1
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McMillen P, Levin M. Collective intelligence: A unifying concept for integrating biology across scales and substrates. Commun Biol 2024; 7:378. [PMID: 38548821 PMCID: PMC10978875 DOI: 10.1038/s42003-024-06037-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/11/2024] [Indexed: 04/01/2024] Open
Abstract
A defining feature of biology is the use of a multiscale architecture, ranging from molecular networks to cells, tissues, organs, whole bodies, and swarms. Crucially however, biology is not only nested structurally, but also functionally: each level is able to solve problems in distinct problem spaces, such as physiological, morphological, and behavioral state space. Percolating adaptive functionality from one level of competent subunits to a higher functional level of organization requires collective dynamics: multiple components must work together to achieve specific outcomes. Here we overview a number of biological examples at different scales which highlight the ability of cellular material to make decisions that implement cooperation toward specific homeodynamic endpoints, and implement collective intelligence by solving problems at the cell, tissue, and whole-organism levels. We explore the hypothesis that collective intelligence is not only the province of groups of animals, and that an important symmetry exists between the behavioral science of swarms and the competencies of cells and other biological systems at different scales. We then briefly outline the implications of this approach, and the possible impact of tools from the field of diverse intelligence for regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Patrick McMillen
- Department of Biology, Tufts University, Medford, MA, 02155, USA
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, 02155, USA.
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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2
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Tung A, Sperry MM, Clawson W, Pavuluri A, Bulatao S, Yue M, Flores RM, Pai VP, McMillen P, Kuchling F, Levin M. Embryos assist morphogenesis of others through calcium and ATP signaling mechanisms in collective teratogen resistance. Nat Commun 2024; 15:535. [PMID: 38233424 PMCID: PMC10794468 DOI: 10.1038/s41467-023-44522-2] [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: 06/22/2023] [Accepted: 12/17/2023] [Indexed: 01/19/2024] Open
Abstract
Information for organismal patterning can come from a variety of sources. We investigate the possibility that instructive influences for normal embryonic development are provided not only at the level of cells within the embryo, but also via interactions between embryos. To explore this, we challenge groups of embryos with disruptors of normal development while varying group size. Here, we show that Xenopus laevis embryos are much more sensitive to a diverse set of chemical and molecular-biological perturbations when allowed to develop alone or in small groups, than in large groups. Keeping per-embryo exposure constant, we find that increasing the number of exposed embryos in a cohort increases the rate of survival while incidence of defects decreases. This inter-embryo assistance effect is mediated by short-range diffusible signals and involves the P2 ATP receptor. Our data and computational model emphasize that morphogenesis is a collective phenomenon not only at the level of cells, but also of whole bodies, and that cohort size is a crucial variable in studies of ecotoxicology, teratogenesis, and developmental plasticity.
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Affiliation(s)
- Angela Tung
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Megan M Sperry
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Wesley Clawson
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Ananya Pavuluri
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Sydney Bulatao
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michelle Yue
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Ramses Martinez Flores
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Vaibhav P Pai
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Patrick McMillen
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Franz Kuchling
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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3
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Hutchison A, Sibanda C, Hulme M, Anwar S, Gur B, Thomas R, Lowery LA. Re-examining the evidence that ivermectin induces a melanoma-like state in Xenopus embryos. Bioessays 2024; 46:e2300143. [PMID: 37985957 PMCID: PMC10841629 DOI: 10.1002/bies.202300143] [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: 08/01/2023] [Revised: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
Modeling metastasis in animal systems has been an important focus for developing cancer therapeutics. Xenopus laevis is a well-established model, known for its use in identifying genetic mechanisms underlying diseases and disorders in humans. Prior literature has suggested that the drug, ivermectin, can be used in Xenopus to induce melanocytes to convert into a metastatic melanoma-like state, and thus could be ideal for testing possible melanoma therapies in vivo. However, there are notable inconsistencies between ivermectin studies in Xenopus and the application of ivermectin in mammalian systems, that are relevant to cancer and melanoma research. In this review, we examine the ivermectin-induced phenotypes in Xenopus, and we explore the current uses of ivermectin in human research. We conclude that while ivermectin may be a useful drug for many biomedical purposes, it is not ideal to induce a metastatic melanocyte phenotype in Xenopus for testing the effects of potential melanoma therapeutics.
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Affiliation(s)
- Ainsley Hutchison
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Chiedza Sibanda
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Mackenzie Hulme
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Sarah Anwar
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Bengisu Gur
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Rachael Thomas
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
| | - Laura Anne Lowery
- Alfred B. Nobel Section of Hematology and Medical Oncology, Boston University Chobanian and Avedisian School of Medicine and Boston Medical Center, Boston, Massachusetts, USA
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4
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Mathews J, Levin M. Cancer's unique bioelectric properties: From cells to body-wide networks: Comment on: "The distinguishing electrical properties of cancer cells" by Elisabetta Di Gregorio, Simone Israel, Michael Staelens, Gabriella Tankel, Karthik Shankar, and Jack A. Tuszynski (this issue). Phys Life Rev 2023; 47:113-115. [PMID: 37837910 DOI: 10.1016/j.plrev.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/16/2023]
Affiliation(s)
- J Mathews
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - M Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
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5
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Abstract
Tissue regeneration is not simply a local repair event occurring in isolation from the distant, uninjured parts of the body. Rather, evidence indicates that regeneration is a whole-animal process involving coordinated interactions between different organ systems. Here, we review recent studies that reveal how remote uninjured tissues and organ systems respond to and engage in regeneration. We also discuss the need for toolkits and technological advancements to uncover and dissect organ communication during regeneration.
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Affiliation(s)
- Fei Sun
- Duke Regeneration Center, Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
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6
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Jones E, McLaughlin KA. A Novel Perspective on Neuronal Control of Anatomical Patterning, Remodeling, and Maintenance. Int J Mol Sci 2023; 24:13358. [PMID: 37686164 PMCID: PMC10488252 DOI: 10.3390/ijms241713358] [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: 07/20/2023] [Revised: 08/14/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
While the nervous system may be best known as the sensory communication center of an organism, recent research has revealed a myriad of multifaceted roles for both the CNS and PNS from early development to adult regeneration and remodeling. These systems work to orchestrate tissue pattern formation during embryonic development and continue shaping pattering through transitional periods such as metamorphosis and growth. During periods of injury or wounding, the nervous system has also been shown to influence remodeling and wound healing. The neuronal mechanisms responsible for these events are largely conserved across species, suggesting this evidence may be important in understanding and resolving many human defects and diseases. By unraveling these diverse roles, this paper highlights the necessity of broadening our perspective on the nervous system beyond its conventional functions. A comprehensive understanding of the complex interactions and contributions of the nervous system throughout development and adulthood has the potential to revolutionize therapeutic strategies and open new avenues for regenerative medicine and tissue engineering. This review highlights an important role for the nervous system during the patterning and maintenance of complex tissues and provides a potential avenue for advancing biomedical applications.
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Affiliation(s)
| | - Kelly A. McLaughlin
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA;
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7
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Levin M. Darwin's agential materials: evolutionary implications of multiscale competency in developmental biology. Cell Mol Life Sci 2023; 80:142. [PMID: 37156924 PMCID: PMC10167196 DOI: 10.1007/s00018-023-04790-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023]
Abstract
A critical aspect of evolution is the layer of developmental physiology that operates between the genotype and the anatomical phenotype. While much work has addressed the evolution of developmental mechanisms and the evolvability of specific genetic architectures with emergent complexity, one aspect has not been sufficiently explored: the implications of morphogenetic problem-solving competencies for the evolutionary process itself. The cells that evolution works with are not passive components: rather, they have numerous capabilities for behavior because they derive from ancestral unicellular organisms with rich repertoires. In multicellular organisms, these capabilities must be tamed, and can be exploited, by the evolutionary process. Specifically, biological structures have a multiscale competency architecture where cells, tissues, and organs exhibit regulative plasticity-the ability to adjust to perturbations such as external injury or internal modifications and still accomplish specific adaptive tasks across metabolic, transcriptional, physiological, and anatomical problem spaces. Here, I review examples illustrating how physiological circuits guiding cellular collective behavior impart computational properties to the agential material that serves as substrate for the evolutionary process. I then explore the ways in which the collective intelligence of cells during morphogenesis affect evolution, providing a new perspective on the evolutionary search process. This key feature of the physiological software of life helps explain the remarkable speed and robustness of biological evolution, and sheds new light on the relationship between genomes and functional anatomical phenotypes.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave. 334 Research East, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan St., Boston, MA, 02115, USA.
