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Neagu AN, Whitham D, Bruno P, Arshad A, Seymour L, Morrissiey H, Hukovic AI, Darie CC. Onco-Breastomics: An Eco-Evo-Devo Holistic Approach. Int J Mol Sci 2024; 25:1628. [PMID: 38338903 PMCID: PMC10855488 DOI: 10.3390/ijms25031628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/21/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Known as a diverse collection of neoplastic diseases, breast cancer (BC) can be hyperbolically characterized as a dynamic pseudo-organ, a living organism able to build a complex, open, hierarchically organized, self-sustainable, and self-renewable tumor system, a population, a species, a local community, a biocenosis, or an evolving dynamical ecosystem (i.e., immune or metabolic ecosystem) that emphasizes both developmental continuity and spatio-temporal change. Moreover, a cancer cell community, also known as an oncobiota, has been described as non-sexually reproducing species, as well as a migratory or invasive species that expresses intelligent behavior, or an endangered or parasite species that fights to survive, to optimize its features inside the host's ecosystem, or that is able to exploit or to disrupt its host circadian cycle for improving the own proliferation and spreading. BC tumorigenesis has also been compared with the early embryo and placenta development that may suggest new strategies for research and therapy. Furthermore, BC has also been characterized as an environmental disease or as an ecological disorder. Many mechanisms of cancer progression have been explained by principles of ecology, developmental biology, and evolutionary paradigms. Many authors have discussed ecological, developmental, and evolutionary strategies for more successful anti-cancer therapies, or for understanding the ecological, developmental, and evolutionary bases of BC exploitable vulnerabilities. Herein, we used the integrated framework of three well known ecological theories: the Bronfenbrenner's theory of human development, the Vannote's River Continuum Concept (RCC), and the Ecological Evolutionary Developmental Biology (Eco-Evo-Devo) theory, to explain and understand several eco-evo-devo-based principles that govern BC progression. Multi-omics fields, taken together as onco-breastomics, offer better opportunities to integrate, analyze, and interpret large amounts of complex heterogeneous data, such as various and big-omics data obtained by multiple investigative modalities, for understanding the eco-evo-devo-based principles that drive BC progression and treatment. These integrative eco-evo-devo theories can help clinicians better diagnose and treat BC, for example, by using non-invasive biomarkers in liquid-biopsies that have emerged from integrated omics-based data that accurately reflect the biomolecular landscape of the primary tumor in order to avoid mutilating preventive surgery, like bilateral mastectomy. From the perspective of preventive, personalized, and participatory medicine, these hypotheses may help patients to think about this disease as a process governed by natural rules, to understand the possible causes of the disease, and to gain control on their own health.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of Iași, Carol I bvd. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Aneeta Arshad
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Logan Seymour
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Angiolina I. Hukovic
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
| | - Costel C. Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA; (D.W.); (P.B.); (A.A.); (L.S.); (H.M.); (A.I.H.)
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Freund F, Kerdoncuff E, Matuszewski S, Lapierre M, Hildebrandt M, Jensen JD, Ferretti L, Lambert A, Sackton TB, Achaz G. Interpreting the pervasive observation of U-shaped Site Frequency Spectra. PLoS Genet 2023; 19:e1010677. [PMID: 36952570 PMCID: PMC10072462 DOI: 10.1371/journal.pgen.1010677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 04/04/2023] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
The standard neutral model of molecular evolution has traditionally been used as the null model for population genomics. We gathered a collection of 45 genome-wide site frequency spectra from a diverse set of species, most of which display an excess of low and high frequency variants compared to the expectation of the standard neutral model, resulting in U-shaped spectra. We show that multiple merger coalescent models often provide a better fit to these observations than the standard Kingman coalescent. Hence, in many circumstances these under-utilized models may serve as the more appropriate reference for genomic analyses. We further discuss the underlying evolutionary processes that may result in the widespread U-shape of frequency spectra.
