1
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Alibardi L. Progressive modifications during evolution involving epigenetic changes have determined loss of regeneration mainly in terrestrial animals: A hypothesis. Dev Biol 2024; 515:169-177. [PMID: 39029569 DOI: 10.1016/j.ydbio.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 07/21/2024]
Abstract
In order to address a biological explanation for the different regenerative abilities present among animals, a new evolutionary speculation is presented. It is hypothesized that epigenetic mechanisms have lowered or erased regeneration during the evolution of terrestrial invertebrates and vertebrates. The hypothesis indicates that a broad regeneration can only occur in marine or freshwater conditions, and that life on land does not allow for high regeneration. This is due to the physical, chemical and microbial conditions present in the terrestrial environment with respect to those of the aquatic environment. The present speculation provides examples of hypothetic evolutionary animal lineages that colonized the land, such as parasitic annelids, terrestrial mollusks, arthropods and amniotes. These are the animals where regeneration is limited or absent and their injuries are only repaired through limited healing or scarring. It is submitted that this loss derived from changes in the developmental gene pathways sustaining regeneration in the aquatic environment but that cannot be expressed on land. Once regeneration was erased in terrestrial species, re-adaptation to freshwater niches could not reactivate the previously altered gene pathways that determined regeneration. Therefore a broad regeneration was no longer possible or became limited and heteromorphic in the derived, extant animals. Only in few cases extensive healing abilities or regengrow, a healing process where regeneration overlaps with somatic growth, have evolved among arthropods and amniotes. The present paper is an extension of previous speculations trying to explain in biological terms the different regenerative abilities present among metazoans.
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2
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Fujita T, Aoki N, Mori C, Homma KJ, Yamaguchi S. SoxC and MmpReg promote blastema formation in whole-body regeneration of fragmenting potworms Enchytraeus japonensis. Nat Commun 2024; 15:6659. [PMID: 39174502 PMCID: PMC11341731 DOI: 10.1038/s41467-024-50865-1] [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: 10/03/2022] [Accepted: 07/22/2024] [Indexed: 08/24/2024] Open
Abstract
Regeneration in many animals involves the formation of a blastema, which differentiates and organizes into the appropriate missing body parts. Although the mechanisms underlying blastema formation are often fundamental to regeneration biology, information on the cellular and molecular basis of blastema formation remains limited. Here, we focus on a fragmenting potworm (Enchytraeus japonensis), which can regenerate its whole body from small fragments. We find soxC and mmpReg as upregulated genes in the blastema. RNAi of soxC and mmpReg reduce the number of blastema cells, indicating that soxC and mmpReg promote blastema formation. Expression analyses show that soxC-expressing cells appear to gradually accumulate in blastema and constitute a large part of the blastema. Additionally, similar expression dynamics of SoxC orthologue genes in frog (Xenopus laevis) are found in the regeneration blastema of tadpole tail. Our findings provide insights into the cellular and molecular mechanisms underlying blastema formation across species.
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Affiliation(s)
- Toshiyuki Fujita
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Naoya Aoki
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Chihiro Mori
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Koichi J Homma
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan
| | - Shinji Yamaguchi
- Department of Biological Sciences, Faculty of Pharmaceutical Sciences, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, Japan.
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3
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Parey E, Ortega-Martinez O, Delroisse J, Piovani L, Czarkwiani A, Dylus D, Arya S, Dupont S, Thorndyke M, Larsson T, Johannesson K, Buckley KM, Martinez P, Oliveri P, Marlétaz F. The brittle star genome illuminates the genetic basis of animal appendage regeneration. Nat Ecol Evol 2024; 8:1505-1521. [PMID: 39030276 PMCID: PMC11310086 DOI: 10.1038/s41559-024-02456-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/29/2024] [Indexed: 07/21/2024]
Abstract
Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars are a species-rich class of echinoderms with outstanding regenerative abilities, but investigations into the genetic bases of regeneration in this group have been hindered by the limited genomic resources. Here we report a chromosome-scale genome assembly for the brittle star Amphiura filiformis. We show that the brittle star genome is the most rearranged among echinoderms sequenced so far, featuring a reorganized Hox cluster reminiscent of the rearrangements observed in sea urchins. In addition, we performed an extensive profiling of gene expression during brittle star adult arm regeneration and identified sequential waves of gene expression governing wound healing, proliferation and differentiation. We conducted comparative transcriptomic analyses with other invertebrate and vertebrate models for appendage regeneration and uncovered hundreds of genes with conserved expression dynamics, particularly during the proliferative phase of regeneration. Our findings emphasize the crucial importance of echinoderms to detect long-range expression conservation between vertebrates and classical invertebrate regeneration model systems.
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Affiliation(s)
- Elise Parey
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Olga Ortega-Martinez
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | - Jérôme Delroisse
- Biology of Marine Organisms and Biomimetics Unit, Research Institute for Biosciences, University of Mons, Mons, Belgium
| | - Laura Piovani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anna Czarkwiani
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Technische Universität Dresden, Center for Regenerative Therapies Dresden (CRTD), Dresden, Germany
| | - David Dylus
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- Roche Pharmaceutical Research and Early Development (pRED), Cardiovascular and Metabolism, Immunology, Infectious Disease, and Ophthalmology (CMI2O), F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Srishti Arya
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK
- MRC Laboratory of Medical Sciences, Imperial College London, London, UK
| | - Samuel Dupont
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
- IAEA Marine Environment Laboratories, Radioecology Laboratory, Quai Antoine 1er, Monaco
| | - Michael Thorndyke
- Department of Biology and Environmental Science, University of Gothenburg, Kristineberg Marine Research Station, Fiskebäckskil, Sweden
| | - Tomas Larsson
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Johannesson
- Tjärnö Marine Laboratory, Department of Marine Sciences, University of Gothenburg, Strömstad, Sweden
| | | | - Pedro Martinez
- Departament de Genètica, Microbiologia, i Estadística, Universitat de Barcelona, Barcelona, Spain
- Institut Català de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Paola Oliveri
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Ferdinand Marlétaz
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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4
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Hulett RE, Rivera-López C, Gehrke AR, Gompers A, Srivastava M. A wound-induced differentiation trajectory for neurons. Proc Natl Acad Sci U S A 2024; 121:e2322864121. [PMID: 38976727 PMCID: PMC11260127 DOI: 10.1073/pnas.2322864121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 05/03/2024] [Indexed: 07/10/2024] Open
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully functional new organs, including new brains, de novo. The regeneration of a new brain requires the formation of diverse neural cell types and their assembly into an organized structure with correctly wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neural subpopulations, however, how these transcriptional programs are initiated in response to injury remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia, to study wound-induced transcriptional regulatory events that lead to the production of neurons and subsequently a functional brain. Footprinting analysis using chromatin accessibility data on a chromosome-scale genome assembly revealed that binding sites for the Nuclear Factor Y (NFY) transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal function. Single-cell transcriptome analysis combined with functional studies identified soxC+ stem cells as a putative progenitor population for multiple neural subtypes. Further, we found that wound-induced soxC expression is likely under direct transcriptional control by NFY, uncovering a mechanism for the initiation of a neural differentiation pathway by early wound-induced binding of a transcriptional regulator.
