KTA, Bareham B, Butler TM, Harvey LMR, Cagan A, Menzies A, Moore L, Colquhoun AJ, Turner W, Thomas B, Gnanapragasam V, Williams N, Rassl DM, Vöhringer H, Zumalave S, Nangalia J, Tubío JMC, Gerstung M, Saeb-Parsy K, Stratton MR, Campbell PJ, Mitchell TJ, Martincorena I. Extensive heterogeneity in somatic mutation and selection in the human bladder. Science 2020; 370:75-82. [PMID: 33004514 DOI: 10.1126/science.aba8347] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/05/2020] [Indexed: 12/17/2022]
Abstract
The extent of somatic mutation and clonal selection in the human bladder remains unknown. We sequenced 2097 bladder microbiopsies from 20 individuals using targeted (n = 1914 microbiopsies), whole-exome (n = 655), and whole-genome (n = 88) sequencing. We found widespread positive selection in 17 genes. Chromatin remodeling genes were frequently mutated, whereas mutations were absent in several major bladder cancer genes. There was extensive interindividual variation in selection, with different driver genes dominating the clonal landscape across individuals. Mutational signatures were heterogeneous across clones and individuals, which suggests differential exposure to mutagens in the urine. Evidence of APOBEC mutagenesis was found in 22% of the microbiopsies. Sequencing multiple microbiopsies from five patients with bladder cancer enabled comparisons with cancer-free individuals and across histological features. This study reveals a rich landscape of mutational processes and selection in normal urothelium with large heterogeneity across clones and individuals.
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Affiliation(s)
- Andrew R J Lawson
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Federico Abascal
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Laura O'Neill
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Calli Latimer
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Keiran Raine
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam 3015 GD, Netherlands
| | - Anne Y Warren
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Krishnaa T A Mahbubani
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Bethany Bareham
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Timothy M Butler
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Luke M R Harvey
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Alex Cagan
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Andrew Menzies
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Luiza Moore
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Alexandra J Colquhoun
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - William Turner
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Benjamin Thomas
- The Royal Melbourne Hospital, Parkville, Victoria 3010, Australia
- Department of Surgery, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Vincent Gnanapragasam
- Academic Urology Group, Department of Surgery and Oncology, University of Cambridge, Cambridge CB2 0QQ, UK
- Cambridge Urology Translational Research and Clinical Trials Office, University of Cambridge CB2 0QQ, UK
| | - Nicholas Williams
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Doris M Rassl
- Department of Pathology, Royal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0AY, UK
| | - Harald Vöhringer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Sonia Zumalave
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
| | - Jyoti Nangalia
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - José M C Tubío
- Mobile Genomes and Disease, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela 15706, Spain
- The Biomedical Research Centre (CINBIO), University of Vigo, Vigo 36310, Spain
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton CB10 1SD, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Urology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Iñigo Martincorena
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
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30
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Patchett AL, Coorens THH, Darby J, Wilson R, McKay MJ, Kamath KS, Rubin A, Wakefield M, Mcintosh L, Mangiola S, Pye RJ, Flies AS, Corcoran LM, Lyons AB, Woods GM, Murchison EP, Papenfuss AT, Tovar C. Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii). Cell Mol Life Sci 2020; 77:1847-1858. [PMID: 31375869 PMCID: PMC11104932 DOI: 10.1007/s00018-019-03259-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/25/2019] [Accepted: 07/26/2019] [Indexed: 01/01/2023]
Abstract
Devil facial tumour disease (DFTD) comprises two genetically distinct transmissible cancers (DFT1 and DFT2) endangering the survival of the Tasmanian devil (Sarcophilus harrisii) in the wild. DFT1 first arose from a cell of the Schwann cell lineage; however, the tissue-of-origin of the recently discovered DFT2 cancer is unknown. In this study, we compared the transcriptome and proteome of DFT2 tumours to DFT1 and normal Tasmanian devil tissues to determine the tissue-of-origin of the DFT2 cancer. Our findings demonstrate that DFT2 expresses a range of Schwann cell markers and exhibits expression patterns consistent with a similar origin to the DFT1 cancer. Furthermore, DFT2 cells express genes associated with the repair response to peripheral nerve damage. These findings suggest that devils may be predisposed to transmissible cancers of Schwann cell origin. The combined effect of factors such as frequent nerve damage from biting, Schwann cell plasticity and low genetic diversity may allow these cancers to develop on rare occasions. The emergence of two independent transmissible cancers from the same tissue in the Tasmanian devil presents an unprecedented opportunity to gain insight into cancer development, evolution and immune evasion in mammalian species.
