1
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Cannataro VL, Glasmacher KA, Hampson CE. Mutations, substitutions, and selection: Linking mutagenic processes to cancer using evolutionary theory. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167268. [PMID: 38823460 DOI: 10.1016/j.bbadis.2024.167268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/25/2024] [Accepted: 05/25/2024] [Indexed: 06/03/2024]
Abstract
Cancers are the product of evolutionary events, where molecular variation occurs and accumulates in tissues and tumors. Sequencing of this molecular variation informs not only which variants are driving tumorigenesis, but also the mechanisms behind what is fueling mutagenesis. Both of these details are crucial for preventing premature deaths due to cancer, whether it is by targeting the variants driving the cancer phenotype or by measures to prevent exogenous mutations from contributing to somatic evolution. Here, we review tools to determine both molecular signatures and cancer drivers, and avenues by which these metrics may be linked.
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Affiliation(s)
| | - Kira A Glasmacher
- Emmanuel College, 400 Fenway, Boston, MA 02115, United States of America
| | - Caralynn E Hampson
- Emmanuel College, 400 Fenway, Boston, MA 02115, United States of America
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2
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Montazid S, Bandyopadhyay S, Hart DW, Gao N, Johnson B, Thrumurthy SG, Penn DJ, Wernisch B, Bansal M, Altrock PM, Rost F, Gazinska P, Ziolkowski P, Hayee B, Liu Y, Han J, Tessitore A, Koth J, Bodmer WF, East JE, Bennett NC, Tomlinson I, Irshad S. Adult stem cell activity in naked mole rats for long-term tissue maintenance. Nat Commun 2023; 14:8484. [PMID: 38123565 PMCID: PMC10733326 DOI: 10.1038/s41467-023-44138-6] [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: 03/25/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The naked mole rat (NMR), Heterocephalus glaber, the longest-living rodent, provides a unique opportunity to explore how evolution has shaped adult stem cell (ASC) activity and tissue function with increasing lifespan. Using cumulative BrdU labelling and a quantitative imaging approach to track intestinal ASCs (Lgr5+) in their native in vivo state, we find an expanded pool of Lgr5+ cells in NMRs, and these cells specifically at the crypt base (Lgr5+CBC) exhibit slower division rates compared to those in short-lived mice but have a similar turnover as human LGR5+CBC cells. Instead of entering quiescence (G0), NMR Lgr5+CBC cells reduce their division rates by prolonging arrest in the G1 and/or G2 phases of the cell cycle. Moreover, we also observe a higher proportion of differentiated cells in NMRs that confer enhanced protection and function to the intestinal mucosa which is able to detect any chemical imbalance in the luminal environment efficiently, triggering a robust pro-apoptotic, anti-proliferative response within the stem/progenitor cell zone.
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Affiliation(s)
- Shamir Montazid
- Nuffield Department of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK
| | | | - Daniel W Hart
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, 0028, Republic of South Africa
| | - Nan Gao
- Department of Biological Sciences, Rutgers University, Newark, 07102, NJ, USA
| | - Brian Johnson
- Division of Biomedical Informatics, Department of Medicine, University of California San Diego, 9500 Gilman Dr, La Jolla, 92093, CA, USA
| | - Sri G Thrumurthy
- Endoscopy, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Dustin J Penn
- Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, 1160, Austria
| | - Bettina Wernisch
- Konrad Lorenz Institute of Ethology, Department of Interdisciplinary Life Sciences, University of Veterinary Medicine, Vienna, 1160, Austria
| | | | - Philipp M Altrock
- Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, 24306, Ploen, Germany
| | - Fabian Rost
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Patrycja Gazinska
- Biobank Research Group, Lukasiewicz Research Network, PORT Polish Center for Technology Development, Wroclaw, Poland
| | - Piotr Ziolkowski
- Department of Clinical and Experimental Pathology, Wroclaw Medical University, 50-368, Wroclaw, Poland
| | - Bu'Hussain Hayee
- Endoscopy, King's College Hospital NHS Foundation Trust, London, SE5 9RS, UK
| | - Yue Liu
- Department of Biological Sciences, Rutgers University, Newark, 07102, NJ, USA
| | - Jiangmeng Han
- Department of Biological Sciences, Rutgers University, Newark, 07102, NJ, USA
| | | | - Jana Koth
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Walter F Bodmer
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - James E East
- Translational Gastroenterology Unit, Experimental Medicine Division, Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DU, UK
| | - Nigel C Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria, 0028, Republic of South Africa
| | - Ian Tomlinson
- Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
| | - Shazia Irshad
- Nuffield Department of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, OX3 9DU, UK.