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Affiliation(s)
- Fabian Freund
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Elise Kerdoncuff
- Department of Genetics, University of California, Berkeley, California, United States of America
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Marguerite Lapierre
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Jeffrey D Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Luca Ferretti
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Amaury Lambert
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, Paris, France
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
| | - Timothy B Sackton
- Éco-anthropologie, Muséum National d'Histoire Naturelle, Université Paris-Cité, Paris, France
| | - Guillaume Achaz
- Informatics Group, Harvard University, Cambridge, Massachusetts, United States of America
- SMILE group, Center for Interdisciplinary Research in Biology (CIRB), Collège de France, Paris, France
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3
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Árnason E, Koskela J, Halldórsdóttir K, Eldon B. Sweepstakes reproductive success via pervasive and recurrent selective sweeps. eLife 2023; 12:80781. [PMID: 36806325 PMCID: PMC9940914 DOI: 10.7554/elife.80781] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 12/28/2022] [Indexed: 02/22/2023] Open
Abstract
Highly fecund natural populations characterized by high early mortality abound, yet our knowledge about their recruitment dynamics is somewhat rudimentary. This knowledge gap has implications for our understanding of genetic variation, population connectivity, local adaptation, and the resilience of highly fecund populations. The concept of sweepstakes reproductive success, which posits a considerable variance and skew in individual reproductive output, is key to understanding the distribution of individual reproductive success. However, it still needs to be determined whether highly fecund organisms reproduce through sweepstakes and, if they do, the relative roles of neutral and selective sweepstakes. Here, we use coalescent-based statistical analysis of population genomic data to show that selective sweepstakes likely explain recruitment dynamics in the highly fecund Atlantic cod. We show that the Kingman coalescent (modelling no sweepstakes) and the Xi-Beta coalescent (modelling random sweepstakes), including complex demography and background selection, do not provide an adequate fit for the data. The Durrett-Schweinsberg coalescent, in which selective sweepstakes result from recurrent and pervasive selective sweeps of new mutations, offers greater explanatory power. Our results show that models of sweepstakes reproduction and multiple-merger coalescents are relevant and necessary for understanding genetic diversity in highly fecund natural populations. These findings have fundamental implications for understanding the recruitment variation of fish stocks and general evolutionary genomics of high-fecundity organisms.
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Affiliation(s)
- Einar Árnason
- Institute of Life- and environmental Sciences, University of IcelandReykjavikIceland,Department of Organismal and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Jere Koskela
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Katrín Halldórsdóttir
- Institute of Life- and environmental Sciences, University of IcelandReykjavikIceland
| | - Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science, Museum für NaturkundeBerlinGermany
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4
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Ní Leathlobhair M, Lenski RE. Population genetics of clonally transmissible cancers. Nat Ecol Evol 2022; 6:1077-1089. [PMID: 35879542 DOI: 10.1038/s41559-022-01790-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Populations of cancer cells are subject to the same core evolutionary processes as asexually reproducing, unicellular organisms. Transmissible cancers are particularly striking examples of these processes. These unusual cancers are clonal lineages that can spread through populations via physical transfer of living cancer cells from one host individual to another, and they have achieved long-term success in the colonization of at least eight different host species. Population genetic theory provides a useful framework for understanding the shift from a multicellular sexual animal into a unicellular asexual clone and its long-term effects on the genomes of these cancers. In this Review, we consider recent findings from transmissible cancer research with the goals of developing an evolutionarily informed perspective on transmissible cancers, examining possible implications for their long-term fate and identifying areas for future research on these exceptional lineages.
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Affiliation(s)
- Máire Ní Leathlobhair
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland.