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Affiliation(s)
- Ryan E. Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA02138
| | - Andrew R. Gehrke
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA02138
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5
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Gąsiorowski L, Chai C, Rozanski A, Purandare G, Ficze F, Mizi A, Wang B, Rink JC. Regeneration in the absence of canonical neoblasts in an early branching flatworm. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.24.595708. [PMID: 38853907 PMCID: PMC11160568 DOI: 10.1101/2024.05.24.595708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The remarkable regenerative abilities of flatworms are closely linked to neoblasts - adult pluripotent stem cells that are the only division-competent cell type outside of the reproductive system. Although the presence of neoblast-like cells and whole-body regeneration in other animals has led to the idea that these features may represent the ancestral metazoan state, the evolutionary origin of both remains unclear. Here we show that the catenulid Stenostomum brevipharyngium, a member of the earliest-branching flatworm lineage, lacks conventional neoblasts despite being capable of whole-body regeneration and asexual reproduction. Using a combination of single-nuclei transcriptomics, in situ gene expression analysis, and functional experiments, we find that cell divisions are not restricted to a single cell type and are associated with multiple fully differentiated somatic tissues. Furthermore, the cohort of germline multipotency genes, which are considered canonical neoblast markers, are not expressed in dividing cells, but in the germline instead, and we experimentally show that they are neither necessary for proliferation nor regeneration. Overall, our results challenge the notion that canonical neoblasts are necessary for flatworm regeneration and open up the possibility that neoblast-like cells may have evolved convergently in different animals, independent of their regenerative capacity.
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Affiliation(s)
- Ludwik Gąsiorowski
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Chew Chai
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Andrei Rozanski
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Gargi Purandare
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Fruzsina Ficze
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Athanasia Mizi
- Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany
| | - Bo Wang
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Jochen C Rink
- Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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6
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Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Del Olmo I, Peron S, Salamanca-Díaz DA, Mason V, Metzger B, Bely AE, Kenny NJ, Özpolat BD, Solana J. Annelid adult cell type diversity and their pluripotent cellular origins. Nat Commun 2024; 15:3194. [PMID: 38609365 PMCID: PMC11014941 DOI: 10.1038/s41467-024-47401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/27/2024] [Indexed: 04/14/2024] Open
Abstract
Many annelids can regenerate missing body parts or reproduce asexually, generating all cell types in adult stages. However, the putative adult stem cell populations involved in these processes, and the diversity of cell types generated by them, are still unknown. To address this, we recover 75,218 single cell transcriptomes of the highly regenerative and asexually-reproducing annelid Pristina leidyi. Our results uncover a rich cell type diversity including annelid specific types as well as novel types. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. We find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors, in piwi+ cells. Finally, lineage reconstruction analyses reveal computational differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids by single cell transcriptomics and suggest that a piwi+ cell population with a pluripotent stem cell signature is associated with adult cell type differentiation.
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Affiliation(s)
- Patricia Álvarez-Campos
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain.
| | - Helena García-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Elena Emili
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alberto Pérez-Posada
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Irene Del Olmo
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Sophie Peron
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - David A Salamanca-Díaz
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Living Systems Institute, University of Exeter, Exeter, UK
| | - Vincent Mason
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Bria Metzger
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA
| | - Alexandra E Bely
- Department of Biology, University of Maryland, College Park, MD, 20742, USA
| | - Nathan J Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa, New Zealand
| | - B Duygu Özpolat
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, 05432, USA.
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, Saint Louis, MO, 63130, USA.
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
- Living Systems Institute, University of Exeter, Exeter, UK.
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7
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Tan FH, Bronner ME. Regenerative loss in the animal kingdom as viewed from the mouse digit tip and heart. Dev Biol 2024; 507:44-63. [PMID: 38145727 PMCID: PMC10922877 DOI: 10.1016/j.ydbio.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 11/30/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
The myriad regenerative abilities across the animal kingdom have fascinated us for centuries. Recent advances in developmental, molecular, and cellular biology have allowed us to unearth a surprising diversity of mechanisms through which these processes occur. Developing an all-encompassing theory of animal regeneration has thus proved a complex endeavor. In this chapter, we frame the evolution and loss of animal regeneration within the broad developmental constraints that may physiologically inhibit regenerative ability across animal phylogeny. We then examine the mouse as a model of regeneration loss, specifically the experimental systems of the digit tip and heart. We discuss the digit tip and heart as a positionally-limited system of regeneration and a temporally-limited system of regeneration, respectively. We delve into the physiological processes involved in both forms of regeneration, and how each phase of the healing and regenerative process may be affected by various molecular signals, systemic changes, or microenvironmental cues. Lastly, we also discuss the various approaches and interventions used to induce or improve the regenerative response in both contexts, and the implications they have for our understanding regenerative ability more broadly.