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3
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Kok RNU, Tans SJ, van Zon JS. Minimizing cell number fluctuations in self-renewing tissues with a stem-cell niche. Phys Rev E 2023; 108:064403. [PMID: 38243426 DOI: 10.1103/physreve.108.064403] [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: 11/18/2022] [Accepted: 11/02/2023] [Indexed: 01/21/2024]
Abstract
Self-renewing tissues require that a constant number of proliferating cells is maintained over time. This maintenance can be ensured at the single-cell level or the population level. Maintenance at the population level leads to fluctuations in the number of proliferating cells over time. Often, it is assumed that those fluctuations can be reduced by increasing the number of asymmetric divisions, i.e., divisions where only one of the daughter cells remains proliferative. Here, we study a model of cell proliferation that incorporates a stem-cell niche of fixed size, and explicitly model the cells inside and outside the niche. We find that in this model, fluctuations are minimized when the difference in growth rate between the niche and the rest of the tissue is maximized and all divisions are symmetric divisions, producing either two proliferating or two nonproliferating daughters. We show that this optimal state leaves visible signatures in clone size distributions and could thus be detected experimentally.
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Affiliation(s)
- Rutger N U Kok
- Autonomous Matter, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Sander J Tans
- Autonomous Matter, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
| | - Jeroen S van Zon
- Autonomous Matter, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands
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4
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Pradeu T, Daignan-Fornier B, Ewald A, Germain PL, Okasha S, Plutynski A, Benzekry S, Bertolaso M, Bissell M, Brown JS, Chin-Yee B, Chin-Yee I, Clevers H, Cognet L, Darrason M, Farge E, Feunteun J, Galon J, Giroux E, Green S, Gross F, Jaulin F, Knight R, Laconi E, Larmonier N, Maley C, Mantovani A, Moreau V, Nassoy P, Rondeau E, Santamaria D, Sawai CM, Seluanov A, Sepich-Poore GD, Sisirak V, Solary E, Yvonnet S, Laplane L. Reuniting philosophy and science to advance cancer research. Biol Rev Camb Philos Soc 2023; 98:1668-1686. [PMID: 37157910 PMCID: PMC10869205 DOI: 10.1111/brv.12971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/10/2023]
Abstract
Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer.
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Affiliation(s)
- Thomas Pradeu
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
| | - Bertrand Daignan-Fornier
- CNRS UMR 5095 Institut de Biochimie et Génétique Cellulaires, University of Bordeaux, 1 rue Camille St Saens, Bordeaux 33077, France
| | - Andrew Ewald
- Departments of Cell Biology and Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Pierre-Luc Germain
- Department of Health Sciences and Technology, Institute for Neurosciences, Eidgenössische Technische Hochschule (ETH) Zürich, Universitätstrasse 2, Zürich 8092, Switzerland
- Department of Molecular Life Sciences, Laboratory of Statistical Bioinformatics, Universität Zürich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Samir Okasha
- Department of Philosophy, University of Bristol, Cotham House, Bristol, BS6 6JL, UK
| | - Anya Plutynski
- Department of Philosophy, Washington University in St. Louis, and Associate with Division of Biology and Biomedical Sciences, St. Louis, MO 63105, USA
| | - Sébastien Benzekry
- Computational Pharmacology and Clinical Oncology (COMPO) Unit, Inria Sophia Antipolis-Méditerranée, Cancer Research Center of Marseille, Inserm UMR1068, CNRS UMR7258, Aix Marseille University UM105, 27, bd Jean Moulin, Marseille 13005, France
| | - Marta Bertolaso
- Research Unit of Philosophy of Science and Human Development, Università Campus Bio-Medico di Roma, Via Àlvaro del Portillo, 21-00128, Rome, Italy
- Centre for Cancer Biomarkers, University of Bergen, Bergen 5007, Norway
| | - Mina Bissell
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, Berkeley, CA 94720, USA
| | - Joel S. Brown
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Benjamin Chin-Yee
- Division of Hematology, Department of Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