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
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5
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Ono H, Arai Y, Furukawa E, Narushima D, Matsuura T, Nakamura H, Shiokawa D, Nagai M, Imai T, Mimori K, Okamoto K, Hippo Y, Shibata T, Kato M. Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model. BMC Biol 2021; 19:207. [PMID: 34548081 PMCID: PMC8456589 DOI: 10.1186/s12915-021-01147-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/06/2021] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Intra-tumor heterogeneity (ITH) encompasses cellular differences in tumors and is related to clinical outcomes such as drug resistance. However, little is known about the dynamics of ITH, owing to the lack of time-series analysis at the single-cell level. Mouse models that recapitulate cancer development are useful for controlled serial time sampling. RESULTS We performed single-cell exome and transcriptome sequencing of 200 cells to investigate how ITH is generated in a mouse colorectal cancer model. In the model, a single normal intestinal cell is grown into organoids that mimic the intestinal crypt structure. Upon RNAi-mediated downregulation of a tumor suppressor gene APC, the transduced organoids were serially transplanted into mice to allow exposure to in vivo microenvironments, which play relevant roles in cancer development. The ITH of the transcriptome increased after the transplantation, while that of the exome decreased. Mutations generated during organoid culture did not greatly change at the bulk-cell level upon the transplantation. The RNA ITH increase was due to the emergence of new transcriptional subpopulations. In contrast to the initial cells expressing mesenchymal-marker genes, new subpopulations repressed these genes after the transplantation. Analyses of colorectal cancer data from The Cancer Genome Atlas revealed a high proportion of metastatic cases in human subjects with expression patterns similar to the new cell subpopulations in mouse. These results suggest that the birth of transcriptional subpopulations may be a key for adaptation to drastic micro-environmental changes when cancer cells have sufficient genetic alterations at later tumor stages. CONCLUSIONS This study revealed an evolutionary dynamics of single-cell RNA and DNA heterogeneity in tumor progression, giving insights into the mesenchymal-epithelial transformation of tumor cells at metastasis in colorectal cancer.
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Affiliation(s)
- Hanako Ono
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Eisaku Furukawa
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daichi Narushima
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Tetsuya Matsuura
- Department of Animal Experimentation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Daisuke Shiokawa
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Momoko Nagai
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Toshio Imai
- Department of Animal Experimentation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, 101 Hasamamachiidaigaoka, Yufu, Oita, 879-5593, Japan
| | - Koji Okamoto
- Division of Cancer Differentiation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
| | - Yoshitaka Hippo
- Department of Animal Experimentation, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Division of Biochemistry and Molecular Carcinogenesis, Chiba Cancer Center Research Institute, 666-2 Nitona-cho, Chiba Chuo-ku, Chiba, 260-8717, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shiroganedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Mamoru Kato
- Division of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan.
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Menardo F, Gagneux S, Freund F. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis. Mol Biol Evol 2021; 38:290-306. [PMID: 32667991 PMCID: PMC8480183 DOI: 10.1093/molbev/msaa179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Freund
- Department of Plant Biodiversity and Breeding Informatics, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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7
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Freund F, Siri-Jégousse A. The impact of genetic diversity statistics on model selection between coalescents. Comput Stat Data Anal 2021. [DOI: 10.1016/j.csda.2020.107055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Abstract
Natural highly fecund populations abound. These range from viruses to gadids. Many highly fecund populations are economically important. Highly fecund populations provide an important contrast to the low-fecundity organisms that have traditionally been applied in evolutionary studies. A key question regarding high fecundity is whether large numbers of offspring are produced on a regular basis, by few individuals each time, in a sweepstakes mode of reproduction. Such reproduction characteristics are not incorporated into the classical Wright-Fisher model, the standard reference model of population genetics, or similar types of models, in which each individual can produce only small numbers of offspring relative to the population size. The expected genomic footprints of population genetic models of sweepstakes reproduction are very different from those of the Wright-Fisher model. A key, immediate issue involves identifying the footprints of sweepstakes reproduction in genomic data. Whole-genome sequencing data can be used to distinguish the patterns made by sweepstakes reproduction from the patterns made by population growth in a population evolving according to the Wright-Fisher model (or similar models). If the hypothesis of sweepstakes reproduction cannot be rejected, then models of sweepstakes reproduction and associated multiple-merger coalescents will become at least as relevant as the Wright-Fisher model (or similar models) and the Kingman coalescent, the cornerstones of mathematical population genetics, in further discussions of evolutionary genomics of highly fecund populations.
