1
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Riew TR, Kim YS. Mutational Landscapes of Normal Skin and Their Potential Implications in the Development of Skin Cancer: A Comprehensive Narrative Review. J Clin Med 2024; 13:4815. [PMID: 39200957 PMCID: PMC11355262 DOI: 10.3390/jcm13164815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024] Open
Abstract
Recent evidence suggests that physiologically normal skin harbors pervasive mutant clones with cancer drivers. Normal skin has the highest burden of somatic mutations due to persistent ultraviolet exposure throughout life. The mutation burden exponentially increases with age and is further modified by skin site, sun-damage history, and skin phototype. Driver gene profiles in normal skin are similar to those in cutaneous squamous cell carcinoma where NOTCH family, FAT family, and TP53 are consistently reported, while other reported profiles include PPM1D, KMT2D, ASXL1, and RBM10. Normal skin seldom harbors canonical hotspot mutations with therapeutic relevance. The pathologic role of mutant clones with cancer drivers in normal skin is classically considered precursors for skin cancer; however, recent evidence also suggests their putative cancer-protective role. Copy number alterations and other structural variants are rare in normal skin with loss in 9q region encompassing NOTCH1 being the most common. Study methodologies should be carefully designed to obtain an adequate number of cells for sequencing, and a comparable number of cells and read depth across samples. In conclusion, this review provides mutational landscapes of normal skin and discusses their potential implications in the development of skin cancer, highlighting the role of driver genes in early malignant progression.
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Affiliation(s)
- Tae-Ryong Riew
- Department of Anatomy, Catholic Neuroscience Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Yoon-Seob Kim
- Department of Dermatology, Bucheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
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2
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West J, Robertson-Tessi M, Anderson ARA. Agent-based methods facilitate integrative science in cancer. Trends Cell Biol 2023; 33:300-311. [PMID: 36404257 PMCID: PMC10918696 DOI: 10.1016/j.tcb.2022.10.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/25/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022]
Abstract
In this opinion, we highlight agent-based modeling as a key tool for exploration of cell-cell and cell-environment interactions that drive cancer progression, therapeutic resistance, and metastasis. These biological phenomena are particularly suited to be captured at the cell-scale resolution possible only within agent-based or individual-based mathematical models. These modeling approaches complement experimental work (in vitro and in vivo systems) through parameterization and data extrapolation but also feed forward to drive new experiments that test model-generated predictions.
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Affiliation(s)
- Jeffrey West
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Mark Robertson-Tessi
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Alexander R A Anderson
- Integrated Mathematical Oncology Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA.
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3
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Homeostasis limits keratinocyte evolution. Proc Natl Acad Sci U S A 2022; 119:e2006487119. [PMID: 35998218 PMCID: PMC9436311 DOI: 10.1073/pnas.2006487119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Human skin is riddled with mutations creating subclones of variable sizes. Some of these mutations are driver mutations, implicated in cancer development and progression, that appear to be under positive selection due to their relative sizes. We show how these driver and nondriver “passenger” mutations encode their history of division and loss within the tissue using a simple model combined with realistic mutation tracking. Using a three-dimensional in silico homeostatic epidermis model, we reveal that many mutations likely lack functional heterogeneity and are, instead, simply those that arise earlier in life within the basal layer. We use our model to reveal how functional differences conveyed by driver mutations could lead to a persistence phenotype while maintaining homeostasis. Recent studies have revealed that normal human tissues accumulate many somatic mutations. In particular, human skin is riddled with mutations, with multiple subclones of variable sizes. Driver mutations are frequent and tend to have larger subclone sizes, suggesting selection. To begin to understand the histories encoded by these complex somatic mutations, we incorporated genomes into a simple agent-based skin-cell model whose prime directive is homeostasis. In this model, stem-cell survival is random and dependent on proximity to the basement membrane. This simple homeostatic skin model recapitulates the observed log-linear distributions of somatic mutations, where most mutations are found in increasingly smaller subclones that are typically lost with time. Hence, neutral mutations are “passengers” whose fates depend on the random survival of their stem cells, where a rarer larger subclone reflects the survival and spread of mutations acquired earlier in life. The model can also maintain homeostasis and accumulate more frequent and larger driver subclones if these mutations (NOTCH1 and TP53) confer relatively higher persistence in normal skin or during tissue damage (sunlight). Therefore, a relatively simple model of epithelial turnover indicates how observed passenger and driver somatic mutations could accumulate without violating the prime directive of homeostasis in normal human tissues.