- Rotman Institute of Philosophy, Western University, 1151 Richmond Street North, London, ON, Canada
| | - Ian Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, 800 Commissioners Rd E, London, ON, Canada
| | - Hans Clevers
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, Basel 4070, Switzerland
- Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Uppsalalaan 8, Utrecht 3584 CT, The Netherlands
| | - Laurent Cognet
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Marie Darrason
- Department of Pneumology and Thoracic Oncology, University Hospital of Lyon, 165 Chem. du Grand Revoyet, 69310 Pierre Bénite, Lyon, France
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Emmanuel Farge
- Mechanics and Genetics of Embryonic and Tumor Development group, Institut Curie, CNRS, UMR168, Inserm, Centre Origines et conditions d’apparition de la vie (OCAV) Paris Sciences Lettres Research University, Sorbonne University, Institut Curie, 11 rue Pierre et Marie Curie, Paris 75005, France
| | - Jean Feunteun
- INSERM U981, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Jérôme Galon
- INSERM UMRS1138, Integrative Cancer Immunology, Cordelier Research Center, Sorbonne Université, Université Paris Cité, 15 rue de l’École de Médecine, Paris 75006, France
| | - Elodie Giroux
- Lyon Institute of Philosophical Research, Lyon 3 Jean Moulin University, 1 Av. des Frères Lumière, Lyon 69007, France
| | - Sara Green
- Section for History and Philosophy of Science, Department of Science Education, University of Copenhagen, Rådmandsgade 64, Copenhagen 2200, Denmark
| | - Fridolin Gross
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Fanny Jaulin
- INSERM U1279, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
| | - Rob Knight
- Department of Bioengineering, University of California San Diego, 3223 Voigt Dr, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA 92093, USA
| | - Ezio Laconi
- Department of Biomedical Sciences, School of Medicine, University of Cagliari, Via Università 40, Cagliari 09124, Italy
| | - Nicolas Larmonier
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Carlo Maley
- Arizona Cancer Evolution Center, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- School of Life Sciences, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
- Biodesign Center for Biocomputing, Security and Society, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, 1001 S McAllister Ave, Tempe, AZ 85287, USA
- Center for Evolution and Medicine, Arizona State University, 427 East Tyler Mall, Tempe, AZ 85287, USA
| | - Alberto Mantovani
- Department of Biomedical Sciences, Humanitas University, 4 Via Rita Levi Montalcini, 20090 Pieve Emanuele, Milan, Italy
- Department of Immunology and Inflammation, Istituto Clinico Humanitas Humanitas Cancer Center (IRCCS) Humanitas Research Hospital, Via Manzoni 56, Rozzano, Milan 20089, Italy
- The William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Violaine Moreau
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Pierre Nassoy
- CNRS UMR 5298, Laboratoire Photonique Numérique et Nanosciences, University of Bordeaux, Rue François Mitterrand, Talence 33400, France
| | - Elena Rondeau
- INSERM U1111, ENS Lyon and Centre International de Recherche en Infectionlogie (CIRI), 46 Allée d’Italie, Lyon 69007, France
| | - David Santamaria
- Molecular Mechanisms of Cancer Program, Centro de Investigación del Cáncer, Consejo Superior de Investigaciones Científicas (CSIC)-University of Salamanca, Salamanca 37007, Spain
| | - Catherine M. Sawai
- INSERM UMR1312, Bordeaux Institute of Oncology (BRIC), University of Bordeaux, 146 Rue Léo Saignat, Bordeaux 33076, France
| | - Andrei Seluanov
- Department of Biology and Medicine, University of Rochester, Rochester, NY 14627, USA
| | | | - Vanja Sisirak
- CNRS UMR5164 ImmunoConcEpT, University of Bordeaux, 146 rue Leo Saignat, Bordeaux 33076, France
| | - Eric Solary
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Département d’hématologie, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Université Paris-Saclay, Faculté de Médecine, 63 Rue Gabriel Péri, Le Kremlin-Bicêtre 94270, France
| | - Sarah Yvonnet
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen DK-2200, Denmark
| | - Lucie Laplane
- CNRS UMR8590, Institut d’Histoire et Philosophie des Sciences et des Technique, University Paris I Panthéon-Sorbonne, 13 rue du Four, Paris 75006, France
- INSERM U1287, Gustave Roussy, 114 Rue Edouard Vaillant, Villejuif 94800, France