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8
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Pio-Lopez L, Levin M. Morphoceuticals: perspectives for discovery of drugs targeting anatomical control mechanisms in regenerative medicine, cancer and aging. Drug Discov Today 2023; 28:103585. [PMID: 37059328 DOI: 10.1016/j.drudis.2023.103585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/18/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Morphoceuticals are a new class of interventions that target the setpoints of anatomical homeostasis for efficient, modular control of growth and form. Here, we focus on a subclass: electroceuticals, which specifically target the cellular bioelectrical interface. Cellular collectives in all tissues form bioelectrical networks via ion channels and gap junctions that process morphogenetic information, controlling gene expression and allowing cell networks to adaptively and dynamically control growth and pattern formation. Recent progress in understanding this physiological control system, including predictive computational models, suggests that targeting bioelectrical interfaces can control embryogenesis and maintain shape against injury, senescence and tumorigenesis. We propose a roadmap for drug discovery focused on manipulating endogenous bioelectric signaling for regenerative medicine, cancer suppression and antiaging therapeutics. Teaser: By taking advantage of the native problem-solving competencies of cells and tissues, a new kind of top-down approach to biomedicine becomes possible. Bioelectricity offers an especially tractable interface for interventions targeting the software of life for regenerative medicine applications.
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Affiliation(s)
- Léo Pio-Lopez
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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9
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McMillen P, Walker SI, Levin M. Information Theory as an Experimental Tool for Integrating Disparate Biophysical Signaling Modules. Int J Mol Sci 2022; 23:ijms23179580. [PMID: 36076979 PMCID: PMC9455895 DOI: 10.3390/ijms23179580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/13/2022] [Accepted: 08/14/2022] [Indexed: 11/16/2022] Open
Abstract
There is a growing appreciation in the fields of cell biology and developmental biology that cells collectively process information in time and space. While many powerful molecular tools exist to observe biophysical dynamics, biologists must find ways to quantitatively understand these phenomena at the systems level. Here, we present a guide for the application of well-established information theory metrics to biological datasets and explain these metrics using examples from cell, developmental and regenerative biology. We introduce a novel computational tool named after its intended purpose, calcium imaging, (CAIM) for simple, rigorous application of these metrics to time series datasets. Finally, we use CAIM to study calcium and cytoskeletal actin information flow patterns between Xenopus laevis embryonic animal cap stem cells. The tools that we present here should enable biologists to apply information theory to develop a systems-level understanding of information processing across a diverse array of experimental systems.
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Affiliation(s)
- Patrick McMillen
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
| | - Sara I. Walker
- Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ 85281, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA
- Correspondence:
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10
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Grodstein J, Levin M. A Computational Approach to Explaining Bioelectrically Induced Persistent, Stochastic Changes of Axial Polarity in Planarian Regeneration. Bioelectricity 2022. [DOI: 10.1089/bioe.2021.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Joel Grodstein
- Department of Electrical and Computer Engineering, Tufts University, Medford, Massachusetts, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, Massachusetts, USA
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11
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Abstract
Extracting mechanistic knowledge from the spatial and temporal phenotypes of morphogenesis is a current challenge due to the complexity of biological regulation and their feedback loops. Furthermore, these regulatory interactions are also linked to the biophysical forces that shape a developing tissue, creating complex interactions responsible for emergent patterns and forms. Here we show how a computational systems biology approach can aid in the understanding of morphogenesis from a mechanistic perspective. This methodology integrates the modeling of tissues and whole-embryos with dynamical systems, the reverse engineering of parameters or even whole equations with machine learning, and the generation of precise computational predictions that can be tested at the bench. To implement and perform the computational steps in the methodology, we present user-friendly tools, computer code, and guidelines. The principles of this methodology are general and can be adapted to other model organisms to extract mechanistic knowledge of their morphogenesis.
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Affiliation(s)
- Jason M Ko
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Reza Mousavi
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
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12
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Lobo D. Formalizing Phenotypes of Regeneration. Methods Mol Biol 2022; 2450:663-679. [PMID: 35359335 PMCID: PMC9761515 DOI: 10.1007/978-1-0716-2172-1_36] [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] [Indexed: 06/14/2023]
Abstract
Regeneration experiments can produce complex phenotypes including morphological outcomes and gene expression patterns that are crucial for the understanding of the mechanisms of regeneration. However, due to their inherent complexity, variability between individuals, and heterogeneous data spreading across the literature, extracting mechanistic knowledge from them is a current challenge. Toward this goal, here we present protocols to unambiguously formalize the phenotypes of regeneration and their experimental procedures using precise mathematical morphological descriptions and standardized gene expression patterns. We illustrate the application of the methodology with step-by-step protocols for planaria and limb regeneration phenotypes. The curated datasets with these methods are not only helpful for human scientists, but they represent a key formalized resource that can be easily integrated into downstream reverse engineering methodologies for the automatic extraction of mechanistic knowledge. This approach can pave the way for discovering comprehensive systems-level models of regeneration.
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Affiliation(s)
- Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, USA.
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13
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McMillen P, Oudin MJ, Levin M, Payne SL. Beyond Neurons: Long Distance Communication in Development and Cancer. Front Cell Dev Biol 2021; 9:739024. [PMID: 34621752 PMCID: PMC8491768 DOI: 10.3389/fcell.2021.739024] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022] Open
Abstract
Cellular communication is important in all aspects of tissue and organism functioning, from the level of single cells, two discreet populations, and distant tissues of the body. Long distance communication networks integrate individual cells into tissues to maintain a complex organism during development, but when communication between cells goes awry, disease states such as cancer emerge. Herein we discuss the growing body of evidence suggesting that communication methods known to be employed by neurons, also exist in other cell types. We identify three major areas of long-distance communication: bioelectric signaling, tunneling nanotubes (TNTs), and macrophage modulation of networks, and draw comparisons about how these systems operate in the context of development and cancer. Bioelectric signaling occurs between cells through exchange of ions and tissue-level electric fields, leading to changes in biochemical gradients and molecular signaling pathways to control normal development and tumor growth and invasion in cancer. TNTs transport key morphogens and other cargo long distances, mediating electrical coupling, tissue patterning, and malignancy of cancer cells. Lastly macrophages maintain long distance signaling networks through trafficking of vesicles during development, providing communication relays and priming favorable microenvironments for cancer metastasis. By drawing comparisons between non-neural long distance signaling in the context of development and cancer we aim to encourage crosstalk between the two fields to cultivate new hypotheses and potential therapeutic strategies.
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Affiliation(s)
- Patrick McMillen
- Department of Biology, Allen Discovery Center, Tufts University, Medford, MA, United States
| | - Madeleine J Oudin
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
| | - Michael Levin
- Department of Biology, Allen Discovery Center, Tufts University, Medford, MA, United States
| | - Samantha L Payne
- Department of Biomedical Engineering, Tufts University, Medford, MA, United States
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14
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Levin M. Bioelectrical approaches to cancer as a problem of the scaling of the cellular self. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 165:102-113. [PMID: 33961843 DOI: 10.1016/j.pbiomolbio.2021.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022]
Abstract
One lens with which to understand the complex phenomenon of cancer is that of developmental biology. Cancer is the inevitable consequence of a breakdown of the communication that enables individual cells to join into computational networks that work towards large-scale, morphogenetic goals instead of more primitive, unicellular objectives. This perspective suggests that cancer may be a physiological disorder, not necessarily due to problems with the genetically-specified protein hardware. One aspect of morphogenetic coordination is bioelectric signaling, and indeed an abnormal bioelectric signature non-invasively reveals the site of incipient tumors in amphibian models. Functionally, a disruption of resting potential states triggers metastatic melanoma phenotypes in embryos with no genetic defects or carcinogen exposure. Conversely, optogenetic or molecular-biological modulation of bioelectric states can override powerful oncogenic mutations and prevent or normalize tumors. The bioelectrically-mediated information flows that harness cells toward body-level anatomical outcomes represent a very attractive and tractable endogenous control system, which is being targeted by emerging approaches to cancer.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave., Suite 4600, Medford, MA, 02155, USA.