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Affiliation(s)
- Fayth Hui Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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8
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Mitchell DG, Edgar A, Mateu JR, Ryan JF, Martindale MQ. The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor. Commun Biol 2024; 7:203. [PMID: 38374160 PMCID: PMC10876535 DOI: 10.1038/s42003-024-05901-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024] Open
Abstract
Regenerative potential is widespread but unevenly distributed across animals. However, our understanding of the molecular mechanisms underlying regenerative processes is limited to a handful of model organisms, restricting robust comparative analyses. Here, we conduct a time course of RNA-seq during whole body regeneration in Mnemiopsis leidyi (Ctenophora) to uncover gene expression changes that correspond with key events during the regenerative timeline of this species. We identified several genes highly enriched in this dataset beginning as early as 10 minutes after surgical bisection including transcription factors in the early timepoints, peptidases in the middle timepoints, and cytoskeletal genes in the later timepoints. We validated the expression of early response transcription factors by whole mount in situ hybridization, showing that these genes exhibited high expression in tissues surrounding the wound site. These genes exhibit a pattern of transient upregulation as seen in a variety of other organisms, suggesting that they may be initiators of an ancient gene regulatory network linking wound healing to the initiation of a regenerative response.
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Affiliation(s)
- Dorothy G Mitchell
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Allison Edgar
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Júlia Ramon Mateu
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
| | - Joseph F Ryan
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - Mark Q Martindale
- Whitney Laboratory for Marine Bioscience, University of Florida, Saint Augustine, FL, USA.
- Department of Biology, University of Florida, Gainesville, FL, USA.
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9
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Paré L, Bideau L, Baduel L, Dalle C, Benchouaia M, Schneider SQ, Laplane L, Clément Y, Vervoort M, Gazave E. Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii. BMC Genomics 2023; 24:583. [PMID: 37784028 PMCID: PMC10546743 DOI: 10.1186/s12864-023-09602-z] [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: 05/25/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered. RESULTS We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process. CONCLUSIONS In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
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Affiliation(s)
- Louis Paré
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loïc Bideau
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loeiza Baduel
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Caroline Dalle
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Médine Benchouaia
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Stephan Q Schneider
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Lucie Laplane
- Université Paris I Panthéon-Sorbonne, CNRS UMR 8590 Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST), Paris, France
- Gustave Roussy, UMR 1287, Villejuif, France
| | - Yves Clément
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France.
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10
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Sumner JT, Andrasz CL, Johnson CA, Wax S, Anderson P, Keeling EL, Davidson JM. De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus. G3 (BETHESDA, MD.) 2023; 13:jkad181. [PMID: 37555394 PMCID: PMC10542563 DOI: 10.1093/g3journal/jkad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp, and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from nonmodel organisms in the investigation of biological phenomena.
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Affiliation(s)
- Jack T Sumner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Cassidy L Andrasz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Christine A Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Sarah Wax
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Elena L Keeling
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Jean M Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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11
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Tajer B, Savage AM, Whited JL. The salamander blastema within the broader context of metazoan regeneration. Front Cell Dev Biol 2023; 11:1206157. [PMID: 37635872 PMCID: PMC10450636 DOI: 10.3389/fcell.2023.1206157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/29/2023] Open
Abstract
Throughout the animal kingdom regenerative ability varies greatly from species to species, and even tissue to tissue within the same organism. The sheer diversity of structures and mechanisms renders a thorough comparison of molecular processes truly daunting. Are "blastemas" found in organisms as distantly related as planarians and axolotls derived from the same ancestral process, or did they arise convergently and independently? Is a mouse digit tip blastema orthologous to a salamander limb blastema? In other fields, the thorough characterization of a reference model has greatly facilitated these comparisons. For example, the amphibian Spemann-Mangold organizer has served as an amazingly useful comparative template within the field of developmental biology, allowing researchers to draw analogies between distantly related species, and developmental processes which are superficially quite different. The salamander limb blastema may serve as the best starting point for a comparative analysis of regeneration, as it has been characterized by over 200 years of research and is supported by a growing arsenal of molecular tools. The anatomical and evolutionary closeness of the salamander and human limb also add value from a translational and therapeutic standpoint. Tracing the evolutionary origins of the salamander blastema, and its relatedness to other regenerative processes throughout the animal kingdom, will both enhance our basic biological understanding of regeneration and inform our selection of regenerative model systems.
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Affiliation(s)
| | | | - Jessica L. Whited
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, United States
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12
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Hulett RE, Gehrke AR, Gompers A, Rivera-López C, Srivastava M. A wound-induced differentiation trajectory for neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.10.540286. [PMID: 37214981 PMCID: PMC10197691 DOI: 10.1101/2023.05.10.540286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Animals capable of whole-body regeneration can replace any missing cell type and regenerate fully-functional new organs, de novo . The regeneration of a new brain requires the formation of diverse neuronal cell types and their assembly into an organized structure and correctly-wired circuits. Recent work in various regenerative animals has revealed transcriptional programs required for the differentiation of distinct neuronal subpopulations, however how these transcriptional programs are initiated upon amputation remains unknown. Here, we focused on the highly regenerative acoel worm, Hofstenia miamia , to study wound-induced transcriptional regulatory events that lead to the production of neurons. Footprinting analysis using chromatin accessibility data on an improved genome assembly revealed that binding sites for the NFY transcription factor complex were significantly bound during regeneration, showing a dynamic increase in binding within one hour upon amputation specifically in tail fragments, which will regenerate a new brain. Strikingly, NFY targets were highly enriched for genes with neuronal functional. Single-cell transcriptome analysis combined with functional studies identified sox4 + stem cells as the likely progenitor population for multiple neuronal subtypes. Further, we found that wound-induced sox4 expression is likely under direct transcriptional control by NFY, uncovering a mechanism for how early wound-induced binding of a transcriptional regulator results in the initiation of a neuronal differentiation pathway. Highlights A new chromosome-scale assembly for Hofstenia enables comprehensive analysis of transcription factor binding during regeneration NFY motifs become dynamically bound by 1hpa in regenerating tail fragments, particularly in the loci of neural genes A sox4 + neural-specialized stem cell is identified using scRNA-seq sox4 is wound-induced and required for differentiation of multiple neural cell types NFY regulates wound-induced expression of sox4 during regeneration.