- Center for Biology and Society, College of Liberal Arts and Sciences, Arizona State University, 1100 S McAllister Ave, Tempe, AZ 85281, USA
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Jaime-Rodríguez M, Cadena-Hernández AL, Rosales-Valencia LD, Padilla-Sánchez JM, Chavez-Santoscoy RA. Are genetic drift and stem cell adherence in laboratory culture issues for cultivated meat production? Front Nutr 2023; 10:1189664. [PMID: 37701376 PMCID: PMC10493286 DOI: 10.3389/fnut.2023.1189664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/11/2023] [Indexed: 09/14/2023] Open
Abstract
Mesenchymal stem cell-based cultivated meat is a promising solution to the ecological and ethical problems posed by traditional meat production, since it exhibits a protein content and composition that is more comparable to original meat proteins than any other source of cultivated meat products, including plants, bacteria, and fungi. Nonetheless, the nature and laboratory behavior of mesenchymal stem cells pose two significant challenges for large-scale production: genetic drift and adherent growth in culture. Culture conditions used in the laboratory expose the cells to a selective pressure that causes genetic drift, which may give rise to oncogene activation and the loss of "stemness." This is why genetic and functional analysis of the cells during culture is required to determine the maximum number of passages within the laboratory where no significant mutations or loss of function are detected. Moreover, the adherent growth of mesenchymal stem cells can be an obstacle for their large-scale production since volume to surface ratio is limited for high volume containers. Multi-tray systems, roller bottles, and microcarriers have been proposed as potential solutions to scale-up the production of adherent cells required for cultivated meat. The most promising solutions for the safety problems and large-scale obstacles for cultivated meat production are the determination of a limit number of passages based on a genetic analysis and the use of microcarriers from edible materials to maximize the volume to surface proportion and decrease the downstream operations needed for cultivated meat production.
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Richter H. Spectral dynamics of guided edge removals and identifying transient amplifiers for death-Birth updating. J Math Biol 2023; 87:3. [PMID: 37284903 DOI: 10.1007/s00285-023-01937-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 01/03/2023] [Accepted: 05/19/2023] [Indexed: 06/08/2023]
Abstract
The paper deals with two interrelated topics: (1) identifying transient amplifiers in an iterative process, and (2) analyzing the process by its spectral dynamics, which is the change in the graph spectra by edge manipulation. Transient amplifiers are networks representing population structures which shift the balance between natural selection and random drift. Thus, amplifiers are highly relevant for understanding the relationships between spatial structures and evolutionary dynamics. We study an iterative procedure to identify transient amplifiers for death-Birth updating. The algorithm starts with a regular input graph and iteratively removes edges until desired structures are achieved. Thus, a sequence of candidate graphs is obtained. The edge removals are guided by quantities derived from the sequence of candidate graphs. Moreover, we are interested in the Laplacian spectra of the candidate graphs and analyze the iterative process by its spectral dynamics. The results show that although transient amplifiers for death-Birth updating are generally rare, a substantial number of them can be obtained by the proposed procedure. The graphs identified share structural properties and have some similarity to dumbbell and barbell graphs. We analyze amplification properties of these graphs and also two more families of bell-like graphs and show that further transient amplifiers for death-Birth updating can be found. Finally, it is demonstrated that the spectral dynamics possesses characteristic features useful for deducing links between structural and spectral properties. These feature can also be taken for distinguishing transient amplifiers among evolutionary graphs in general.
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Affiliation(s)
- Hendrik Richter
- Faculty of Engineering, HTWK Leipzig University of Applied Sciences, Leipzig, Germany.