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15
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Pezzulo G, LaPalme J, Durant F, Levin M. Bistability of somatic pattern memories: stochastic outcomes in bioelectric circuits underlying regeneration. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190765. [PMID: 33550952 PMCID: PMC7935058 DOI: 10.1098/rstb.2019.0765] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 02/06/2023] Open
Abstract
Nervous systems' computational abilities are an evolutionary innovation, specializing and speed-optimizing ancient biophysical dynamics. Bioelectric signalling originated in cells' communication with the outside world and with each other, enabling cooperation towards adaptive construction and repair of multicellular bodies. Here, we review the emerging field of developmental bioelectricity, which links the field of basal cognition to state-of-the-art questions in regenerative medicine, synthetic bioengineering and even artificial intelligence. One of the predictions of this view is that regeneration and regulative development can restore correct large-scale anatomies from diverse starting states because, like the brain, they exploit bioelectric encoding of distributed goal states-in this case, pattern memories. We propose a new interpretation of recent stochastic regenerative phenotypes in planaria, by appealing to computational models of memory representation and processing in the brain. Moreover, we discuss novel findings showing that bioelectric changes induced in planaria can be stored in tissue for over a week, thus revealing that somatic bioelectric circuits in vivo can implement a long-term, re-writable memory medium. A consideration of the mechanisms, evolution and functionality of basal cognition makes novel predictions and provides an integrative perspective on the evolution, physiology and biomedicine of information processing in vivo. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Giovanni Pezzulo
- Institute of Cognitive Sciences and Technologies, National Research Council, Rome, Italy
| | - Joshua LaPalme
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Fallon Durant
- Allen Discovery Center, Tufts University, Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA
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16
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Levin M. The Biophysics of Regenerative Repair Suggests New Perspectives on Biological Causation. Bioessays 2020; 42:e1900146. [PMID: 31994772 DOI: 10.1002/bies.201900146] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 12/03/2019] [Indexed: 12/13/2022]
Abstract
Evolution exploits the physics of non-neural bioelectricity to implement anatomical homeostasis: a process in which embryonic patterning, remodeling, and regeneration achieve invariant anatomical outcomes despite external interventions. Linear "developmental pathways" are often inadequate explanations for dynamic large-scale pattern regulation, even when they accurately capture relationships between molecular components. Biophysical and computational aspects of collective cell activity toward a target morphology reveal interesting aspects of causation in biology. This is critical not only for unraveling evolutionary and developmental events, but also for the design of effective strategies for biomedical intervention. Bioelectrical controls of growth and form, including stochastic behavior in such circuits, highlight the need for the formulation of nuanced views of pathways, drivers of system-level outcomes, and modularity, borrowing from concepts in related disciplines such as cybernetics, control theory, computational neuroscience, and information theory. This approach has numerous practical implications for basic research and for applications in regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
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17
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Hwang J, Hari A, Cheng R, Gardner JG, Lobo D. Kinetic modeling of microbial growth, enzyme activity, and gene deletions: An integrated model of β-glucosidase function in Cellvibrio japonicus. Biotechnol Bioeng 2020; 117:3876-3890. [PMID: 32833226 DOI: 10.1002/bit.27544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/11/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022]
Abstract
Understanding the complex growth and metabolic dynamics in microorganisms requires advanced kinetic models containing both metabolic reactions and enzymatic regulation to predict phenotypic behaviors under different conditions and perturbations. Most current kinetic models lack gene expression dynamics and are separately calibrated to distinct media, which consequently makes them unable to account for genetic perturbations or multiple substrates. This challenge limits our ability to gain a comprehensive understanding of microbial processes towards advanced metabolic optimizations that are desired for many biotechnology applications. Here, we present an integrated computational and experimental approach for the development and optimization of mechanistic kinetic models for microbial growth and metabolic and enzymatic dynamics. Our approach integrates growth dynamics, gene expression, protein secretion, and gene-deletion phenotypes. We applied this methodology to build a dynamic model of the growth kinetics in batch culture of the bacterium Cellvibrio japonicus grown using either cellobiose or glucose media. The model parameters were inferred from an experimental data set using an evolutionary computation method. The resulting model was able to explain the growth dynamics of C. japonicus using either cellobiose or glucose media and was also able to accurately predict the metabolite concentrations in the wild-type strain as well as in β-glucosidase gene deletion mutant strains. We validated the model by correctly predicting the non-diauxic growth and metabolite consumptions of the wild-type strain in a mixed medium containing both cellobiose and glucose, made further predictions of mutant strains growth phenotypes when using cellobiose and glucose media, and demonstrated the utility of the model for designing industrially-useful strains. Importantly, the model is able to explain the role of the different β-glucosidases and their behavior under genetic perturbations. This integrated approach can be extended to other metabolic pathways to produce mechanistic models for the comprehensive understanding of enzymatic functions in multiple substrates.
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Affiliation(s)
- Jeanice Hwang
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Archana Hari
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Raymond Cheng
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
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18
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Yang M, James AD, Suman R, Kasprowicz R, Nelson M, O'Toole PJ, Brackenbury WJ. Voltage-dependent activation of Rac1 by Na v 1.5 channels promotes cell migration. J Cell Physiol 2020; 235:3950-3972. [PMID: 31612502 PMCID: PMC6973152 DOI: 10.1002/jcp.29290] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/30/2019] [Indexed: 12/17/2022]
Abstract
Ion channels can regulate the plasma membrane potential (Vm ) and cell migration as a result of altered ion flux. However, the mechanism by which Vm regulates motility remains unclear. Here, we show that the Nav 1.5 sodium channel carries persistent inward Na+ current which depolarizes the resting Vm at the timescale of minutes. This Nav 1.5-dependent Vm depolarization increases Rac1 colocalization with phosphatidylserine, to which it is anchored at the leading edge of migrating cells, promoting Rac1 activation. A genetically encoded FRET biosensor of Rac1 activation shows that depolarization-induced Rac1 activation results in acquisition of a motile phenotype. By identifying Nav 1.5-mediated Vm depolarization as a regulator of Rac1 activation, we link ionic and electrical signaling at the plasma membrane to small GTPase-dependent cytoskeletal reorganization and cellular migration. We uncover a novel and unexpected mechanism for Rac1 activation, which fine tunes cell migration in response to ionic and/or electric field changes in the local microenvironment.
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Affiliation(s)
- Ming Yang
- Department of BiologyUniversity of YorkYorkUK
| | - Andrew D. James
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Rakesh Suman
- Phase Focus Ltd, Electric WorksSheffield Digital CampusSheffieldUK
| | | | - Michaela Nelson
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
| | - Peter J. O'Toole
- Bioscience Technology Facility, Department of BiologyUniversity of YorkYorkUK
| | - William J. Brackenbury
- Department of BiologyUniversity of YorkYorkUK
- York Biomedical Research InstituteUniversity of YorkYorkUK
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19
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Jajoo A, Donlon C, Shnayder S, Levin M, McVey M. Sertraline induces DNA damage and cellular toxicity in Drosophila that can be ameliorated by antioxidants. Sci Rep 2020; 10:4512. [PMID: 32161356 PMCID: PMC7066164 DOI: 10.1038/s41598-020-61362-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 02/26/2020] [Indexed: 11/22/2022] Open
Abstract
Sertraline hydrochloride is a commonly prescribed antidepressant medication that acts by amplifying serotonin signaling. Numerous studies have suggested that children of women taking sertraline during pregnancy have an increased risk of developmental defects. Resolving the degree of risk for human fetuses requires comprehensive knowledge of the pathways affected by this drug. We utilized a Drosophila melanogaster model system to assess the effects of sertraline throughout development. Ingestion of sertraline by females did not affect their fecundity or embryogenesis in their progeny. However, larvae that consumed sertraline experienced delayed developmental progression and reduced survival at all stages of development. Genetic experiments showed that these effects were mostly independent of aberrant extracellular serotonin levels. Using an ex vivo imaginal disc culture system, we showed that mitotically active sertraline-treated tissues accumulate DNA double-strand breaks and undergo apoptosis at increased frequencies. Remarkably, the sertraline-induced genotoxicity was partially rescued by co-incubation with ascorbic acid, suggesting that sertraline induces oxidative DNA damage. These findings may have implications for the biomedicine of sertraline-induced birth defects.