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13
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Hulett RE, Kimura JO, Bolaños DM, Luo YJ, Rivera-López C, Ricci L, Srivastava M. Acoel single-cell atlas reveals expression dynamics and heterogeneity of adult pluripotent stem cells. Nat Commun 2023; 14:2612. [PMID: 37147314 PMCID: PMC10163032 DOI: 10.1038/s41467-023-38016-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/11/2023] [Indexed: 05/07/2023] Open
Abstract
Adult pluripotent stem cell (aPSC) populations underlie whole-body regeneration in many distantly-related animal lineages, but how the underlying cellular and molecular mechanisms compare across species is unknown. Here, we apply single-cell RNA sequencing to profile transcriptional cell states of the acoel worm Hofstenia miamia during postembryonic development and regeneration. We identify cell types shared across stages and their associated gene expression dynamics during regeneration. Functional studies confirm that the aPSCs, also known as neoblasts, are the source of differentiated cells and reveal transcription factors needed for differentiation. Subclustering of neoblasts recovers transcriptionally distinct subpopulations, the majority of which are likely specialized to differentiated lineages. One neoblast subset, showing enriched expression of the histone variant H3.3, appears to lack specialization. Altogether, the cell states identified in this study facilitate comparisons to other species and enable future studies of stem cell fate potentials.
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Affiliation(s)
- Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - D Marcela Bolaños
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Carlos Rivera-López
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
- Department of Molecular and Cell Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, 02138, USA.
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14
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Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Salamanca-Díaz DA, Mason V, Metzger B, Bely AE, Kenny N, Özpolat BD, Solana J. Annelid adult cell type diversity and their pluripotent cellular origins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.537979. [PMID: 37163014 PMCID: PMC10168269 DOI: 10.1101/2023.04.25.537979] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Annelids are a broadly distributed, highly diverse, economically and environmentally important group of animals. Most species can regenerate missing body parts, and many are able to reproduce asexually. Therefore, many annelids can generate all adult cell types in adult stages. However, the putative adult stem cell populations involved in these processes, as well as the diversity of adult cell types generated by them, are still unknown. Here, we recover 75,218 single cell transcriptomes of Pristina leidyi, a highly regenerative and asexually-reproducing freshwater annelid. We characterise all major annelid adult cell types, and validate many of our observations by HCR in situ hybridisation. Our results uncover complex patterns of regionally expressed genes in the annelid gut, as well as neuronal, muscle and epidermal specific genes. We also characterise annelid-specific cell types such as the chaetal sacs and globin+ cells, and novel cell types of enigmatic affinity, including a vigilin+ cell type, a lumbrokinase+ cell type, and a diverse set of metabolic cells. Moreover, we characterise transcription factors and gene networks that are expressed specifically in these populations. Finally, we uncover a broadly abundant cluster of putative stem cells with a pluripotent signature. This population expresses well-known stem cell markers such as vasa, piwi and nanos homologues, but also shows heterogeneous expression of differentiated cell markers and their transcription factors. In these piwi+ cells, we also find conserved expression of pluripotency regulators, including multiple chromatin remodelling and epigenetic factors. Finally, lineage reconstruction analyses reveal the existence of differentiation trajectories from piwi+ cells to diverse adult types. Our data reveal the cell type diversity of adult annelids for the first time and serve as a resource for studying annelid cell types and their evolution. On the other hand, our characterisation of a piwi+ cell population with a pluripotent stem cell signature will serve as a platform for the study of annelid stem cells and their role in regeneration.
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Affiliation(s)
- Patricia Álvarez-Campos
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM) & Departamento de Biología (Zoología), Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Helena García-Castro
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Elena Emili
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Alberto Pérez-Posada
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | | | - Vincent Mason
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Bria Metzger
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, USA, 05432
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, MO, USA, 63130
| | | | - Nathan Kenny
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
- Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, Aotearoa New Zealand
| | - B Duygu Özpolat
- Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA, USA, 05432
- Department of Biology, Washington University in St. Louis. 1 Brookings Dr. Saint Louis, MO, USA, 63130
| | - Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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15
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Merino MM, Garcia-Sanz JA. Stemming Tumoral Growth: A Matter of Grotesque Organogenesis. Cells 2023; 12:872. [PMID: 36980213 PMCID: PMC10047265 DOI: 10.3390/cells12060872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
The earliest metazoans probably evolved from single-celled organisms which found the colonial system to be a beneficial organization. Over the course of their evolution, these primary colonial organisms increased in size, and division of labour among the cells became a remarkable feature, leading to a higher level of organization: the biological organs. Primitive metazoans were the first organisms in evolution to show organ-type structures, which set the grounds for complex organs to evolve. Throughout evolution, and concomitant with organogenesis, is the appearance of tissue-specific stem cells. Tissue-specific stem cells gave rise to multicellular living systems with distinct organs which perform specific physiological functions. This setting is a constructive role of evolution; however, rebel cells can take over the molecular mechanisms for other purposes: nowadays we know that cancer stem cells, which generate aberrant organ-like structures, are at the top of a hierarchy. Furthermore, cancer stem cells are the root of metastasis, therapy resistance, and relapse. At present, most therapeutic drugs are unable to target cancer stem cells and therefore, treatment becomes a challenging issue. We expect that future research will uncover the mechanistic "forces" driving organ growth, paving the way to the implementation of new strategies to impair human tumorigenesis.