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Affiliation(s)
- Amanda L Patchett
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia.
| | - Tim H H Coorens
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Jocelyn Darby
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS, 7001, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Karthik S Kamath
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Alan Rubin
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Matthew Wakefield
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Lachlan Mcintosh
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Stefano Mangiola
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Surgery, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Ruth J Pye
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Andrew S Flies
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | - Lynn M Corcoran
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - A Bruce Lyons
- School of Medicine, University of Tasmania, Hobart, TAS, 7000, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
| | | | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3000, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3000, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Cesar Tovar
- Menzies Institute for Medical Research, University of Tasmania, 17 Liverpool Street, Hobart, TAS, 7000, Australia
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31
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Moore L, Leongamornlert D, Coorens THH, Sanders MA, Ellis P, Dentro SC, Dawson KJ, Butler T, Rahbari R, Mitchell TJ, Maura F, Nangalia J, Tarpey PS, Brunner SF, Lee-Six H, Hooks Y, Moody S, Mahbubani KT, Jimenez-Linan M, Brosens JJ, Iacobuzio-Donahue CA, Martincorena I, Saeb-Parsy K, Campbell PJ, Stratton MR. The mutational landscape of normal human endometrial epithelium. Nature 2020; 580:640-646. [PMID: 32350471 DOI: 10.1038/s41586-020-2214-z] [Citation(s) in RCA: 260] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/20/2020] [Indexed: 12/13/2022]
Abstract
All normal somatic cells are thought to acquire mutations, but understanding of the rates, patterns, causes and consequences of somatic mutations in normal cells is limited. The uterine endometrium adopts multiple physiological states over a lifetime and is lined by a gland-forming epithelium1,2. Here, using whole-genome sequencing, we show that normal human endometrial glands are clonal cell populations with total mutation burdens that increase at about 29 base substitutions per year and that are many-fold lower than those of endometrial cancers. Normal endometrial glands frequently carry 'driver' mutations in cancer genes, the burden of which increases with age and decreases with parity. Cell clones with drivers often originate during the first decades of life and subsequently progressively colonize the epithelial lining of the endometrium. Our results show that mutational landscapes differ markedly between normal tissues-perhaps shaped by differences in their structure and physiology-and indicate that the procession of neoplastic change that leads to endometrial cancer is initiated early in life.
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Affiliation(s)
- Luiza Moore
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Daniel Leongamornlert
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Tim H H Coorens
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Mathijs A Sanders
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter Ellis
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
- Inivata Ltd, Cambridge, UK
| | - Stefan C Dentro
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK
| | - Kevin J Dawson
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Tim Butler
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Raheleh Rahbari
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Thomas J Mitchell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Francesco Maura
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jyoti Nangalia
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Patrick S Tarpey
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Simon F Brunner
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Henry Lee-Six
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Yvette Hooks
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Sarah Moody
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mercedes Jimenez-Linan
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Jan J Brosens
- Tommy's National Miscarriage Research Centre, Warwick Medical School, University of Warwick, Coventry, UK
| | - Christine A Iacobuzio-Donahue
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Inigo Martincorena
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Peter J Campbell
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK
| | - Michael R Stratton
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Cambridge, UK.