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4
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Fowler JC, Jones PH. Somatic Mutation: What Shapes the Mutational Landscape of Normal Epithelia? Cancer Discov 2022; 12:1642-1655. [PMID: 35397477 PMCID: PMC7613026 DOI: 10.1158/2159-8290.cd-22-0145] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 04/01/2022] [Indexed: 11/16/2022]
Abstract
Epithelial stem cells accumulate mutations throughout life. Some of these mutants increase competitive fitness and may form clones that colonize the stem cell niche and persist to acquire further genome alterations. After a transient expansion, mutant stem cells must revert to homeostatic behavior so normal tissue architecture is maintained. Some positively selected mutants may promote cancer development, whereas others inhibit carcinogenesis. Factors that shape the mutational landscape include wild-type and mutant stem cell dynamics, competition for the niche, and environmental exposures. Understanding these processes may give new insight into the basis of cancer risk and opportunities for cancer prevention. SIGNIFICANCE Recent advances in sequencing have found somatic mutations in all epithelial tissues studied to date. Here we review how the mutational landscape of normal epithelia is shaped by clonal competition within the stem cell niche combined with environmental exposures. Some of the selected mutant genes are oncogenic, whereas others may be inhibitory of transformation. Discoveries in this area leave many open questions, such as the definition of cancer driver genes, the mechanisms by which tissues constrain a high proportion of oncogenic mutant cells, and whether clonal fitness can be modulated to decrease cancer risk.
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Affiliation(s)
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton CB10 1SA, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
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5
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Gabbutt C, Wright NA, Baker A, Shibata D, Graham TA. Lineage tracing in human tissues. J Pathol 2022; 257:501-512. [PMID: 35415852 PMCID: PMC9253082 DOI: 10.1002/path.5911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/21/2022] [Accepted: 04/09/2022] [Indexed: 11/11/2022]
Abstract
The dynamical process of cell division that underpins homeostasis in the human body cannot be directly observed in vivo, but instead is measurable from the pattern of somatic genetic or epigenetic mutations that accrue in tissues over an individual's lifetime. Because somatic mutations are heritable, they serve as natural lineage tracing markers that delineate clonal expansions. Mathematical analysis of the distribution of somatic clone sizes gives a quantitative readout of the rates of cell birth, death, and replacement. In this review we explore the broad range of somatic mutation types that have been used for lineage tracing in human tissues, introduce the mathematical concepts used to infer dynamical information from these clone size data, and discuss the insights of this lineage tracing approach for our understanding of homeostasis and cancer development. We use the human colon as a particularly instructive exemplar tissue. There is a rich history of human somatic cell dynamics surreptitiously written into the cell genomes that is being uncovered by advances in sequencing and careful mathematical analysis lineage of tracing data. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Calum Gabbutt
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Evolution and CancerInstitute of Cancer ResearchSuttonUK
- London Interdisciplinary Doctoral Training Programme (LIDo)LondonUK
| | - Nicholas A Wright
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Ann‐Marie Baker
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Evolution and CancerInstitute of Cancer ResearchSuttonUK
| | - Darryl Shibata
- Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Trevor A Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Evolution and CancerInstitute of Cancer ResearchSuttonUK
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6
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Colom B, Herms A, Hall MWJ, Dentro SC, King C, Sood RK, Alcolea MP, Piedrafita G, Fernandez-Antoran D, Ong SH, Fowler JC, Mahbubani KT, Saeb-Parsy K, Gerstung M, Hall BA, Jones PH. Mutant clones in normal epithelium outcompete and eliminate emerging tumours. Nature 2021; 598:510-514. [PMID: 34646013 PMCID: PMC7612642 DOI: 10.1038/s41586-021-03965-7] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 08/26/2021] [Indexed: 02/08/2023]
Abstract
Human epithelial tissues accumulate cancer-driver mutations with age1-9, yet tumour formation remains rare. The positive selection of these mutations suggests that they alter the behaviour and fitness of proliferating cells10-12. Thus, normal adult tissues become a patchwork of mutant clones competing for space and survival, with the fittest clones expanding by eliminating their less competitive neighbours11-14. However, little is known about how such dynamic competition in normal epithelia influences early tumorigenesis. Here we show that the majority of newly formed oesophageal tumours are eliminated through competition with mutant clones in the adjacent normal epithelium. We followed the fate of nascent, microscopic, pre-malignant tumours in a mouse model of oesophageal carcinogenesis and found that most were rapidly lost with no indication of tumour cell death, decreased proliferation or an anti-tumour immune response. However, deep sequencing of ten-day-old and one-year-old tumours showed evidence of selection on the surviving neoplasms. Induction of highly competitive clones in transgenic mice increased early tumour removal, whereas pharmacological inhibition of clonal competition reduced tumour loss. These results support a model in which survival of early neoplasms depends on their competitive fitness relative to that of mutant clones in the surrounding normal tissue. Mutant clones in normal epithelium have an unexpected anti-tumorigenic role in purging early tumours through cell competition, thereby preserving tissue integrity.