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Affiliation(s)
- Marisa M. Merino
- Department of Biochemistry, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland
| | - Jose A. Garcia-Sanz
- Department of Molecular Biomedicine, Centro de Investigaciones Biologicas Margarita Salas, Spanish National Research Council (CIB-CSIC), 28040 Madrid, Spain
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16
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Rennolds CW, Bely AE. Integrative biology of injury in animals. Biol Rev Camb Philos Soc 2023; 98:34-62. [PMID: 36176189 PMCID: PMC10087827 DOI: 10.1111/brv.12894] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 01/12/2023]
Abstract
Mechanical injury is a prevalent challenge in the lives of animals with myriad potential consequences for organisms, including reduced fitness and death. Research on animal injury has focused on many aspects, including the frequency and severity of wounding in wild populations, the short- and long-term consequences of injury at different biological scales, and the variation in the response to injury within or among individuals, species, ontogenies, and environmental contexts. However, relevant research is scattered across diverse biological subdisciplines, and the study of the effects of injury has lacked synthesis and coherence. Furthermore, the depth of knowledge across injury biology is highly uneven in terms of scope and taxonomic coverage: much injury research is biomedical in focus, using mammalian model systems and investigating cellular and molecular processes, while research at organismal and higher scales, research that is explicitly comparative, and research on invertebrate and non-mammalian vertebrate species is less common and often less well integrated into the core body of knowledge about injury. The current state of injury research presents an opportunity to unify conceptually work focusing on a range of relevant questions, to synthesize progress to date, and to identify fruitful avenues for future research. The central aim of this review is to synthesize research concerning the broad range of effects of mechanical injury in animals. We organize reviewed work by four broad and loosely defined levels of biological organization: molecular and cellular effects, physiological and organismal effects, behavioural effects, and ecological and evolutionary effects of injury. Throughout, we highlight the diversity of injury consequences within and among taxonomic groups while emphasizing the gaps in taxonomic coverage, causal understanding, and biological endpoints considered. We additionally discuss the importance of integrating knowledge within and across biological levels, including how initial, localized responses to injury can lead to long-term consequences at the scale of the individual animal and beyond. We also suggest important avenues for future injury biology research, including distinguishing better between related yet distinct injury phenomena, expanding the subjects of injury research to include a greater variety of species, and testing how intrinsic and extrinsic conditions affect the scope and sensitivity of injury responses. It is our hope that this review will not only strengthen understanding of animal injury but will contribute to building a foundation for a more cohesive field of 'injury biology'.
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17
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V KN, O KY, Yu DI. Regeneration of the digestive system in the crinoid Lamprometra palmata (Mariametridae, Comatulida). Cell Tissue Res 2023; 391:87-109. [PMID: 34633568 DOI: 10.1007/s00441-021-03526-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/09/2021] [Indexed: 01/18/2023]
Abstract
The morphology and regeneration of the digestive system and tegmen after autotomy of the visceral mass in the crinoid Lamprometra palmata (Clark 1921) was studied. The gut has a five-lobed shape and is covered by a tegmen. The tegmen consists of epidermis and underlying connective tissue. The digestive tube can be divided into three parts: esophagus, intestine, and rectum. At 6 h post-autotomy, the calyx surface is covered by a layer of amoebocytes and juxtaligamental cells (JLCs). At 14-18 h, post-autotomy transdifferentiation of JLCs begins and give rise to the epidermis and cells of digestive system. On days 1-2 post-autotomy, JLCs undergo the mesenchymal-epithelial transition. Some JLCs turn into typical epidermal cells, while other JLCs form small closed epithelial structures that represent the gut anlage. On day 4 post-autotomy, the animals have a mouth opening and a small anal cone. On day 7 post-autotomy, the visceral mass and the digestive system become fully formed but are smaller than normal. A 24-h exposure of L. palmata individuals to a 10-7 M colchicine solution did not slow down regeneration, and the timing of gut formation was similar to that in the control animals. We conclude that JLCs are the major cell source for gut and epidermis regeneration in L. palmata. The main mechanisms of morphogenesis are cell migration, mesenchymal-epithelial transition, and transdifferentiation.
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Affiliation(s)
- Kalacheva Nadezhda V
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia.
| | - Kamenev Yaroslav O
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Dolmatov Igor Yu
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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18
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Kimura JO, Bolaños DM, Ricci L, Srivastava M. Embryonic origins of adult pluripotent stem cells. Cell 2022; 185:4756-4769.e13. [PMID: 36493754 PMCID: PMC9761687 DOI: 10.1016/j.cell.2022.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 08/16/2022] [Accepted: 11/08/2022] [Indexed: 12/13/2022]
Abstract
Although adult pluripotent stem cells (aPSCs) are found in many animal lineages, mechanisms for their formation during embryogenesis are unknown. Here, we leveraged Hofstenia miamia, a regenerative worm that possesses collectively pluripotent aPSCs called neoblasts and produces manipulable embryos. Lineage tracing and functional experiments revealed that one pair of blastomeres gives rise to cells that resemble neoblasts in distribution, behavior, and gene expression. In Hofstenia, aPSCs include transcriptionally distinct subpopulations that express markers associated with differentiated tissues; our data suggest that despite their heterogeneity, aPSCs are derived from one lineage, not from multiple tissue-specific lineages during development. Next, we combined single-cell transcriptome profiling across development with neoblast cell-lineage tracing and identified a molecular trajectory for neoblast formation that includes transcription factors Hes, FoxO, and Tbx. This identification of a cellular mechanism and molecular trajectory for aPSC formation opens the door for in vivo studies of aPSC regulation and evolution.
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Affiliation(s)
- Julian O Kimura
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - D Marcela Bolaños
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA.
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19
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Tracing the origin of everything. Cell 2022; 185:4677-4679. [PMID: 36493749 DOI: 10.1016/j.cell.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/07/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022]
Abstract
Highly potent adult stem cells fuel lifelong tissue homeostasis and regeneration in many aquatic invertebrates, yet their developmental backstories remain obscure. In this issue of Cell, Kimura and colleagues reveal the cellular origin of adult pluripotent stem cells and propose a molecular trajectory for their specification during acoel embryogenesis.