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32
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Coorens THH, Treger TD, Al-Saadi R, Moore L, Tran MGB, Mitchell TJ, Tugnait S, Thevanesan C, Young MD, Oliver TRW, Oostveen M, Collord G, Tarpey PS, Cagan A, Hooks Y, Brougham M, Reynolds BC, Barone G, Anderson J, Jorgensen M, Burke GAA, Visser J, Nicholson JC, Smeulders N, Mushtaq I, Stewart GD, Campbell PJ, Wedge DC, Martincorena I, Rampling D, Hook L, Warren AY, Coleman N, Chowdhury T, Sebire N, Drost J, Saeb-Parsy K, Stratton MR, Straathof K, Pritchard-Jones K, Behjati S. Embryonal precursors of Wilms tumor. Science 2019; 366:1247-1251. [PMID: 31806814 PMCID: PMC6914378 DOI: 10.1126/science.aax1323] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [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: 02/25/2019] [Revised: 07/04/2019] [Accepted: 11/06/2019] [Indexed: 12/27/2022]
Abstract
Adult cancers often arise from premalignant clonal expansions. Whether the same is true of childhood tumors has been unclear. To investigate whether Wilms tumor (nephroblastoma; a childhood kidney cancer) develops from a premalignant background, we examined the phylogenetic relationship between tumors and corresponding normal tissues. In 14 of 23 cases studied (61%), we found premalignant clonal expansions in morphologically normal kidney tissues that preceded tumor development. These clonal expansions were defined by somatic mutations shared between tumor and normal tissues but absent from blood cells. We also found hypermethylation of the H19 locus, a known driver of Wilms tumor development, in 58% of the expansions. Phylogenetic analyses of bilateral tumors indicated that clonal expansions can evolve before the divergence of left and right kidney primordia. These findings reveal embryonal precursors from which unilateral and multifocal cancers develop.
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Affiliation(s)
| | - Taryn D Treger
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Reem Al-Saadi
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Luiza Moore
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Maxine G B Tran
- UCL Division of Surgery and Interventional Science, Royal Free Hospital, London NW3 2PS, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London NW3 2PS, UK
| | - Thomas J Mitchell
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Suzanne Tugnait
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
| | | | | | - Thomas R W Oliver
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Minou Oostveen
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Grace Collord
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Patrick S Tarpey
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Alex Cagan
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
| | | | - Mark Brougham
- Department of Haematology and Oncology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK
| | - Ben C Reynolds
- Department of Paediatric Nephrology, Royal Hospital for Children, Glasgow G51 4TF, UK
| | - Giuseppe Barone
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - John Anderson
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Mette Jorgensen
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - G A Amos Burke
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Johannes Visser
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - James C Nicholson
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Naima Smeulders
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Imran Mushtaq
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Grant D Stewart
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - David C Wedge
- Big Data Institute, University of Oxford, Oxford OX3 7LF, UK
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | | | - Dyanne Rampling
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Liz Hook
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Anne Y Warren
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Tanzina Chowdhury
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Neil Sebire
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Jarno Drost
- Princess Máxima Center for Pediatric Oncology, Oncode Institute, 3584 CS Utrecht, Netherlands
| | - Kourosh Saeb-Parsy
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | | | - Karin Straathof
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Kathy Pritchard-Jones
- UCL Great Ormond Street Institute of Child Health, London WC1N 1EH, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Sam Behjati
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK.
- Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
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33
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Lee-Six H, Olafsson S, Ellis P, Osborne RJ, Sanders MA, Moore L, Georgakopoulos N, Torrente F, Noorani A, Goddard M, Robinson P, Coorens THH, O'Neill L, Alder C, Wang J, Fitzgerald RC, Zilbauer M, Coleman N, Saeb-Parsy K, Martincorena I, Campbell PJ, Stratton MR. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 2019; 574:532-537. [PMID: 31645730 DOI: 10.1038/s41586-019-1672-7] [Citation(s) in RCA: 364] [Impact Index Per Article: 72.8] [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: 09/11/2018] [Accepted: 09/11/2019] [Indexed: 02/06/2023]
Abstract
The colorectal adenoma-carcinoma sequence has provided a paradigmatic framework for understanding the successive somatic genetic changes and consequent clonal expansions that lead to cancer1. However, our understanding of the earliest phases of colorectal neoplastic changes-which may occur in morphologically normal tissue-is comparatively limited, as for most cancer types. Here we use whole-genome sequencing to analyse hundreds of normal crypts from 42 individuals. Signatures of multiple mutational processes were revealed; some of these were ubiquitous and continuous, whereas others were only found in some individuals, in some crypts or during certain periods of life. Probable driver mutations were present in around 1% of normal colorectal crypts in middle-aged individuals, indicating that adenomas and carcinomas are rare outcomes of a pervasive process of neoplastic change across morphologically normal colorectal epithelium. Colorectal cancers exhibit substantially increased mutational burdens relative to normal cells. Sequencing normal colorectal cells provides quantitative insights into the genomic and clonal evolution of cancer.