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Affiliation(s)
- Arpita Jajoo
- Department of Biology, Tufts University, Medford, MA, USA
| | | | - Sarah Shnayder
- Department of Biology, Tufts University, Medford, MA, USA
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, USA
- Allen Discovery Center at Tufts University, Medford, MA, USA
| | - Mitch McVey
- Department of Biology, Tufts University, Medford, MA, USA.
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20
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Abstract
Selective serotonin reuptake inhibitor (SSRI) drugs, targeting serotonin transport, are widely used. A puzzling and biomedically important phenomenon concerns the persistent sexual dysfunction following SSRI use seen in some patients. What could be the mechanism of a persistent physiological state brought on by a transient exposure to serotonin transport blockers? In this study, we briefly review the clinical facts concerning this side effect of serotonin reuptake inhibitors and suggest a possible mechanism. Bioelectric circuits (among neural or non-neural cells) could persistently maintain alterations of bioelectric cell properties (resting potential), resulting in long-term changes in electrophysiology and signaling. We present new data revealing this phenomenon in planarian flatworms, in which brief SSRI exposures induce long-lasting changes in resting potential profile. We also briefly review recent data linking neurotransmitter signaling to developmental bioelectrics. Further study of tissue bioelectric memory could enable the design of ionoceutical interventions to counteract side effects of SSRIs and similar drugs.
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Affiliation(s)
- David Healy
- Hergest Unit, Department of Psychiatry, Bangor University, Bangor, Wales
| | - Joshua LaPalme
- Allen Discovery Center, Tufts University, Medford, Massachusetts
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, Massachusetts
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21
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Levin M, Selberg J, Rolandi M. Endogenous Bioelectrics in Development, Cancer, and Regeneration: Drugs and Bioelectronic Devices as Electroceuticals for Regenerative Medicine. iScience 2019; 22:519-533. [PMID: 31837520 PMCID: PMC6920204 DOI: 10.1016/j.isci.2019.11.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/15/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
A major frontier in the post-genomic era is the investigation of the control of coordinated growth and three-dimensional form. Dynamic remodeling of complex organs in regulative embryogenesis, regeneration, and cancer reveals that cells and tissues make decisions that implement complex anatomical outcomes. It is now essential to understand not only the genetics that specifies cellular hardware but also the physiological software that implements tissue-level plasticity and robust morphogenesis. Here, we review recent discoveries about the endogenous mechanisms of bioelectrical communication among non-neural cells that enables them to cooperate in vivo. We discuss important advances in bioelectronics, as well as computational and pharmacological tools that are enabling the taming of biophysical controls toward applications in regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, USA.
| | - John Selberg
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA 95064, USA
| | - Marco Rolandi
- Electrical and Computer Engineering Department, University of California, Santa Cruz, CA 95064, USA
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22
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Levin M. The Computational Boundary of a "Self": Developmental Bioelectricity Drives Multicellularity and Scale-Free Cognition. Front Psychol 2019; 10:2688. [PMID: 31920779 PMCID: PMC6923654 DOI: 10.3389/fpsyg.2019.02688] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/14/2019] [Indexed: 12/12/2022] Open
Abstract
All epistemic agents physically consist of parts that must somehow comprise an integrated cognitive self. Biological individuals consist of subunits (organs, cells, and molecular networks) that are themselves complex and competent in their own native contexts. How do coherent biological Individuals result from the activity of smaller sub-agents? To understand the evolution and function of metazoan creatures' bodies and minds, it is essential to conceptually explore the origin of multicellularity and the scaling of the basal cognition of individual cells into a coherent larger organism. In this article, I synthesize ideas in cognitive science, evolutionary biology, and developmental physiology toward a hypothesis about the origin of Individuality: "Scale-Free Cognition." I propose a fundamental definition of an Individual based on the ability to pursue goals at an appropriate level of scale and organization and suggest a formalism for defining and comparing the cognitive capacities of highly diverse types of agents. Any Self is demarcated by a computational surface - the spatio-temporal boundary of events that it can measure, model, and try to affect. This surface sets a functional boundary - a cognitive "light cone" which defines the scale and limits of its cognition. I hypothesize that higher level goal-directed activity and agency, resulting in larger cognitive boundaries, evolve from the primal homeostatic drive of living things to reduce stress - the difference between current conditions and life-optimal conditions. The mechanisms of developmental bioelectricity - the ability of all cells to form electrical networks that process information - suggest a plausible set of gradual evolutionary steps that naturally lead from physiological homeostasis in single cells to memory, prediction, and ultimately complex cognitive agents, via scale-up of the basic drive of infotaxis. Recent data on the molecular mechanisms of pre-neural bioelectricity suggest a model of how increasingly sophisticated cognitive functions emerge smoothly from cell-cell communication used to guide embryogenesis and regeneration. This set of hypotheses provides a novel perspective on numerous phenomena, such as cancer, and makes several unique, testable predictions for interdisciplinary research that have implications not only for evolutionary developmental biology but also for biomedicine and perhaps artificial intelligence and exobiology.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States
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23
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Ko JM, Lobo D. Continuous Dynamic Modeling of Regulated Cell Adhesion: Sorting, Intercalation, and Involution. Biophys J 2019; 117:2166-2179. [PMID: 31732144 PMCID: PMC6895740 DOI: 10.1016/j.bpj.2019.10.032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/19/2019] [Accepted: 10/22/2019] [Indexed: 12/14/2022] Open
Abstract
Cell-cell adhesion is essential for tissue growth and multicellular pattern formation and crucial for the cellular dynamics during embryogenesis and cancer progression. Understanding the dynamical gene regulation of cell adhesion molecules (CAMs) responsible for the emerging spatial tissue behaviors is a current challenge because of the complexity of these nonlinear interactions and feedback loops at different levels of abstraction-from genetic regulation to whole-organism shape formation. To extend our understanding of cell and tissue behaviors due to the regulation of adhesion molecules, here we present a novel, to our knowledge, model for the spatial dynamics of cellular patterning, growth, and shape formation due to the differential expression of CAMs and their regulation. Capturing the dynamic interplay between genetic regulation, CAM expression, and differential cell adhesion, the proposed continuous model can explain the complex and emergent spatial behaviors of cell populations that change their adhesion properties dynamically because of inter- and intracellular genetic regulation. This approach can demonstrate the mechanisms responsible for classical cell-sorting behaviors, cell intercalation in proliferating populations, and the involution of germ layer cells induced by a diffusing morphogen during gastrulation. The model makes predictions on the physical parameters controlling the amplitude and wavelength of a cellular intercalation interface, as well as the crucial role of N-cadherin regulation for the involution and migration of cells beyond the gradient of the morphogen Nodal during zebrafish gastrulation. Integrating the emergent spatial tissue behaviors with the regulation of genes responsible for essential cellular properties such as adhesion will pave the way toward understanding the genetic regulation of large-scale complex patterns and shapes formation in developmental, regenerative, and cancer biology.
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Affiliation(s)
- Jason M Ko
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland; Department of Computer Science and Electrical Engineering, University of Maryland, Baltimore County, Baltimore, Maryland; Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland, Baltimore, Maryland.
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24
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Toward Decoding Bioelectric Events in Xenopus Embryogenesis: New Methodology for Tracking Interplay Between Calcium and Resting Potentials In Vivo. J Mol Biol 2019; 432:605-620. [PMID: 31711960 DOI: 10.1016/j.jmb.2019.10.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 10/07/2019] [Accepted: 10/15/2019] [Indexed: 12/16/2022]
Abstract
Although chemical signaling during embryogenesis is readily addressed by a plethora of available techniques, the developmental functions of ionic signaling are still poorly understood. It is increasingly realized that bioelectric events in nonneural cells are critical for pattern regulation, but their study has been hampered by difficulties in monitoring and manipulating them in vivo. Recent developments in visualizing electrical signaling dynamics in the field of neuroscience have facilitated functional experiments that reveal instructive developmental bioelectric signals. However, there is a pressing need for additional tools to explore time-dependent ionic signaling to understand complex endogenous dynamics. Here, we present methodological advances, including 4D imaging and data analysis, for improved tracking of calcium flux in the Xenopus laevis embryo, lowering the barrier for in vivo physiology work in this important model system. Using these techniques, we investigated the relationship between bioelectric ion channel activity and calcium, finding that cell hyperpolarization and depolarization both induce persistent static elevation of cytoplasmic calcium levels that fade over developmental time. These calcium changes correlate with increased cell mobility in early embryos and abnormal craniofacial morphology in later embryos. We thus highlight membrane potential modulation as a tractable tool for modulation of signaling cascades that rely on calcium as a transduction mechanism. The methods we describe facilitate the study of important novel aspects of developmental physiology, are extendable to numerous classes of existing and forthcoming fluorescent physiological reporters, and establish highly accessible, inexpensive protocols for their investigation.