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Affiliation(s)
- B Colom
- Wellcome Sanger Institute, Hinxton, UK
| | - A Herms
- Wellcome Sanger Institute, Hinxton, UK
| | - M W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK
| | - S C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - C King
- Wellcome Sanger Institute, Hinxton, UK
| | - R K Sood
- Wellcome Sanger Institute, Hinxton, UK
| | - M P Alcolea
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK
| | - G Piedrafita
- Wellcome Sanger Institute, Hinxton, UK
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - D Fernandez-Antoran
- Wellcome Sanger Institute, Hinxton, UK
- Wellcome Trust-Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - S H Ong
- Wellcome Sanger Institute, Hinxton, UK
| | | | - K T Mahbubani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - K Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - M Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - B A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - P H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK.
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7
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Kostiou V, Hall MWJ, Jones PH, Hall BA. Simulations reveal that different responses to cell crowding determine the expansion of p53 and Notch mutant clones in squamous epithelia. J R Soc Interface 2021; 18:20210607. [PMID: 34637643 PMCID: PMC8510697 DOI: 10.1098/rsif.2021.0607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 12/31/2022] Open
Abstract
During ageing, normal epithelial tissues progressively accumulate clones carrying mutations that increase mutant cell fitness above that of wild-type cells. Such mutants spread widely through the tissues, yet despite this cellular homeostasis and functional integrity of the epithelia are maintained. Two of the genes most commonly mutated in human skin and oesophagus are p53 and Notch1, both of which are also recurrently mutated in cancers of these tissues. From observations taken in human and mouse epithelia, we find that clones carrying p53 and Notch pathway mutations have different clone dynamics which can be explained by their different responses to local cell crowding. p53 mutant clone growth in mouse epidermis approximates a logistic curve, but feedbacks responding to local crowding are required to maintain tissue homeostasis. We go on to show that the observed ability of Notch pathway mutant cells to displace the wild-type population in the mouse oesophageal epithelium reflects a local density feedback that affects both mutant and wild-type cells equally. We then show how these distinct feedbacks are consistent with the distribution of mutations observed in human datasets and are suggestive of a putative mechanism to constrain these cancer-associated mutants.
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Affiliation(s)
- Vasiliki Kostiou
- Department of medical physics and biomedical engineering, UCL, Gower Street, London WC1E 6BT, UK
| | - Michael W. J. Hall
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Philip H. Jones
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Benjamin A. Hall
- Department of medical physics and biomedical engineering, UCL, Gower Street, London WC1E 6BT, UK
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8
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Pereira D, Sequeira I. A Scarless Healing Tale: Comparing Homeostasis and Wound Healing of Oral Mucosa With Skin and Oesophagus. Front Cell Dev Biol 2021; 9:682143. [PMID: 34381771 PMCID: PMC8350526 DOI: 10.3389/fcell.2021.682143] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Epithelial tissues are the most rapidly dividing tissues in the body, holding a natural ability for renewal and regeneration. This ability is crucial for survival as epithelia are essential to provide the ultimate barrier against the external environment, protecting the underlying tissues. Tissue stem and progenitor cells are responsible for self-renewal and repair during homeostasis and following injury. Upon wounding, epithelial tissues undergo different phases of haemostasis, inflammation, proliferation and remodelling, often resulting in fibrosis and scarring. In this review, we explore the phenotypic differences between the skin, the oesophagus and the oral mucosa. We discuss the plasticity of these epithelial stem cells and contribution of different fibroblast subpopulations for tissue regeneration and wound healing. While these epithelial tissues share global mechanisms of stem cell behaviour for tissue renewal and regeneration, the oral mucosa is known for its outstanding healing potential with minimal scarring. We aim to provide an updated review of recent studies that combined cell therapy with bioengineering exporting the unique scarless properties of the oral mucosa to improve skin and oesophageal wound healing and to reduce fibrotic tissue formation. These advances open new avenues toward the ultimate goal of achieving scarless wound healing.
