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Fanchon E, Stéphanou A. Is Cancer Metabolism an Atavism? Cancers (Basel) 2024; 16:2415. [PMID: 39001477 PMCID: PMC11240651 DOI: 10.3390/cancers16132415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2024] [Revised: 06/28/2024] [Accepted: 06/28/2024] [Indexed: 07/16/2024] Open
Abstract
The atavistic theory of cancer posits that cancer emerges and progresses through the reversion of cellular phenotypes to more ancestral types with genomic and epigenetic changes deactivating recently evolved genetic modules and activating ancient survival mechanisms. This theory aims at explaining the known cancer hallmarks and the paradox of cancer's predictable progression despite the randomness of genetic mutations. Lineweaver and colleagues recently proposed the Serial Atavism Model (SAM), an enhanced version of the atavistic theory, which suggests that cancer progression involves multiple atavistic reversions where cells regress through evolutionary stages, losing recently evolved traits first and reactivating primitive ones later. The Warburg effect, where cancer cells upregulate glycolysis and lactate production in the presence of oxygen instead of using oxidative phosphorylation, is one of the key feature of the SAM. It is associated with the metabolism of ancient cells living on Earth before the oxygenation of the atmosphere. This review addresses the question of whether cancer metabolism can be considered as an atavistic reversion. By analyzing several known characteristics of cancer metabolism, we reach the conclusion that this version of the atavistic theory does not provide an adequate conceptual frame for cancer research. Cancer metabolism spans a whole spectrum of metabolic states which cannot be fully explained by a sequential reversion to an ancient state. Moreover, we interrogate the nature of cancer metabolism and discuss its characteristics within the framework of the SAM.
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Affiliation(s)
- Eric Fanchon
- Université Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
| | - Angélique Stéphanou
- Université Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, TIMC, 38000 Grenoble, France
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2
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Simpson K, L'Homme A, Keymer J, Federici F. Spatial biology of Ising-like synthetic genetic networks. BMC Biol 2023; 21:185. [PMID: 37667283 PMCID: PMC10478219 DOI: 10.1186/s12915-023-01681-4] [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: 12/20/2022] [Accepted: 08/11/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Understanding how spatial patterns of gene expression emerge from the interaction of individual gene networks is a fundamental challenge in biology. Developing a synthetic experimental system with a common theoretical framework that captures the emergence of short- and long-range spatial correlations (and anti-correlations) from interacting gene networks could serve to uncover generic scaling properties of these ubiquitous phenomena. RESULTS Here, we combine synthetic biology, statistical mechanics models, and computational simulations to study the spatial behavior of synthetic gene networks (SGNs) in Escherichia coli quasi-2D colonies growing on hard agar surfaces. Guided by the combined mechanisms of the contact process lattice simulation and two-dimensional Ising model (CPIM), we describe the spatial behavior of bi-stable and chemically coupled SGNs that self-organize into patterns of long-range correlations with power-law scaling or short-range anti-correlations. These patterns, resembling ferromagnetic and anti-ferromagnetic configurations of the Ising model near critical points, maintain their scaling properties upon changes in growth rate and cell shape. CONCLUSIONS Our findings shed light on the spatial biology of coupled and bistable gene networks in growing cell populations. This emergent spatial behavior could provide insights into the study and engineering of self-organizing gene patterns in eukaryotic tissues and bacterial consortia.
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Affiliation(s)
- Kevin Simpson
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile
| | - Alfredo L'Homme
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan Keymer
- Institute for Advanced Studies, Shenzhen X-Institute, Shenzhen, China.
- Schools of Physics and Biology, Pontificia Universidad Católica de Chile, Santiago, Chile.
- Department of Natural Sciences and Technology, Universidad de Aysén, Coyhaique, Chile.