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25
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Abstract
As the leading cause of death in cancer, there is an urgent need to develop treatments to target the dissemination of primary tumor cells to secondary organs, known as metastasis. Bioelectric signaling has emerged in the last century as an important controller of cell growth, and with the development of current molecular tools we are now beginning to identify its role in driving cell migration and metastasis in a variety of cancer types. This review summarizes the currently available research for bioelectric signaling in solid tumor metastasis. We review the steps of metastasis and discuss how these can be controlled by bioelectric cues at the level of a cell, a population of cells, and the tissue. The role of ion channel, pump, and exchanger activity and ion flux is discussed, along with the importance of the membrane potential and the relationship between ion flux and membrane potential. We also provide an overview of the evidence for control of metastasis by external electric fields (EFs) and draw from examples in embryogenesis and regeneration to discuss the implications for endogenous EFs. By increasing our understanding of the dynamic properties of bioelectric signaling, we can develop new strategies that target metastasis to be translated into the clinic.
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Affiliation(s)
- Samantha L. Payne
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, Massachusetts
| | - Madeleine J. Oudin
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts
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26
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Tuszynski J, Tilli TM, Levin M. Ion Channel and Neurotransmitter Modulators as Electroceutical Approaches to the Control of Cancer. Curr Pharm Des 2019; 23:4827-4841. [PMID: 28554310 PMCID: PMC6340161 DOI: 10.2174/1381612823666170530105837] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/17/2017] [Accepted: 05/23/2017] [Indexed: 11/22/2022]
Abstract
The activities of individual cells must be tightly coordinated in order to build and maintain complex 3-dimensional body structures during embryogenesis and regeneration. Thus, one way to view cancer is within systems biology as a network disorder affecting the ability of cells to properly interact with a morphodynamic field of instructive signals that keeps proliferation and migration orchestrated toward the anatomical needs of the host or-ganism. One layer of this set of instructive microenvironmental cues is bioelectrical. Voltage gradients among all somatic cells (not just excitable nerve and muscle) control cell behavior, and the ionic coupling of cells into networks via electrochemical synapses allows them to implement tissue-level patterning decisions. These gradients have been increasingly impli-cated in the induction and suppression of tumorigenesis and metastasis, in the emerging links between developmental bioelectricity to the cancer problem. Consistent with the well-known role of neurotransmitter molecules in transducing electrical activity to downstream cascades in the brain, serotonergic signaling has likewise been implicated in cancer. Here, we review these recent data and propose new approaches for manipulating bioelectric and neurotransmitter pathways in cancer biology based on a bioelectric view of cancer. To sup-port this methodology, we present new data on the effects of the SSRI Prozac and its analog (ZINC ID = ZINC06811610) on survival of both cancer (MCF7) and normal (MCF10A) breast cells exposed to these compounds. We found an IC50 concentration (25 μM for Pro-zac and 100 μM for the Prozac analog) at which these compounds inhibited tumor cell sur-vival and proliferation. Additionally, at these concentrations, we did not observe alterations in a non-tumoral cell line. This constitutes a proof-of-concept demonstration for our hy-pothesis that the use of both existing and novel drugs as electroceuticals could serve as an alternative to highly toxic chemotherapy strategies replacing or augmenting them with less toxic alternatives. We believe this new approach forms an exciting roadmap for future bio-medical advances.
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Affiliation(s)
- Jack Tuszynski
- Department of Oncology, Faculty of Medicine & Dentistry, University of Alberta, Edmonton, Alberta. Canada
| | - Tatiana M Tilli
- Laboratory of Biological System Modeling, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT/IDN), Center for Technological Development in Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro. Brazil
| | - Michael Levin
- Biology Department, and Allen Discovery Center, Tufts University, Medford, MA, 02155. United States
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27
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Levin M, Pietak AM, Bischof J. Planarian regeneration as a model of anatomical homeostasis: Recent progress in biophysical and computational approaches. Semin Cell Dev Biol 2019; 87:125-144. [PMID: 29635019 PMCID: PMC6234102 DOI: 10.1016/j.semcdb.2018.04.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 12/22/2022]
Abstract
Planarian behavior, physiology, and pattern control offer profound lessons for regenerative medicine, evolutionary biology, morphogenetic engineering, robotics, and unconventional computation. Despite recent advances in the molecular genetics of stem cell differentiation, this model organism's remarkable anatomical homeostasis provokes us with truly fundamental puzzles about the origin of large-scale shape and its relationship to the genome. In this review article, we first highlight several deep mysteries about planarian regeneration in the context of the current paradigm in this field. We then review recent progress in understanding of the physiological control of an endogenous, bioelectric pattern memory that guides regeneration, and how modulating this memory can permanently alter the flatworm's target morphology. Finally, we focus on computational approaches that complement reductive pathway analysis with synthetic, systems-level understanding of morphological decision-making. We analyze existing models of planarian pattern control and highlight recent successes and remaining knowledge gaps in this interdisciplinary frontier field.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States; Biology Department, Tufts University, Medford, MA 02155, United States.
| | - Alexis M Pietak
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States
| | - Johanna Bischof
- Allen Discovery Center at Tufts University, Medford, MA 02155, United States; Biology Department, Tufts University, Medford, MA 02155, United States
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28
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Churchill CDM, Winter P, Tuszynski JA, Levin M. EDEn-Electroceutical Design Environment: Ion Channel Tissue Expression Database with Small Molecule Modulators. iScience 2019; 11:42-56. [PMID: 30590250 PMCID: PMC6308252 DOI: 10.1016/j.isci.2018.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/22/2018] [Accepted: 12/06/2018] [Indexed: 02/06/2023] Open
Abstract
The emerging field of bioelectricity has revealed numerous new roles for ion channels beyond the nervous system, which can be exploited for applications in regenerative medicine. Developing such biomedical interventions for birth defects, cancer, traumatic injury, and bioengineering first requires knowledge of ion channel targets expressed in tissues of interest. This information can then be used to select combinations of small molecule inhibitors and/or activators that manipulate the bioelectric state. Here, we provide an overview of electroceutical design environment (EDEn), the first bioinformatic platform that facilitates the design of such therapeutic strategies. This database includes information on ion channels and ion pumps, linked to known chemical modulators and their properties. The database also provides information about the expression levels of the ion channels in over 100 tissue types. The graphical interface allows the user to readily identify chemical entities that can alter the electrical properties of target cells and tissues.
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Affiliation(s)
| | - Philip Winter
- Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB T6G 2E1, Canada; Department of Oncology, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Michael Levin
- Allen Discovery Center, Tufts University, 200 Boston Avenue, Suite 4600, Medford, MA 02155, USA.
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29
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Feltes BC, Grisci BI, Poloni JDF, Dorn M. Perspectives and applications of machine learning for evolutionary developmental biology. Mol Omics 2018; 14:289-306. [PMID: 30168572 DOI: 10.1039/c8mo00111a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Evolutionary Developmental Biology (Evo-Devo) is an ever-expanding field that aims to understand how development was modulated by the evolutionary process. In this sense, "omic" studies emerged as a powerful ally to unravel the molecular mechanisms underlying development. In this scenario, bioinformatics tools become necessary to analyze the growing amount of information. Among computational approaches, machine learning stands out as a promising field to generate knowledge and trace new research perspectives for bioinformatics. In this review, we aim to expose the current advances of machine learning applied to evolution and development. We draw clear perspectives and argue how evolution impacted machine learning techniques.
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Affiliation(s)
- Bruno César Feltes
- Institute of Informatics, Federal University of Rio Grande do Sul, Porto Alegre, Brazil.