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Affiliation(s)
| | - Inês Sequeira
- Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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9
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Fowler JC, King C, Bryant C, Hall MWJ, Sood R, Ong SH, Earp E, Fernandez-Antoran D, Koeppel J, Dentro SC, Shorthouse D, Durrani A, Fife K, Rytina E, Milne D, Roshan A, Mahububani K, Saeb-Parsy K, Hall BA, Gerstung M, Jones PH. Selection of Oncogenic Mutant Clones in Normal Human Skin Varies with Body Site. Cancer Discov 2021; 11:340-361. [PMID: 33087317 PMCID: PMC7116717 DOI: 10.1158/2159-8290.cd-20-1092] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/24/2020] [Accepted: 10/15/2020] [Indexed: 11/16/2022]
Abstract
Skin cancer risk varies substantially across the body, yet how this relates to the mutations found in normal skin is unknown. Here we mapped mutant clones in skin from high- and low-risk sites. The density of mutations varied by location. The prevalence of NOTCH1 and FAT1 mutations in forearm, trunk, and leg skin was similar to that in keratinocyte cancers. Most mutations were caused by ultraviolet light, but mutational signature analysis suggested differences in DNA-repair processes between sites. Eleven mutant genes were under positive selection, with TP53 preferentially selected in the head and FAT1 in the leg. Fine-scale mapping revealed 10% of clones had copy-number alterations. Analysis of hair follicles showed mutations in the upper follicle resembled adjacent skin, but the lower follicle was sparsely mutated. Normal skin is a dense patchwork of mutant clones arising from competitive selection that varies by location. SIGNIFICANCE: Mapping mutant clones across the body reveals normal skin is a dense patchwork of mutant cells. The variation in cancer risk between sites substantially exceeds that in mutant clone density. More generally, mutant genes cannot be assigned as cancer drivers until their prevalence in normal tissue is known.See related commentary by De Dominici and DeGregori, p. 227.This article is highlighted in the In This Issue feature, p. 211.
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Affiliation(s)
| | | | | | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, United Kingdom
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Roshan Sood
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Eleanor Earp
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
| | - David Shorthouse
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Amer Durrani
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Fife
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Edward Rytina
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Doreen Milne
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Amit Roshan
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Krishnaa Mahububani
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Cambridge, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, Cambridge, United Kingdom
| | - Benjamin A Hall
- Department of Medical Physics and Biomedical Engineering, University College London, London, United Kingdom
| | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, United Kingdom
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, United Kingdom.
- MRC Cancer Unit, University of Cambridge, Hutchison-MRC Research Centre, Cambridge Biomedical Campus, Cambridge, United Kingdom
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10
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Colom B, Alcolea MP, Piedrafita G, Hall MWJ, Wabik A, Dentro SC, Fowler JC, Herms A, King C, Ong SH, Sood RK, Gerstung M, Martincorena I, Hall BA, Jones PH. Spatial competition shapes the dynamic mutational landscape of normal esophageal epithelium. Nat Genet 2020; 52:604-614. [PMID: 32424351 PMCID: PMC7116672 DOI: 10.1038/s41588-020-0624-3] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/07/2020] [Indexed: 12/29/2022]
Abstract
During aging, progenitor cells acquire mutations, which may generate clones that colonize the surrounding tissue. By middle age, normal human tissues, including the esophageal epithelium (EE), become a patchwork of mutant clones. Despite their relevance for understanding aging and cancer, the processes that underpin mutational selection in normal tissues remain poorly understood. Here, we investigated this issue in the esophageal epithelium of mutagen-treated mice. Deep sequencing identified numerous mutant clones with multiple genes under positive selection, including Notch1, Notch2 and Trp53, which are also selected in human esophageal epithelium. Transgenic lineage tracing revealed strong clonal competition that evolved over time. Clone dynamics were consistent with a simple model in which the proliferative advantage conferred by positively selected mutations depends on the nature of the neighboring cells. When clones with similar competitive fitness collide, mutant cell fate reverts towards homeostasis, a constraint that explains how selection operates in normal-appearing epithelium.