| | - Fernán Federici
- ANID - Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
- Institute for Biological and Medical Engineering, Schools of Engineering, Medicine and Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
- FONDAP Center for Genome Regulation - Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Artime O, De Domenico M. From the origin of life to pandemics: emergent phenomena in complex systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200410. [PMID: 35599559 PMCID: PMC9125231 DOI: 10.1098/rsta.2020.0410] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 05/31/2023]
Abstract
When a large number of similar entities interact among each other and with their environment at a low scale, unexpected outcomes at higher spatio-temporal scales might spontaneously arise. This non-trivial phenomenon, known as emergence, characterizes a broad range of distinct complex systems-from physical to biological and social-and is often related to collective behaviour. It is ubiquitous, from non-living entities such as oscillators that under specific conditions synchronize, to living ones, such as birds flocking or fish schooling. Despite the ample phenomenological evidence of the existence of systems' emergent properties, central theoretical questions to the study of emergence remain unanswered, such as the lack of a widely accepted, rigorous definition of the phenomenon or the identification of the essential physical conditions that favour emergence. We offer here a general overview of the phenomenon of emergence and sketch current and future challenges on the topic. Our short review also serves as an introduction to the theme issue Emergent phenomena in complex physical and socio-technical systems: from cells to societies, where we provide a synthesis of the contents tackled in the issue and outline how they relate to these challenges, spanning from current advances in our understanding on the origin of life to the large-scale propagation of infectious diseases. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Oriol Artime
- Fondazione Bruno Kessler, Via Sommarive 18, Povo, TN 38123, Italy
| | - Manlio De Domenico
- Department of Physics and Astronomy ‘Galileo Galilei’, University of Padua, Padova, Veneto, Italy
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Bonforti A, Solé R. Unicellular-multicellular evolutionary branching driven by resource limitations. J R Soc Interface 2022; 19:20220018. [PMID: 35642429 DOI: 10.1098/rsif.2022.0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Multicellular life forms have evolved many times on our planet, suggesting that this is a common evolutionary innovation. Multiple advantages have been proposed for the emergence of multicellularity (MC). In this paper, we address the problem of how the first precondition for MC, namely 'stay together', might have occurred under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of evolved cell-cell adhesion among growing and dividing cells that exploit a localized resource with a given size, we show that a transition occurs at a critical resource size separating a phase of evolved multicellular aggregates from a phase where unicellularity (UC) is favoured. The two phases are separated by an intermediate domain where both UC and MC can be selected by evolution. This model provides a minimal approach to the early stages that were required to transition from individuality to cohesive groups of cells associated with a physical cooperative effect: when resources are present only in a localized portion of the habitat, MC is a desirable property as it helps cells to keep close to the available local nutrients.
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Affiliation(s)
- Adriano Bonforti
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain
| | - Ricard Solé
- ICREA-Complex Systems Lab, UPF-PRBB, Dr. Aiguader 80, 08003 Barcelona, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Passeig Maritim de la Barceloneta 37, 08003 Barcelona, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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Ivanov I, Castellanos SL, Balasbas S, Otrin L, Marušič N, Vidaković-Koch T, Sundmacher K. Bottom-Up Synthesis of Artificial Cells: Recent Highlights and Future Challenges. Annu Rev Chem Biomol Eng 2021; 12:287-308. [PMID: 34097845 DOI: 10.1146/annurev-chembioeng-092220-085918] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The bottom-up approach in synthetic biology aims to create molecular ensembles that reproduce the organization and functions of living organisms and strives to integrate them in a modular and hierarchical fashion toward the basic unit of life-the cell-and beyond. This young field stands on the shoulders of fundamental research in molecular biology and biochemistry, next to synthetic chemistry, and, augmented by an engineering framework, has seen tremendous progress in recent years thanks to multiple technological and scientific advancements. In this timely review of the research over the past decade, we focus on three essential features of living cells: the ability to self-reproduce via recursive cycles of growth and division, the harnessing of energy to drive cellular processes, and the assembly of metabolic pathways. In addition, we cover the increasing efforts to establish multicellular systems via different communication strategies and critically evaluate the potential applications.
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Affiliation(s)
- Ivan Ivanov
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; , , , ,
| | - Sebastián López Castellanos
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; , , , ,
| | - Severo Balasbas
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; , , , ,
| | - Lado Otrin
- Electrochemical Energy Conversion, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; ,
| | - Nika Marušič
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; , , , ,
| | - Tanja Vidaković-Koch
- Electrochemical Energy Conversion, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; ,
| | - Kai Sundmacher
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany; , , , , .,Department of Process Systems Engineering, Otto-von-Guericke University Magdeburg, 39106 Magdeburg, Germany
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Abstract
Increased control of biological growth and form is an essential gateway to transformative medical advances. Repairing of birth defects, restoring lost or damaged organs, normalizing tumors, all depend on understanding how cells cooperate to make specific, functional large-scale structures. Despite advances in molecular genetics, significant gaps remain in our understanding of the meso-scale rules of morphogenesis. An engineering approach to this problem is the creation of novel synthetic living forms, greatly extending available model systems beyond evolved plant and animal lineages. Here, we review recent advances in the emerging field of synthetic morphogenesis, the bioengineering of novel multicellular living bodies. Emphasizing emergent self-organization, tissue-level guided self-assembly, and active functionality, this work is the essential next generation of synthetic biology. Aside from useful living machines for specific functions, the rational design and analysis of new, coherent anatomies will greatly increase our understanding of foundational questions in evolutionary developmental and cell biology.