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30
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Abstract
Biological systems respond to and communicate through biophysical cues, such as electrical, thermal, mechanical and topographical signals. However, precise tools for introducing localized physical stimuli and/or for sensing biological responses to biophysical signals with high spatiotemporal resolution are limited. Inorganic semiconductors display many relevant electrical and optical properties, and they can be fabricated into a broad spectrum of electronic and photonic devices. Inorganic semiconductor devices enable the formation of functional interfaces with biological material, ranging from proteins to whole organs. In this Review, we discuss fundamental semiconductor physics and operation principles, with a focus on their behaviour in physiological conditions, and highlight the advantages of inorganic semiconductors for the establishment of biointerfaces. We examine semiconductor device design and synthesis and discuss typical signal transduction mechanisms at bioelectronic and biophotonic interfaces for electronic and optoelectronic sensing, optoelectronic and photothermal stimulation and photoluminescent in vivo imaging of cells and tissues. Finally, we evaluate cytotoxicity and highlight possible new material components and biological targets of inorganic semiconductor devices.
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31
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Sullivan KG, Levin M. Inverse Drug Screening of Bioelectric Signaling and Neurotransmitter Roles: Illustrated Using a Xenopus Tail Regeneration Assay. Cold Spring Harb Protoc 2018; 2018:pdb.prot099937. [PMID: 29437995 DOI: 10.1101/pdb.prot099937] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Xenopus embryos and larvae are an ideal model system in which to study the interplay between genetics, physiology, and anatomy in the control of structure and function. An important emerging field is the study of bioelectric signaling, the exchange of ion- and neurotransmitter-mediated messages among all types of cells (not just nerve and muscle cells), in the regulation of growth and form during embryogenesis, regeneration, and cancer. To facilitate the mechanistic investigation of bioelectric events in vivo, it is necessary to identify the endogenous signaling machinery involved in any patterning process of interest. This protocol uses the tail regeneration assay in Xenopus to perform an inverse drug screen; tiers of known compounds are used to probe the involvement of increasingly specific classes of bioelectric and neurotransmitter machinery. By using a hierarchical approach, large classes of targets are ruled out in early rounds, focusing attention on progressively narrower sets of proteins. Such a screen avoids many of the limitations of a molecular-genetic targeting approach and provides a rapid and efficient way to focus on specific targets. Usually, <10 experiments are needed to determine whether bioelectrics and/or neurotransmitter signaling are involved in the process of interest. This protocol describes the strategy in the context of a semiquantitative analysis of tail regeneration but can be applied to any assay in Xenopus or other small aquatic model system (e.g., zebrafish). Given the ever-increasing toolkit of chemical genetics, such screens represent a powerful and versatile methodology for probing the physiological circuits underlying pattern regulation.
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Affiliation(s)
- Kelly G Sullivan
- Biology Department, and Allen Discovery Center at Tufts University, Medford, Massachusetts 02155
| | - Michael Levin
- Biology Department, and Allen Discovery Center at Tufts University, Medford, Massachusetts 02155
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32
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Levin M, Martyniuk CJ. The bioelectric code: An ancient computational medium for dynamic control of growth and form. Biosystems 2018; 164:76-93. [PMID: 28855098 PMCID: PMC10464596 DOI: 10.1016/j.biosystems.2017.08.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/20/2017] [Accepted: 08/22/2017] [Indexed: 12/19/2022]
Abstract
What determines large-scale anatomy? DNA does not directly specify geometrical arrangements of tissues and organs, and a process of encoding and decoding for morphogenesis is required. Moreover, many species can regenerate and remodel their structure despite drastic injury. The ability to obtain the correct target morphology from a diversity of initial conditions reveals that the morphogenetic code implements a rich system of pattern-homeostatic processes. Here, we describe an important mechanism by which cellular networks implement pattern regulation and plasticity: bioelectricity. All cells, not only nerves and muscles, produce and sense electrical signals; in vivo, these processes form bioelectric circuits that harness individual cell behaviors toward specific anatomical endpoints. We review emerging progress in reading and re-writing anatomical information encoded in bioelectrical states, and discuss the approaches to this problem from the perspectives of information theory, dynamical systems, and computational neuroscience. Cracking the bioelectric code will enable much-improved control over biological patterning, advancing basic evolutionary developmental biology as well as enabling numerous applications in regenerative medicine and synthetic bioengineering.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, Biology Department, Tufts University, 200 Boston Avenue, Suite 4600 Medford, MA 02155, USA.
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
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33
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Moore D, Walker SI, Levin M. Cancer as a disorder of patterning information: computational and biophysical perspectives on the cancer problem. CONVERGENT SCIENCE PHYSICAL ONCOLOGY 2017. [DOI: 10.1088/2057-1739/aa8548] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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34
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Paré JF, Martyniuk CJ, Levin M. Bioelectric regulation of innate immune system function in regenerating and intact Xenopus laevis. NPJ Regen Med 2017; 2:15. [PMID: 29302351 PMCID: PMC5677984 DOI: 10.1038/s41536-017-0019-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/27/2017] [Accepted: 04/02/2017] [Indexed: 02/07/2023] Open
Abstract
Two key inputs that regulate regeneration are the function of the immune system, and spatial gradients of transmembrane potential (Vmem). Endogenous bioelectric signaling in somatic tissues during regenerative patterning is beginning to be understood, but its role in the context of immune response has never been investigated. Here, we show that Vmem levels modulate innate immunity activity in Xenopus laevis embryos. We developed an assay in which X. laevis embryos are infected with a uropathogenic microorganism, in the presence or absence of reagents that modify Vmem, prior to the ontogenesis of the adaptive immune system. General depolarization of the organism's Vmem by pharmacological or molecular genetic (ion channel misexpression) methods increased resistance to infection, while hyperpolarization made the embryos more susceptible to death by infection. Hyperpolarized specimens harbored a higher load of infectious microorganisms when compared to controls. We identified two mechanisms by which Vmem mediates immune function: serotonergic signaling involving melanocytes and an increase in the number of primitive myeloid cells. Bioinformatics analysis of genes whose transcription is altered by depolarization revealed a number of immune system targets consistent with mammalian data. Remarkably, amputation of the tail bud potentiates systemic resistance to infection by increasing the number of peripheral myeloid cells, revealing an interplay of regenerative response, innate immunity, and bioelectric regulation. Our study identifies bioelectricity as a new mechanism by which innate immune response can be regulated in the context of infection or regeneration. Vmem modulation using drugs already approved for human use could be exploited to improve resistance to infections in clinical settings.
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Affiliation(s)
- Jean-François Paré
- Biology Department, and Allen Discovery Center at Tufts, Tufts University, Medford, MA USA
| | - Christopher J. Martyniuk
- Center for Environmental and Human Toxicology and Department of Physiological Sciences, University of Florida Genetics Institute, College of Veterinary Medicine, University of Florida, Gainesville, FL USA
| | - Michael Levin
- Biology Department, and Allen Discovery Center at Tufts, Tufts University, Medford, MA USA
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Abstract
Uveal melanoma (UM), a rare cancer of the eye, is distinct from cutaneous melanoma by its etiology, the mutation frequency and profile, and its clinical behavior including resistance to targeted therapy and immune checkpoint blockers. Primary disease is efficiently controlled by surgery or radiation therapy, but about half of UMs develop distant metastasis mostly to the liver. Survival of patients with metastasis is below 1 year and has not improved in decades. Recent years have brought a deep understanding of UM biology characterized by initiating mutations in the G proteins GNAQ and GNA11. Cytogenetic alterations, in particular monosomy of chromosome 3 and amplification of the long arm of chromosome 8, and mutation of the BRCA1-associated protein 1, BAP1, a tumor suppressor gene, or the splicing factor SF3B1 determine UM metastasis. Cytogenetic and molecular profiling allow for a very precise prognostication that is still not matched by efficacious adjuvant therapies. G protein signaling has been shown to activate the YAP/TAZ pathway independent of HIPPO, and conventional signaling via the mitogen-activated kinase pathway probably also contributes to UM development and progression. Several lines of evidence indicate that inflammation and macrophages play a pro-tumor role in UM and in its hepatic metastases. UM cells benefit from the immune privilege in the eye and may adopt several mechanisms involved in this privilege for tumor escape that act even after leaving the niche. Here, we review the current knowledge of the biology of UM and discuss recent approaches to UM treatment.