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20
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Angileri KM, Bagia NA, Feschotte C. Transposon control as a checkpoint for tissue regeneration. Development 2022; 149:dev191957. [PMID: 36440631 PMCID: PMC10655923 DOI: 10.1242/dev.191957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022]
Abstract
Tissue regeneration requires precise temporal control of cellular processes such as inflammatory signaling, chromatin remodeling and proliferation. The combination of these processes forms a unique microenvironment permissive to the expression, and potential mobilization of, transposable elements (TEs). Here, we develop the hypothesis that TE activation creates a barrier to tissue repair that must be overcome to achieve successful regeneration. We discuss how uncontrolled TE activity may impede tissue restoration and review mechanisms by which TE activity may be controlled during regeneration. We posit that the diversification and co-evolution of TEs and host control mechanisms may contribute to the wide variation in regenerative competency across tissues and species.
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Affiliation(s)
- Krista M. Angileri
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Nornubari A. Bagia
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, NY 14850, USA
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21
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Latitudinal and temporal variation in injury and its impacts in the invasive Asian shore crab Hemigrapsus sanguineus. Sci Rep 2022; 12:16557. [PMID: 36192531 PMCID: PMC9530151 DOI: 10.1038/s41598-022-21119-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/22/2022] [Indexed: 11/25/2022] Open
Abstract
Nonlethal injury is a pervasive stress on individual animals that can affect large portions of a population at any given time. Yet most studies examine snapshots of injury at a single place and time, making the implicit assumption that the impacts of nonlethal injury are constant. We sampled Asian shore crabs Hemigrapsus sanguineus throughout their invasive North American range and from the spring through fall of 2020. We then documented the prevalence of limb loss over this space and time. We further examined the impacts of limb loss and limb regeneration on food consumption, growth, reproduction, and energy storage. We show that injury differed substantially across sites and was most common towards the southern part of their invaded range on the East Coast of North America. Injury also varied idiosyncratically across sites and through time. It also had strong impacts on individuals via reduced growth and reproduction, despite increased food consumption in injured crabs. Given the high prevalence of nonlethal injury in this species, these negative impacts of injury on individual animals likely scale up to influence population level processes (e.g., population growth), and may be one factor acting against the widespread success of this invader.
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22
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Abstract
POUV is a relatively newly emerged class of POU transcription factors present in jawed vertebrates (Gnathostomata). The function of POUV-class proteins is inextricably linked to zygotic genome activation (ZGA). A large body of evidence now extends the role of these proteins to subsequent developmental stages. While some functions resemble those of other POU-class proteins and are related to neuroectoderm development, others have emerged de novo. The most notable of the latter functions is pluripotency control by Oct4 in mammals. In this review, we focus on these de novo functions in the best-studied species harbouring POUV proteins-zebrafish, Xenopus (anamniotes) and mammals (amniotes). Despite the broad diversity of their biological functions in vertebrates, POUV proteins exert a common feature related to their role in safeguarding the undifferentiated state of cells. Here we summarize numerous pieces of evidence for these specific functions of the POUV-class proteins and recap available loss-of-function data.
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Affiliation(s)
- Evgeny I. Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
| | - Alexey N. Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St Petersburg, Russia
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23
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Srivastava M. Studying development, regeneration, stem cells, and more in the acoel Hofstenia miamia. Curr Top Dev Biol 2022; 147:153-172. [PMID: 35337448 DOI: 10.1016/bs.ctdb.2022.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Acoel worms represent an enigmatic lineage of animals (Acoelomorpha) that has danced around the tree of animal life. Morphology-based classification placed them as flatworms (Phylum Platyhelminthes), with much of their biology being interpreted as a variation on what is observed in better-studied members of that phylum. However, molecular phylogenies suggest that acoels belong to a clade (Xenacoelomorpha) that could be a sister group to other animals with bilateral symmetry (Bilateria) or could belong within deuterostomes, closely related to a group that includes sea stars (Ambulacraria). This change in phylogenetic position has led to renewed interest in the biology of acoels, which can now offer insights into the evolution of many bilaterian traits. The acoel Hofstenia miamia has emerged as a powerful new research organism that enables mechanistic studies of xenacoelomorph biology, especially of developmental and regenerative processes. This article explains the motivation for developing Hofstenia as a new model system, describes Hofstenia biology, highlights the tools and resources that make Hofstenia a good research organism, and considers the questions that Hofstenia is well-positioned to answer. Finally, looking to the future, this article serves as an invitation to new and established scientists to join the growing community of researchers studying this exciting model system.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA, United States.
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24
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Allievi A, Canavesi M, Ferrario C, Sugni M, Bonasoro F. An evo-devo perspective on the regeneration patterns of continuous arm structures in stellate echinoderms. THE EUROPEAN ZOOLOGICAL JOURNAL 2022. [DOI: 10.1080/24750263.2022.2039309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- A. Allievi
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - M. Canavesi
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - C. Ferrario
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - M. Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - F. Bonasoro
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
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25
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Rinkevich B, Ballarin L, Martinez P, Somorjai I, Ben‐Hamo O, Borisenko I, Berezikov E, Ereskovsky A, Gazave E, Khnykin D, Manni L, Petukhova O, Rosner A, Röttinger E, Spagnuolo A, Sugni M, Tiozzo S, Hobmayer B. A pan-metazoan concept for adult stem cells: the wobbling Penrose landscape. Biol Rev Camb Philos Soc 2022; 97:299-325. [PMID: 34617397 PMCID: PMC9292022 DOI: 10.1111/brv.12801] [Citation(s) in RCA: 17] [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: 05/20/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 12/17/2022]
Abstract
Adult stem cells (ASCs) in vertebrates and model invertebrates (e.g. Drosophila melanogaster) are typically long-lived, lineage-restricted, clonogenic and quiescent cells with somatic descendants and tissue/organ-restricted activities. Such ASCs are mostly rare, morphologically undifferentiated, and undergo asymmetric cell division. Characterized by 'stemness' gene expression, they can regulate tissue/organ homeostasis, repair and regeneration. By contrast, analysis of other animal phyla shows that ASCs emerge at different life stages, present both differentiated and undifferentiated phenotypes, and may possess amoeboid movement. Usually pluri/totipotent, they may express germ-cell markers, but often lack germ-line sequestering, and typically do not reside in discrete niches. ASCs may constitute up to 40% of animal cells, and participate in a range of biological phenomena, from whole-body regeneration, dormancy, and agametic asexual reproduction, to indeterminate growth. They are considered legitimate units of selection. Conceptualizing this divergence, we present an alternative stemness metaphor to the Waddington landscape: the 'wobbling Penrose' landscape. Here, totipotent ASCs adopt ascending/descending courses of an 'Escherian stairwell', in a lifelong totipotency pathway. ASCs may also travel along lower stemness echelons to reach fully differentiated states. However, from any starting state, cells can change their stemness status, underscoring their dynamic cellular potencies. Thus, vertebrate ASCs may reflect just one metazoan ASC archetype.