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Mercadal J, Betegón-Putze I, Bosch N, Caño-Delgado AI, Ibañes M. BRAVO self-confined expression through WOX5 in the Arabidopsis root stem-cell niche. Development 2022; 149:dev200510. [PMID: 35899779 PMCID: PMC9440757 DOI: 10.1242/dev.200510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2023]
Abstract
In animals and plants, stem-cell niches are local microenvironments that are tightly regulated to preserve their unique identity while communicating with adjacent cells that will give rise to specialized cell types. In the primary root of Arabidopsis thaliana, two transcription factors, BRAVO and WOX5, among others, are expressed in the stem-cell niche. Intriguingly, BRAVO, a repressor of quiescent center divisions, confines its own gene expression to the stem-cell niche, as evidenced in a bravo mutant background. Here, we propose through mathematical modeling that BRAVO confines its own expression domain to the stem-cell niche by attenuating a WOX5-dependent diffusible activator of BRAVO. This negative feedback drives WOX5 activity to be spatially restricted as well. The results show that WOX5 diffusion and sequestration by binding to BRAVO are sufficient to drive the experimentally observed confined BRAVO expression at the stem-cell niche. We propose that the attenuation of a diffusible activator can be a general mechanism acting at other stem-cell niches to spatially confine genetic activity to a small region while maintaining signaling within them and with the surrounding cells.
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Affiliation(s)
- Josep Mercadal
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Isabel Betegón-Putze
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Nadja Bosch
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Ana I. Caño-Delgado
- Department of Molecular Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB (Cerdanyola del Vallès), 08193 Barcelona, Spain
| | - Marta Ibañes
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, 08028 Barcelona, Spain
- Universitat de Barcelona Institute of Complex Systems (UBICS), Universitat de Barcelona, 08028 Barcelona, Spain
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8
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Vendramin R, Litchfield K, Swanton C. Cancer evolution: Darwin and beyond. EMBO J 2021; 40:e108389. [PMID: 34459009 PMCID: PMC8441388 DOI: 10.15252/embj.2021108389] [Citation(s) in RCA: 120] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/04/2021] [Accepted: 06/25/2021] [Indexed: 12/16/2022] Open
Abstract
Clinical and laboratory studies over recent decades have established branched evolution as a feature of cancer. However, while grounded in somatic selection, several lines of evidence suggest a Darwinian model alone is insufficient to fully explain cancer evolution. First, the role of macroevolutionary events in tumour initiation and progression contradicts Darwin's central thesis of gradualism. Whole-genome doubling, chromosomal chromoplexy and chromothripsis represent examples of single catastrophic events which can drive tumour evolution. Second, neutral evolution can play a role in some tumours, indicating that selection is not always driving evolution. Third, increasing appreciation of the role of the ageing soma has led to recent generalised theories of age-dependent carcinogenesis. Here, we review these concepts and others, which collectively argue for a model of cancer evolution which extends beyond Darwin. We also highlight clinical opportunities which can be grasped through targeting cancer vulnerabilities arising from non-Darwinian patterns of evolution.
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Affiliation(s)
- Roberto Vendramin
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of ExcellenceUniversity College London Cancer InstituteLondonUK
- Cancer Evolution and Genome Instability LaboratoryThe Francis Crick InstituteLondonUK
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9
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Richter H. Spectral analysis of transient amplifiers for death-birth updating constructed from regular graphs. J Math Biol 2021; 82:61. [PMID: 33993365 PMCID: PMC8126557 DOI: 10.1007/s00285-021-01609-y] [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: 01/18/2021] [Revised: 03/31/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
A central question of evolutionary dynamics on graphs is whether or not a mutation introduced in a population of residents survives and eventually even spreads to the whole population, or becomes extinct. The outcome naturally depends on the fitness of the mutant and the rules by which mutants and residents may propagate on the network, but arguably the most determining factor is the network structure. Some structured networks are transient amplifiers. They increase for a certain fitness range the fixation probability of beneficial mutations as compared to a well-mixed population. We study a perturbation method for identifying transient amplifiers for death–birth updating. The method involves calculating the coalescence times of random walks on graphs and finding the vertex with the largest remeeting time. If the graph is perturbed by removing an edge from this vertex, there is a certain likelihood that the resulting perturbed graph is a transient amplifier. We test all pairwise nonisomorphic regular graphs up to a certain order and thus cover the whole structural range expressible by these graphs. For cubic and quartic regular graphs we find a sufficiently large number of transient amplifiers. For these networks we carry out a spectral analysis and show that the graphs from which transient amplifiers can be constructed share certain structural properties. Identifying spectral and structural properties may promote finding and designing such networks.