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Affiliation(s)
- Mo R. Ebrahimkhani
- Department of Pathology, School of Medicine, University of Pittsburgh, A809B Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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Duran-Nebreda S, Pla J, Vidiella B, Piñero J, Conde-Pueyo N, Solé R. Synthetic Lateral Inhibition in Periodic Pattern Forming Microbial Colonies. ACS Synth Biol 2021; 10:277-285. [PMID: 33449631 PMCID: PMC8486170 DOI: 10.1021/acssynbio.0c00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multicellular entities are characterized by intricate spatial patterns, intimately related to the functions they perform. These patterns are often created from isotropic embryonic structures, without external information cues guiding the symmetry breaking process. Mature biological structures also display characteristic scales with repeating distributions of signals or chemical species across space. Many candidate patterning modules have been used to explain processes during development and typically include a set of interacting and diffusing chemicals or agents known as morphogens. Great effort has been put forward to better understand the conditions in which pattern-forming processes can occur in the biological domain. However, evidence and practical knowledge allowing us to engineer symmetry-breaking is still lacking. Here we follow a different approach by designing a synthetic gene circuit in E. coli that implements a local activation long-range inhibition mechanism. The synthetic gene network implements an artificial differentiation process that changes the physicochemical properties of the agents. Using both experimental results and modeling, we show that the proposed system is capable of symmetry-breaking leading to regular spatial patterns during colony growth. Studying how these patterns emerge is fundamental to further our understanding of the evolution of biocomplexity and the role played by self-organization. The artificial system studied here and the engineering perspective on embryogenic processes can help validate developmental theories and identify universal properties underpinning biological pattern formation, with special interest for the area of synthetic developmental biology.
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Affiliation(s)
- Salva Duran-Nebreda
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Evolution of Technology Lab, Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
| | - Jordi Pla
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Blai Vidiella
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Jordi Piñero
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Nuria Conde-Pueyo
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Ricard Solé
- Institut de Biologia Evolutiva (CSIC-UPF), 08003 Barcelona, Spain
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, United States
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Bassel GW. Multicellular Systems Biology: Quantifying Cellular Patterning and Function in Plant Organs Using Network Science. MOLECULAR PLANT 2019; 12:731-742. [PMID: 30794885 DOI: 10.1016/j.molp.2019.02.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 06/09/2023]
Abstract
Organ function is at least partially shaped and constrained by the organization of their constituent cells. Extensive investigation has revealed mechanisms explaining how these patterns are generated, with less being known about their functional relevance. In this paper, a methodology to discretize and quantitatively analyze cellular patterning is described. By performing global organ-scale cellular interaction mapping, the organization of cells can be extracted and analyzed using network science. This provides a means to take the developmental analysis of cellular organization in complex organisms beyond qualitative descriptions and provides data-driven approaches to inferring cellular function. The bridging of a structure-function relationship in hypocotyl epidermal cell patterning through global topological analysis provides support for this approach. The analysis of cellular topologies from patterning mutants further enables the contribution of gene activity toward the organizational properties of tissues to be linked, bridging molecular and tissue scales. This systems-based approach to investigate multicellular complexity paves the way to uncovering the principles of complex organ design and achieving predictive genotype-phenotype mapping.
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Affiliation(s)
- George W Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
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Sekine R, Shibata T, Ebisuya M. Synthetic mammalian pattern formation driven by differential diffusivity of Nodal and Lefty. Nat Commun 2018; 9:5456. [PMID: 30575724 PMCID: PMC6303393 DOI: 10.1038/s41467-018-07847-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 12/03/2018] [Indexed: 01/08/2023] Open
Abstract
A synthetic mammalian reaction-diffusion pattern has yet to be created, and Nodal-Lefty signaling has been proposed to meet conditions for pattern formation: Nodal is a short-range activator whereas Lefty is a long-range inhibitor. However, this pattern forming possibility has never been directly tested, and the underlying mechanisms of differential diffusivity of Nodal and Lefty remain unclear. Here, through a combination of synthetic and theoretical approaches, we show that a reconstituted Nodal-Lefty network in mammalian cells spontaneously gives rise to a pattern. Surprisingly, extracellular Nodal is confined underneath the cells, resulting in a narrow distribution compared with Lefty. The short-range distribution requires the finger 1 domain of Nodal, and transplantation of the finger 1 domain into Lefty shortens the distribution of Lefty, successfully preventing pattern formation. These results indicate that the differences in localization and domain structures between Nodal and Lefty, combined with the activator-inhibitor topology, are sufficient for reaction-diffusion patterning. Nodal-Lefty signaling combines a short-range activator and a long-range inhibitor for axis formation and left-right patterning. Here the authors reconstitute a synthetic biology activator-inhibitor circuit of Nodal-Lefty to drive pattern formation in mammalian cells.
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Affiliation(s)
- Ryoji Sekine
- Laboratory for Reconstitutive Developmental Biology, RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan
| | - Tatsuo Shibata
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan
| | - Miki Ebisuya
- Laboratory for Reconstitutive Developmental Biology, RIKEN Center for Biosystems Dynamics Research (RIKEN BDR), 2-2-3 Minatojima-minamimachi, Chuo-ku, 650-0047, Kobe, Japan. .,European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader, 88, 08003, Barcelona, Spain.
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