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Affiliation(s)
- Baruch Rinkevich
- Israel Oceanographic & Limnological ResearchNational Institute of OceanographyPOB 9753, Tel ShikmonaHaifa3109701Israel
| | - Loriano Ballarin
- Department of BiologyUniversity of PadovaVia Ugo Bassi 58/BPadova35121Italy
| | - Pedro Martinez
- Departament de Genètica, Microbiologia i EstadísticaUniversitat de BarcelonaAv. Diagonal 643Barcelona08028Spain
- Institut Català de Recerca i Estudis Avançats (ICREA)Passeig Lluís Companys 23Barcelona08010Spain
| | - Ildiko Somorjai
- School of BiologyUniversity of St AndrewsSt Andrews, FifeKY16 9ST, ScotlandUK
| | - Oshrat Ben‐Hamo
- Israel Oceanographic & Limnological ResearchNational Institute of OceanographyPOB 9753, Tel ShikmonaHaifa3109701Israel
| | - Ilya Borisenko
- Department of Embryology, Faculty of BiologySaint‐Petersburg State UniversityUniversity Embankment, 7/9Saint‐Petersburg199034Russia
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center GroningenAntonius Deusinglaan 1Groningen9713 AVThe Netherlands
| | - Alexander Ereskovsky
- Department of Embryology, Faculty of BiologySaint‐Petersburg State UniversityUniversity Embankment, 7/9Saint‐Petersburg199034Russia
- Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE), Aix Marseille University, CNRS, IRD, Avignon UniversityJardin du Pharo, 58 Boulevard Charles LivonMarseille13007France
- Koltzov Institute of Developmental Biology of Russian Academy of SciencesUlitsa Vavilova, 26Moscow119334Russia
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques MonodParisF‐75006France
| | - Denis Khnykin
- Department of PathologyOslo University HospitalBygg 19, Gaustad Sykehus, Sognsvannsveien 21Oslo0188Norway
| | - Lucia Manni
- Department of BiologyUniversity of PadovaVia Ugo Bassi 58/BPadova35121Italy
| | - Olga Petukhova
- Collection of Vertebrate Cell CulturesInstitute of Cytology, Russian Academy of SciencesTikhoretsky Ave. 4St. Petersburg194064Russia
| | - Amalia Rosner
- Israel Oceanographic & Limnological ResearchNational Institute of OceanographyPOB 9753, Tel ShikmonaHaifa3109701Israel
| | - Eric Röttinger
- Université Côte d'Azur, CNRS, INSERM, Institute for Research on Cancer and Aging, Nice (IRCAN)Nice06107France
- Université Côte d'Azur, Federative Research Institute – Marine Resources (IFR MARRES)28 Avenue de ValroseNice06103France
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine OrganismsStazione Zoologica Anton DohrnVilla ComunaleNaples80121Italy
| | - Michela Sugni
- Department of Environmental Science and Policy (ESP)Università degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche‐sur‐mer (LBDV)06234 Villefranche‐sur‐MerVillefranche sur MerCedexFrance
| | - Bert Hobmayer
- Institute of Zoology and Center for Molecular Biosciences, University of InnsbruckTechnikerstrInnsbruck256020Austria
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26
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Abstract
In his prominent book Regeneration (1901), T.H. Morgan's collected and synthesized theoretical and experimental findings from a diverse array of regenerating animals and plants. Through his endeavor, he introduced a new way to study regeneration and its evolution, setting a conceptual framework that still guides today's research and that embraces the contemporary evolutionary and developmental approaches.In the first part of the chapter, we summarize Morgan's major tenets and use it as a narrative thread to advocate interpreting regenerative biology through the theoretical tools provided by evolution and developmental biology, but also to highlight potential caveats resulting from the rapid proliferation of comparative studies and from the expansion of experimental laboratory models. In the second part, we review some experimental evo-devo approaches, highlighting their power and some of their interpretative dangers. Finally, in order to further understand the evolution of regenerative abilities, we portray an adaptive perspective on the evolution of regeneration and suggest a framework for investigating the adaptive nature of regeneration.
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Affiliation(s)
| | - Alexandre Alié
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France
| | - Stefano Tiozzo
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Villefranche-sur-Mer, France.
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27
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Abrams MJ, Tan FH, Li Y, Basinger T, Heithe ML, Sarma A, Lee IT, Condiotte ZJ, Raffiee M, Dabiri JO, Gold DA, Goentoro L. A conserved strategy for inducing appendage regeneration in moon jellyfish, Drosophila, and mice. eLife 2021; 10:65092. [PMID: 34874003 PMCID: PMC8782573 DOI: 10.7554/elife.65092] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Can limb regeneration be induced? Few have pursued this question, and an evolutionarily conserved strategy has yet to emerge. This study reports a strategy for inducing regenerative response in appendages, which works across three species that span the animal phylogeny. In Cnidaria, the frequency of appendage regeneration in the moon jellyfish Aurelia was increased by feeding with the amino acid L-leucine and the growth hormone insulin. In insects, the same strategy induced tibia regeneration in adult Drosophila. Finally, in mammals, L-leucine and sucrose administration induced digit regeneration in adult mice, including dramatically from mid-phalangeal amputation. The conserved effect of L-leucine and insulin/sugar suggests a key role for energetic parameters in regeneration induction. The simplicity by which nutrient supplementation can induce appendage regeneration provides a testable hypothesis across animals.