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Affiliation(s)
- Hendrik Richter
- HTWK Leipzig University of Applied Sciences, Leipzig, Germany.
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10
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Allen B, Sample C, Steinhagen P, Shapiro J, King M, Hedspeth T, Goncalves M. Fixation probabilities in graph-structured populations under weak selection. PLoS Comput Biol 2021; 17:e1008695. [PMID: 33529219 PMCID: PMC7880501 DOI: 10.1371/journal.pcbi.1008695] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 02/12/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
A population's spatial structure affects the rate of genetic change and the outcome of natural selection. These effects can be modeled mathematically using the Birth-death process on graphs. Individuals occupy the vertices of a weighted graph, and reproduce into neighboring vertices based on fitness. A key quantity is the probability that a mutant type will sweep to fixation, as a function of the mutant's fitness. Graphs that increase the fixation probability of beneficial mutations, and decrease that of deleterious mutations, are said to amplify selection. However, fixation probabilities are difficult to compute for an arbitrary graph. Here we derive an expression for the fixation probability, of a weakly-selected mutation, in terms of the time for two lineages to coalesce. This expression enables weak-selection fixation probabilities to be computed, for an arbitrary weighted graph, in polynomial time. Applying this method, we explore the range of possible effects of graph structure on natural selection, genetic drift, and the balance between the two. Using exhaustive analysis of small graphs and a genetic search algorithm, we identify families of graphs with striking effects on fixation probability, and we analyze these families mathematically. Our work reveals the nuanced effects of graph structure on natural selection and neutral drift. In particular, we show how these notions depend critically on the process by which mutations arise.
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Affiliation(s)
- Benjamin Allen
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Christine Sample
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Patricia Steinhagen
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Julia Shapiro
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Matthew King
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Timothy Hedspeth
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
| | - Megan Goncalves
- Department of Mathematics, Emmanuel College, Boston, Massachusetts, United States of America
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11
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Birtwell D, Luebeck G, Maley CC. The evolution of metapopulation dynamics and the number of stem cells in intestinal crypts and other tissue structures in multicellular bodies. Evol Appl 2020; 13:1771-1783. [PMID: 32821281 PMCID: PMC7428809 DOI: 10.1111/eva.13069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/04/2022] Open
Abstract
Carcinogenesis is a process of somatic evolution. Previous models of stem and transient amplifying cells in epithelial proliferating units like colonic crypts showed that intermediate numbers of stem cells in a crypt should optimally prevent progression to cancer. If a stem cell population is too small, it is easy for a mutator mutation to drift to fixation. If it is too large, it is easy for selection to drive cell fitness enhancing carcinogenic mutations to fixation. Here, we show that a multiscale microsimulation, that captures both within-crypt and between-crypt evolutionary dynamics, leads to a different conclusion. Epithelial tissues are metapopulations of crypts. We measured time to initiation of a neoplasm, implemented as inactivation of both alleles of a tumor suppressor gene. In our model, time to initiation is dependent on the spread of mutator clones in the crypts. The proportion of selectively beneficial and deleterious mutations in somatic cells is unknown and so was explored with a parameter. When the majority of non-neutral mutations are deleterious, the fitness of mutator clones tends to decline. When crypts are maintained by few stem cells, intercrypt competition tends to remove crypts with fixed mutators. When there are many stem cells within a crypt, there is virtually no crypt turnover, but mutator clones are suppressed by within-crypt competition. If the majority of non-neutral mutations are beneficial to the clone, then these results are reversed and intermediate-sized crypts provide the most protection against initiation. These results highlight the need to understand the dynamics of turnover and the mechanisms that control homeostasis, both at the level of stem cells within proliferative units and at the tissue level of competing proliferative units. Determining the distribution of fitness effects of somatic mutations will also be crucial to understanding the dynamics of tumor initiation and progression.