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Affiliation(s)
| | | | | | | | - Mathijs A Sanders
- Wellcome Sanger Institute, Hinxton, UK
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Franco Torrente
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
| | - Ayesha Noorani
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Martin Goddard
- Department of Pathology, Papworth Hospital NHS Trust, Cambridge, UK
| | | | | | | | | | | | - Rebecca C Fitzgerald
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Addenbrooke's Hospital, Cambridge, UK
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Nicholas Coleman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge NIHR Biomedical Research Centre, Cambridge Biomedical Campus, Cambridge, UK
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Stammnitz MR, Coorens THH, Gori KC, Hayes D, Fu B, Wang J, Martin-Herranz DE, Alexandrov LB, Baez-Ortega A, Barthorpe S, Beck A, Giordano F, Knowles GW, Kwon YM, Hall G, Price S, Pye RJ, Tubio JMC, Siddle HVT, Sohal SS, Woods GM, McDermott U, Yang F, Garnett MJ, Ning Z, Murchison EP. The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils. Cancer Cell 2018; 33:607-619.e15. [PMID: 29634948 PMCID: PMC5896245 DOI: 10.1016/j.ccell.2018.03.013] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/23/2018] [Accepted: 03/11/2018] [Indexed: 02/07/2023]
Abstract
Transmissible cancers are clonal lineages that spread through populations via contagious cancer cells. Although rare in nature, two facial tumor clones affect Tasmanian devils. Here we perform comparative genetic and functional characterization of these lineages. The two cancers have similar patterns of mutation and show no evidence of exposure to exogenous mutagens or viruses. Genes encoding PDGF receptors have copy number gains and are present on extrachromosomal double minutes. Drug screening indicates causative roles for receptor tyrosine kinases and sensitivity to inhibitors of DNA repair. Y chromosome loss from a male clone infecting a female host suggests immunoediting. These results imply that Tasmanian devils may have inherent susceptibility to transmissible cancers and present a suite of therapeutic compounds for use in conservation.
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Affiliation(s)
- Maximilian R Stammnitz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Tim H H Coorens
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Kevin C Gori
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Dane Hayes
- Mount Pleasant Laboratories, Tasmanian Department of Primary Industries, Parks, Water and the Environment, Prospect, TAS 7250, Australia; School of Health Sciences, Faculty of Health, University of Tasmania, Launceston, TAS 7248, Australia
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Jinhong Wang
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Daniel E Martin-Herranz
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Ludmil B Alexandrov
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Adrian Baez-Ortega
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Syd Barthorpe
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Alexandra Beck
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Francesca Giordano
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Graeme W Knowles
- Mount Pleasant Laboratories, Tasmanian Department of Primary Industries, Parks, Water and the Environment, Prospect, TAS 7250, Australia
| | - Young Mi Kwon
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - George Hall
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Stacey Price
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Ruth J Pye
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Jose M C Tubio
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Hannah V T Siddle
- Centre for Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Sukhwinder Singh Sohal
- School of Health Sciences, Faculty of Health, University of Tasmania, Launceston, TAS 7248, Australia
| | - Gregory M Woods
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
| | - Ultan McDermott
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Mathew J Garnett
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Zemin Ning
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Elizabeth P Murchison
- Transmissible Cancer Group, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK.
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