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Affiliation(s)
| | - Maria P Alcolea
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Oncology, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | - Gabriel Piedrafita
- Wellcome Sanger Institute, Hinxton, UK
- Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Michael W J Hall
- Wellcome Sanger Institute, Hinxton, UK
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Stefan C Dentro
- Wellcome Sanger Institute, Hinxton, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | | | | | | | | | - Moritz Gerstung
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, UK.
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Cambridge Biomedical Campus, Cambridge, UK.
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11
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Williams MJ, Zapata L, Werner B, Barnes CP, Sottoriva A, Graham TA. Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios. eLife 2020; 9:e48714. [PMID: 32223898 PMCID: PMC7105384 DOI: 10.7554/elife.48714] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/09/2020] [Indexed: 12/22/2022] Open
Abstract
The distribution of fitness effects (DFE) defines how new mutations spread through an evolving population. The ratio of non-synonymous to synonymous mutations (dN/dS) has become a popular method to detect selection in somatic cells. However the link, in somatic evolution, between dN/dS values and fitness coefficients is missing. Here we present a quantitative model of somatic evolutionary dynamics that determines the selective coefficients of individual driver mutations from dN/dS estimates. We then measure the DFE for somatic mutant clones in ostensibly normal oesophagus and skin. We reveal a broad distribution of fitness effects, with the largest fitness increases found for TP53 and NOTCH1 mutants (proliferative bias 1-5%). This study provides the theoretical link between dN/dS values and selective coefficients in somatic evolution, and measures the DFE of mutations in human tissues.
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Affiliation(s)
- Marc J Williams
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Luis Zapata
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Benjamin Werner
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
| | - Chris P Barnes
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Andrea Sottoriva
- Evolutionary Genomics and Modelling Lab, Centre for Evolution and Cancer, The Institute of Cancer ResearchLondonUnited Kingdom
| | - Trevor A Graham
- Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of LondonLondonUnited Kingdom
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12
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Fernandez-Antoran D, Piedrafita G, Murai K, Ong SH, Herms A, Frezza C, Jones PH. Outcompeting p53-Mutant Cells in the Normal Esophagus by Redox Manipulation. Cell Stem Cell 2019; 25:329-341.e6. [PMID: 31327664 PMCID: PMC6739485 DOI: 10.1016/j.stem.2019.06.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 05/14/2019] [Accepted: 06/14/2019] [Indexed: 12/20/2022]
Abstract
As humans age, normal tissues, such as the esophageal epithelium, become a patchwork of mutant clones. Some mutations are under positive selection, conferring a competitive advantage over wild-type cells. We speculated that altering the selective pressure on mutant cell populations may cause them to expand or contract. We tested this hypothesis by examining the effect of oxidative stress from low-dose ionizing radiation (LDIR) on wild-type and p53 mutant cells in the transgenic mouse esophagus. We found that LDIR drives wild-type cells to stop proliferating and differentiate. p53 mutant cells are insensitive to LDIR and outcompete wild-type cells following exposure. Remarkably, combining antioxidant treatment and LDIR reverses this effect, promoting wild-type cell proliferation and p53 mutant differentiation, reducing the p53 mutant population. Thus, p53-mutant cells can be depleted from the normal esophagus by redox manipulation, showing that external interventions may be used to alter the mutational landscape of an aging tissue.
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Affiliation(s)
| | | | - Kasumi Murai
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Swee Hoe Ong
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Albert Herms
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Christian Frezza
- MRC Cancer Unit, University of Cambridge, Box 196, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK
| | - Philip H Jones
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; MRC Cancer Unit, University of Cambridge, Box 196, Cambridge Biomedical Campus, Cambridge CB2 0XZ, UK.
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