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Affiliation(s)
- David Birtwell
- Norris Comprehensive Cancer CenterUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Georg Luebeck
- Public Health Sciences DivisionFred Hutchinson Cancer Research CenterSeattleWAUSA
| | - Carlo C. Maley
- Arizona Cancer Evolution CenterBiodesign Institute and School of Life SciencesArizona State UniversityTempeAZUSA
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12
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Chen B, Shi Z, Chen Q, Shen X, Shibata D, Wen H, Wu CI. Tumorigenesis as the Paradigm of Quasi-neutral Molecular Evolution. Mol Biol Evol 2020; 36:1430-1441. [PMID: 30912799 DOI: 10.1093/molbev/msz075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In the absence of both positive and negative selections, coding sequences evolve at a neutral rate (R = 1). Such a high genomic rate is generally not achievable due to the prevalence of negative selection against codon substitutions. Remarkably, somatic evolution exhibits the seemingly neutral rate R ∼ 1 across normal and cancerous tissues. Nevertheless, R ∼ 1 may also mean that positive and negative selections are both strong, but equal in intensity. We refer to this regime as quasi-neutral. Indeed, individual genes in cancer cells often evolve at a much higher, or lower, rate than R ∼ 1. Here, we show that 1) quasi-neutrality is much more likely when populations are small (N < 50); 2) stem-cell populations in single normal tissue niches, from which tumors likely emerge, have a small N (usually <50) but selection at this stage is measurable and strong; 3) when N dips below 50, selection efficacy decreases precipitously; and 4) notably, N is smaller in the stem-cell niche of the small intestine than in the colon. Hence, the ∼70-fold higher rate of phenotypic evolution (observed as cancer risk) in the latter can be explained by the greater efficacy of selection, which then leads to the fixation of more advantageous and fewer deleterious mutations in colon cancers. In conclusion, quasi-neutral evolution sheds a new light on a general evolutionary principle that helps to explain aspects of cancer evolution.
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Affiliation(s)
- Bingjie Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zongkun Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Qingjian Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xu Shen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Darryl Shibata
- Department of Pathology, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - Haijun Wen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, China.,CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,Department of Ecology and Evolution, University of Chicago, Chicago, IL
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13
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Abstract
Kimura's neutral theory argued that positive selection was not responsible for an appreciable fraction of molecular substitutions. Correspondingly, quantitative analysis reveals that the vast majority of substitutions in cancer genomes are not detectably under selection. Insights from the somatic evolution of cancer reveal that beneficial substitutions in cancer constitute a small but important fraction of the molecular variants. The molecular evolution of cancer community will benefit by incorporating the neutral theory of molecular evolution into their understanding and analysis of cancer evolution-and accepting the use of tractable, predictive models, even when there is some evidence that they are not perfect.
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Affiliation(s)
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University, New Haven, CT
- Program in Computational Biology and Bioinformatics
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT
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14
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Cannataro VL, McKinley SA, St Mary CM. The evolutionary trade-off between stem cell niche size, aging, and tumorigenesis. Evol Appl 2017; 10:590-602. [PMID: 28616066 PMCID: PMC5469181 DOI: 10.1111/eva.12476] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Accepted: 02/28/2017] [Indexed: 12/18/2022] Open
Abstract
Many epithelial tissues within multicellular organisms are continually replenished by small independent populations of stem cells largely responsible for maintaining tissue homeostasis. These continually dividing populations are subject to mutations that can lead to tumorigenesis but also contribute to aging. Mutations accumulate in stem cell niches and change the rate of cell division and differentiation; the pace of this process and the fate of specific mutations depend strongly on niche population size. Here, we create a mathematical model of the intestinal stem cell niche, crypt system, and epithelium. We calculate the expected effect of fixed mutations in stem cell niches and their effect on tissue homeostasis throughout the intestinal epithelium over organismal lifetime. We find that, due to the small population size of stem cell niches, mutations predominantly fix via genetic drift and decrease stem cell fitness, leading to niche and tissue attrition, and contributing to organismal aging. We also explore mutation accumulation at various stem cell niche sizes and demonstrate that an evolutionary trade-off exists between niche size, tissue aging, and the risk of tumorigenesis. Further, mouse and human niches exist at a size that minimizes the probability of tumorigenesis, at the expense of accumulating deleterious mutations due to genetic drift. Finally, we show that the trade-off between the probability of tumorigenesis and the extent of aging depends on whether or not mutational effects confer a selective advantage in the stem cell niche.
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Affiliation(s)
- Vincent L Cannataro
- Department of Biostatistics Yale School of Public Health Yale University New Haven CT USA.,Department of Biology University of Florida Gainesville FL USA
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