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Affiliation(s)
- Bjarki Eldon
- Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, D-10115 Berlin, Germany;
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Nagornov IS, Kato M. tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes. Bioinformatics 2020; 36:3597-3599. [PMID: 32170925 PMCID: PMC7267821 DOI: 10.1093/bioinformatics/btaa182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/09/2019] [Accepted: 03/11/2020] [Indexed: 12/20/2022] Open
Abstract
Summary The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH. Availability and implementation The open-source code is available in the repository https://github.com/nagornovys/Cancer_cell_evolution. Contact mamkato@ncc.go.jp Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Iurii S Nagornov
- Department of Bioinformatics, Research Institute, National Cancer Center Japan, Tokyo 104-0045, Japan
| | - Mamoru Kato
- Department of Bioinformatics, Research Institute, National Cancer Center Japan, Tokyo 104-0045, Japan
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Cannings models, population size changes and multiple-merger coalescents. J Math Biol 2020; 80:1497-1521. [PMID: 32008102 PMCID: PMC7052052 DOI: 10.1007/s00285-020-01470-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 01/10/2020] [Indexed: 11/17/2022]
Abstract
Multiple-merger coalescents, e.g. \documentclass[12pt]{minimal}
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\begin{document}$$\varLambda $$\end{document}Λ-n-coalescents, have been proposed as models of the genealogy of n sampled individuals for a range of populations whose genealogical structures are not captured well by Kingman’s n-coalescent. \documentclass[12pt]{minimal}
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\begin{document}$$\varLambda $$\end{document}Λ-n-coalescents can be seen as the limit process of the discrete genealogies of Cannings models with fixed population size, when time is rescaled and population size \documentclass[12pt]{minimal}
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\begin{document}$$N\rightarrow \infty $$\end{document}N→∞. As established for Kingman’s n-coalescent, moderate population size fluctuations in the discrete population model should be reflected by a time-change of the limit coalescent. For \documentclass[12pt]{minimal}
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\begin{document}$$\varLambda $$\end{document}Λ-n-coalescents, this has been explicitly shown for only a limited subclass of \documentclass[12pt]{minimal}
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\begin{document}$$\varLambda $$\end{document}Λ-n-coalescents and exponentially growing populations. This article gives a more general construction of time-changed \documentclass[12pt]{minimal}
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\begin{document}$$\varLambda $$\end{document}Λ-n-coalescents as limits of specific Cannings models with rather arbitrary time changes.
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Kato M, Vasco DA, Sugino R, Narushima D, Krasnitz A. Sweepstake evolution revealed by population-genetic analysis of copy-number alterations in single genomes of breast cancer. ROYAL SOCIETY OPEN SCIENCE 2017; 4:171060. [PMID: 28989791 PMCID: PMC5627131 DOI: 10.1098/rsos.171060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Single-cell sequencing is a promising technology that can address cancer cell evolution by identifying genetic alterations in individual cells. In a recent study, genome-wide DNA copy numbers of single cells were accurately quantified by single-cell sequencing in breast cancers. Phylogenetic-tree analysis revealed genetically distinct populations, each consisting of homogeneous cells. Bioinformatics methods based on population genetics should be further developed to quantitatively analyse the single-cell sequencing data. We developed a bioinformatics framework that was combined with molecular-evolution theories to analyse copy-number losses. This analysis revealed that most deletions in the breast cancers at the single-cell level were generated by simple stochastic processes. A non-standard type of coalescent theory, the multiple-merger coalescent model, aided by approximate Bayesian computation fit well with the data, allowing us to estimate the population-genetic parameters in addition to false-positive and false-negative rates. The estimated parameters suggest that the cancer cells underwent sweepstake evolution, where only one or very few parental cells produced a descendent cell population. We conclude that breast cancer cells successively substitute in a tumour mass, and the high reproduction of only a portion of cancer cells may confer high adaptability to this cancer.
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Affiliation(s)
- Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuuoo-ku, Tokyo 104-0045, Japan
| | - Daniel A. Vasco
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Ryuichi Sugino
- School of Advanced Sciences, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan
| | - Daichi Narushima
- Department of Bioinformatics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuuoo-ku, Tokyo 104-0045, Japan
| | - Alexander Krasnitz
- Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, One Bungtown Road, Cold Spring Harbor, NY 11724, USA
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