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Affiliation(s)
- Adriana Amaro
- Laboratory of Molecular Pathology, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, L.go Rosanna Benzi 10, 16132, Genoa, Italy
| | - Rosaria Gangemi
- Laboratory of Biotherapies, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Francesca Piaggio
- Laboratory of Molecular Pathology, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, L.go Rosanna Benzi 10, 16132, Genoa, Italy
| | - Giovanna Angelini
- Laboratory of Molecular Pathology, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, L.go Rosanna Benzi 10, 16132, Genoa, Italy
| | - Gaia Barisione
- Laboratory of Biotherapies, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Silvano Ferrini
- Laboratory of Biotherapies, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, Genoa, Italy
| | - Ulrich Pfeffer
- Laboratory of Molecular Pathology, Department of Integrated Oncology Therapies, IRCCS AOU San Martino - IST Istituto Nazionale per la Ricerca sul Cancro, L.go Rosanna Benzi 10, 16132, Genoa, Italy.
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Discovering novel phenotypes with automatically inferred dynamic models: a partial melanocyte conversion in Xenopus. Sci Rep 2017; 7:41339. [PMID: 28128301 PMCID: PMC5269672 DOI: 10.1038/srep41339] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 12/16/2016] [Indexed: 12/20/2022] Open
Abstract
Progress in regenerative medicine requires reverse-engineering cellular control networks to infer perturbations with desired systems-level outcomes. Such dynamic models allow phenotypic predictions for novel perturbations to be rapidly assessed in silico. Here, we analyzed a Xenopus model of conversion of melanocytes to a metastatic-like phenotype only previously observed in an all-or-none manner. Prior in vivo genetic and pharmacological experiments showed that individual animals either fully convert or remain normal, at some characteristic frequency after a given perturbation. We developed a Machine Learning method which inferred a model explaining this complex, stochastic all-or-none dataset. We then used this model to ask how a new phenotype could be generated: animals in which only some of the melanocytes converted. Systematically performing in silico perturbations, the model predicted that a combination of altanserin (5HTR2 inhibitor), reserpine (VMAT inhibitor), and VP16-XlCreb1 (constitutively active CREB) would break the all-or-none concordance. Remarkably, applying the predicted combination of three reagents in vivo revealed precisely the expected novel outcome, resulting in partial conversion of melanocytes within individuals. This work demonstrates the capability of automated analysis of dynamic models of signaling networks to discover novel phenotypes and predictively identify specific manipulations that can reach them.
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Lobo D, Levin M. Computing a Worm: Reverse-Engineering Planarian Regeneration. EMERGENCE, COMPLEXITY AND COMPUTATION 2017. [DOI: 10.1007/978-3-319-33921-4_24] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Bertolesi GE, Vazhappilly ST, Hehr CL, McFarlane S. Pharmacological induction of skin pigmentation unveils the neuroendocrine circuit regulated by light. Pigment Cell Melanoma Res 2016; 29:186-98. [PMID: 26582755 DOI: 10.1111/pcmr.12442] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 11/12/2015] [Indexed: 12/24/2022]
Abstract
Light-regulated skin colour change is an important physiological process in invertebrates and lower vertebrates, and includes daily circadian variation and camouflage (i.e. background adaptation). The photoactivation of melanopsin-expressing retinal ganglion cells (mRGCs) in the eye initiates an uncharacterized neuroendocrine circuit that regulates melanin dispersion/aggregation through the secretion of alpha-melanocyte-stimulating hormone (α-MSH). We developed experimental models of normal or enucleated Xenopus embryos, as well as in situ cultures of skin of isolated dorsal head and tails, to analyse pharmacological induction of skin pigmentation and α-MSH synthesis. Both processes are triggered by a melanopsin inhibitor, AA92593, as well as chloride channel modulators. The AA9253 effect is eye-dependent, while functional data in vivo point to GABAA receptors expressed on pituitary melanotrope cells as the chloride channel blocker target. Based on the pharmacological data, we suggest a neuroendocrine circuit linking mRGCs with α-MSH secretion, which is used normally during background adaptation.
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Affiliation(s)
- Gabriel E Bertolesi
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Sherene T Vazhappilly
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Carrie L Hehr
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Sarah McFarlane
- Department of Cell Biology and Anatomy, Hotchkiss Brain Institute, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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Bertolesi GE, Hehr CL, Munn H, McFarlane S. Two light-activated neuroendocrine circuits arising in the eye trigger physiological and morphological pigmentation. Pigment Cell Melanoma Res 2016; 29:688-701. [DOI: 10.1111/pcmr.12531] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 08/22/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Gabriel E. Bertolesi
- Department of Cell Biology and Anatomy; Hotchkiss Brain Institute; Alberta Children's Hospital Research Institute; University of Calgary; Calgary AB Canada
| | - Carrie L. Hehr
- Department of Cell Biology and Anatomy; Hotchkiss Brain Institute; Alberta Children's Hospital Research Institute; University of Calgary; Calgary AB Canada
| | - Hayden Munn
- Department of Cell Biology and Anatomy; Hotchkiss Brain Institute; Alberta Children's Hospital Research Institute; University of Calgary; Calgary AB Canada
| | - Sarah McFarlane
- Department of Cell Biology and Anatomy; Hotchkiss Brain Institute; Alberta Children's Hospital Research Institute; University of Calgary; Calgary AB Canada
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Sullivan KG, Emmons-Bell M, Levin M. Physiological inputs regulate species-specific anatomy during embryogenesis and regeneration. Commun Integr Biol 2016; 9:e1192733. [PMID: 27574538 PMCID: PMC4988443 DOI: 10.1080/19420889.2016.1192733] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/13/2016] [Accepted: 05/16/2016] [Indexed: 12/12/2022] Open
Abstract
A key problem in evolutionary developmental biology is identifying the sources of instructive information that determine species-specific anatomical pattern. Understanding the inputs to large-scale morphology is also crucial for efforts to manipulate pattern formation in regenerative medicine and synthetic bioengineering. Recent studies have revealed a physiological system of communication among cells that regulates pattern during embryogenesis and regeneration in vertebrate and invertebrate models. Somatic tissues form networks using the same ion channels, electrical synapses, and neurotransmitter mechanisms exploited by the brain for information-processing. Experimental manipulation of these circuits was recently shown to override genome default patterning outcomes, resulting in head shapes resembling those of other species in planaria and Xenopus. The ability to drastically alter macroscopic anatomy to that of other extant species, despite a wild-type genomic sequence, suggests exciting new approaches to the understanding and control of patterning. Here, we review these results and discuss hypotheses regarding non-genomic systems of instructive information that determine biological growth and form.
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Affiliation(s)
- Kelly G Sullivan
- Allen Discovery Center at Tufts University, Tufts University , Medford, MA, USA
| | - Maya Emmons-Bell
- Allen Discovery Center at Tufts University, Tufts University , Medford, MA, USA
| | - Michael Levin
- Allen Discovery Center at Tufts University, Tufts University , Medford, MA, USA
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Sullivan KG, Levin M. Neurotransmitter signaling pathways required for normal development in Xenopus laevis embryos: a pharmacological survey screen. J Anat 2016; 229:483-502. [PMID: 27060969 DOI: 10.1111/joa.12467] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2016] [Indexed: 01/08/2023] Open
Abstract
Neurotransmitters are not only involved in brain function but are also important signaling molecules for many diverse cell types. Neurotransmitters are widely conserved, from evolutionarily ancient organisms lacking nervous systems through man. Here, results are reported from a loss- and gain-of-function survey, using pharmacological modulators of several neurotransmitter pathways to examine possible roles for these pathways in normal embryogenesis. Applying reagents targeting the glutamatergic, adrenergic and dopaminergic pathways to embryos of Xenopus laevis from gastrulation to organogenesis stages, we observed and quantified numerous malformations, including craniofacial defects, hyperpigmentation, muscle mispatterning and miscoiling of the gut. These data implicate several key neurotransmitters in new embryonic patterning roles, reveal novel earlier stages for processes involved in eye development, suggest new targets for subsequent molecular-genetic investigation, and highlight the necessity for in-depth toxicology studies of psychoactive compounds to which human embryos might be exposed during pregnancy.
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Affiliation(s)
- Kelly G Sullivan
- Biology Department, Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
| | - Michael Levin
- Biology Department, Center for Regenerative and Developmental Biology, Tufts University, Medford, MA, USA
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Durant F, Lobo D, Hammelman J, Levin M. Physiological controls of large-scale patterning in planarian regeneration: a molecular and computational perspective on growth and form. REGENERATION (OXFORD, ENGLAND) 2016; 3:78-102. [PMID: 27499881 PMCID: PMC4895326 DOI: 10.1002/reg2.54] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/18/2016] [Accepted: 02/22/2016] [Indexed: 12/12/2022]
Abstract
Planaria are complex metazoans that repair damage to their bodies and cease remodeling when a correct anatomy has been achieved. This model system offers a unique opportunity to understand how large-scale anatomical homeostasis emerges from the activities of individual cells. Much progress has been made on the molecular genetics of stem cell activity in planaria. However, recent data also indicate that the global pattern is regulated by physiological circuits composed of ionic and neurotransmitter signaling. Here, we overview the multi-scale problem of understanding pattern regulation in planaria, with specific focus on bioelectric signaling via ion channels and gap junctions (electrical synapses), and computational efforts to extract explanatory models from functional and molecular data on regeneration. We present a perspective that interprets results in this fascinating field using concepts from dynamical systems theory and computational neuroscience. Serving as a tractable nexus between genetic, physiological, and computational approaches to pattern regulation, planarian pattern homeostasis harbors many deep insights for regenerative medicine, evolutionary biology, and engineering.
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Affiliation(s)
- Fallon Durant
- Department of Biology, Allen Discovery Center at Tufts University, Tufts Center for Regenerative and Developmental BiologyTufts UniversityMA02155USA
| | - Daniel Lobo
- Department of Biological SciencesUniversity of MarylandBaltimore County, 1000 Hilltop CircleBaltimoreMD21250USA
| | - Jennifer Hammelman
- Department of Biology, Allen Discovery Center at Tufts University, Tufts Center for Regenerative and Developmental BiologyTufts UniversityMA02155USA
| | - Michael Levin
- Department of Biology, Allen Discovery Center at Tufts University, Tufts Center for Regenerative and Developmental BiologyTufts UniversityMA02155USA
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43
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Gordon NK, Gordon R. The organelle of differentiation in embryos: the cell state splitter. Theor Biol Med Model 2016; 13:11. [PMID: 26965444 PMCID: PMC4785624 DOI: 10.1186/s12976-016-0037-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 02/27/2016] [Indexed: 12/16/2022] Open
Abstract
The cell state splitter is a membraneless organelle at the apical end of each epithelial cell in a developing embryo. It consists of a microfilament ring and an intermediate filament ring subtending a microtubule mat. The microtubules and microfilament ring are in mechanical opposition as in a tensegrity structure. The cell state splitter is bistable, perturbations causing it to contract or expand radially. The intermediate filament ring provides metastability against small perturbations. Once this snap-through organelle is triggered, it initiates signal transduction to the nucleus, which changes gene expression in one of two readied manners, causing its cell to undergo a step of determination and subsequent differentiation. The cell state splitter also triggers the cell state splitters of adjacent cells to respond, resulting in a differentiation wave. Embryogenesis may be represented then as a bifurcating differentiation tree, each edge representing one cell type. In combination with the differentiation waves they propagate, cell state splitters explain the spatiotemporal course of differentiation in the developing embryo. This review is excerpted from and elaborates on "Embryogenesis Explained" (World Scientific Publishing, Singapore, 2016).
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Affiliation(s)
| | - Richard Gordon
- />Retired, University of Manitoba, Winnipeg, Canada
- />Embryogenesis Center, Gulf Specimen Aquarium & Marine Laboratory, 222 Clark Drive, Panacea, FL 32346 USA
- />C.S. Mott Center for Human Growth & Development, Department of Obstetrics & Gynecology, Wayne State University, 275 E. Hancock, Detroit, MI 48201 USA
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Lobo D, Hammelman J, Levin M. MoCha: Molecular Characterization of Unknown Pathways. J Comput Biol 2016; 23:291-7. [PMID: 26950055 DOI: 10.1089/cmb.2015.0211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Automated methods for the reverse-engineering of complex regulatory networks are paving the way for the inference of mechanistic comprehensive models directly from experimental data. These novel methods can infer not only the relations and parameters of the known molecules defined in their input datasets, but also unknown components and pathways identified as necessary by the automated algorithms. Identifying the molecular nature of these unknown components is a crucial step for making testable predictions and experimentally validating the models, yet no specific and efficient tools exist to aid in this process. To this end, we present here MoCha (Molecular Characterization), a tool optimized for the search of unknown proteins and their pathways from a given set of known interacting proteins. MoCha uses the comprehensive dataset of protein-protein interactions provided by the STRING database, which currently includes more than a billion interactions from over 2,000 organisms. MoCha is highly optimized, performing typical searches within seconds. We demonstrate the use of MoCha with the characterization of unknown components from reverse-engineered models from the literature. MoCha is useful for working on network models by hand or as a downstream step of a model inference engine workflow and represents a valuable and efficient tool for the characterization of unknown pathways using known data from thousands of organisms. MoCha and its source code are freely available online under the GPLv3 license.
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Affiliation(s)
- Daniel Lobo
- 1 Department of Biological Sciences, University of Maryland , Baltimore County, Baltimore, Maryland
| | - Jennifer Hammelman
- 2 Center for Regenerative and Developmental Biology, and Department of Biology, Tufts University , Medford, Massachusetts
| | - Michael Levin
- 2 Center for Regenerative and Developmental Biology, and Department of Biology, Tufts University , Medford, Massachusetts
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45
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Rubin BP, Brockes J, Galliot B, Grossniklaus U, Lobo D, Mainardi M, Mirouze M, Prochiantz A, Steger A. A dynamic architecture of life. F1000Res 2015; 4:1288. [PMID: 26949518 PMCID: PMC4760269 DOI: 10.12688/f1000research.7315.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2015] [Indexed: 12/15/2022] Open
Abstract
In recent decades, a profound conceptual transformation has occurred comprising different areas of biological research, leading to a novel understanding of life processes as much more dynamic and changeable. Discoveries in plants and animals, as well as novel experimental approaches, have prompted the research community to reconsider established concepts and paradigms. This development was taken as an incentive to organise a workshop in May 2014 at the Academia Nazionale dei Lincei in Rome. There, experts on epigenetics, regeneration, neuroplasticity, and computational biology, using different animal and plant models, presented their insights on important aspects of a dynamic architecture of life, which comprises all organisational levels of the organism. Their work demonstrates that a dynamic nature of life persists during the entire existence of the organism and permits animals and plants not only to fine-tune their response to particular environmental demands during development, but underlies their continuous capacity to do so. Here, a synthesis of the different findings and their relevance for biological thinking is presented.
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Affiliation(s)
- Beatrix P Rubin
- Collegium Helveticum, University of Zurich and ETH Zurich, Zurich, 8092, Switzerland
| | - Jeremy Brockes
- Department of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Brigitte Galliot
- Department of Genetics and Evolution, University of Geneva, Geneva, 1211, Switzerland
| | - Ueli Grossniklaus
- Department of Plant and Microbial Biology & Zurich-Basel Plant Science Center, University of Zurich, Zurich, 8008, Switzerland
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD, 21250, USA
| | - Marco Mainardi
- CNR Neuroscience Institute, 56124 Pisa, Italy; Institute of Human Physiology, Catholic University, 00168 Rome, Italy
| | - Marie Mirouze
- Institut de Recherche pour le Développement, UMR DIADE, Laboratoire Génome et Développement des Plantes, 66860 Perpignan, France
| | - Alain Prochiantz
- Chaire des Processus Morphogénétiques, Centre Interdisciplinaire de Recherche en Biologie, Paris, 75231, France
| | - Angelika Steger
- Institute of Theoretical Computer Science, ETH Zurich, Zurich, 8092, Switzerland
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46
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Xing J, Lee REC. Putting it all on pigmentation: Heuristics of a bold and stochastic cell fate decision. Sci Signal 2015; 8:fs17. [PMID: 26443702 DOI: 10.1126/scisignal.aad2816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Gradients of transmembrane potential coordinate cell-fate decisions and patterning during embryogenesis and wound-healing. Bioelectrical signaling may also be more important for adult pathologies than currently recognized. In this issue of Science Signaling, Lobikin et al. describe a role for bioelectric signals during the development of Xenopus leavis embryos to instruct an organism-level response reminiscent of neoplastic progression in melanoma.
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Affiliation(s)
- Jianhua Xing
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Robin E C Lee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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