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Affiliation(s)
- Michael J Abrams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Fayth Hui Tan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Yutian Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ty Basinger
- Department of Biology and Allied Health Sciences, Bloomsburg University, Bloomsburg, United States
| | - Martin L Heithe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Anish Sarma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Iris T Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Zevin J Condiotte
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Misha Raffiee
- Department of Bioengineering, Stanford University, Paolo Alto, United States
| | - John O Dabiri
- Graduate Aerospace Laboratories and Mechanical Engineering, California Institute of Technology, Pasadena, United States
| | - David A Gold
- Department of Earth and Planetary Sciences, University of California, Davis, Davis, United States
| | - Lea Goentoro
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
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28
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Dolmatov IY, Kalacheva NV, Tkacheva ES, Shulga AP, Zavalnaya EG, Shamshurina EV, Girich AS, Boyko AV, Eliseikina MG. Expression of Piwi, MMP, TIMP, and Sox during Gut Regeneration in Holothurian Eupentacta fraudatrix (Holothuroidea, Dendrochirotida). Genes (Basel) 2021; 12:1292. [PMID: 34440466 PMCID: PMC8391186 DOI: 10.3390/genes12081292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Mesodermal cells of holothurian Eupentacta fraudatrix can transdifferentiate into enterocytes during the regeneration of the digestive system. In this study, we investigated the expression of several genes involved in gut regeneration in E. fraudatrix. Moreover, the localization of progenitor cells of coelomocytes, juvenile cells, and their participation in the formation of the luminal epithelium of the digestive tube were studied. It was shown that Piwi-positive cells were not involved in the formation of the luminal epithelium of the digestive tube. Ef-72 kDa type IV collagenase and Ef-MMP16 had an individual expression profile and possibly different functions. The Ef-tensilin3 gene exhibited the highest expression and indicates its potential role in regeneration. Ef-Sox9/10 and Ef-Sox17 in E. fraudatrix may participate in the mechanism of transdifferentiation of coelomic epithelial cells. Their transcripts mark the cells that plunge into the connective tissue of the gut anlage and give rise to enterocytes. Ef-Sox9/10 probably controls the switching of mesodermal cells to the enterocyte phenotype, while Ef-Sox17 may be involved in the regulation of the initial stages of transdifferentiation.
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Affiliation(s)
- Igor Yu. Dolmatov
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Palchevsky 17, 690041 Vladivostok, Russia; (N.V.K.); (E.S.T.); (A.P.S.); (E.G.Z.); (E.V.S.); (A.S.G.); (A.V.B.); (M.G.E.)
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29
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Kostyuchenko RP, Kozin VV. Comparative Aspects of Annelid Regeneration: Towards Understanding the Mechanisms of Regeneration. Genes (Basel) 2021; 12:1148. [PMID: 34440322 PMCID: PMC8392629 DOI: 10.3390/genes12081148] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 01/12/2023] Open
Abstract
The question of why animals vary in their ability to regenerate remains one of the most intriguing questions in biology. Annelids are a large and diverse phylum, many members of which are capable of extensive regeneration such as regrowth of a complete head or tail and whole-body regeneration, even from few segments. On the other hand, some representatives of both of the two major annelid clades show very limited tissue regeneration and are completely incapable of segmental regeneration. Here we review experimental and descriptive data on annelid regeneration, obtained at different levels of organization, from data on organs and tissues to intracellular and transcriptomic data. Understanding the variety of the cellular and molecular basis of regeneration in annelids can help one to address important questions about the role of stem/dedifferentiated cells and "molecular morphallaxis" in annelid regeneration as well as the evolution of regeneration in general.
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Affiliation(s)
- Roman P. Kostyuchenko
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7-9, 199034 St. Petersburg, Russia;
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30
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Srivastava M. Beyond Casual Resemblances: Rigorous Frameworks for Comparing Regeneration Across Species. Annu Rev Cell Dev Biol 2021; 37:415-440. [PMID: 34288710 DOI: 10.1146/annurev-cellbio-120319-114716] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The majority of animal phyla have species that can regenerate. Comparing regeneration across animals can reconstruct the molecular and cellular evolutionary history of this process. Recent studies have revealed some similarity in regeneration mechanisms, but rigorous comparative methods are needed to assess whether these resemblances are ancestral pathways (homology) or are the result of convergent evolution (homoplasy). This review aims to provide a framework for comparing regeneration across animals, focusing on gene regulatory networks (GRNs), which are substrates for assessing process homology. The homology of the wound-induced activation of Wnt signaling and of adult stem cells are discussed as examples of ongoing studies of regeneration that enable comparisons in a GRN framework. Expanding the study of regeneration GRNs in currently studied species and broadening taxonomic sampling for these approaches will identify processes that are unifying principles of regeneration biology across animals. These insights are important both for evolutionary studies of regeneration and for human regenerative medicine. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Mansi Srivastava
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;
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31
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Wolff A, Hinman V. The Use of Larval Sea Stars and Sea Urchins in the Discovery of Shared Mechanisms of Metazoan Whole-Body Regeneration. Genes (Basel) 2021; 12:1063. [PMID: 34356079 PMCID: PMC8303351 DOI: 10.3390/genes12071063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 02/07/2023] Open
Abstract
The ability to regenerate is scattered among the metazoan tree of life. Further still, regenerative capacity varies widely within these specific organisms. Numerous organisms, all with different regenerative capabilities, have been studied at length and key similarities and disparities in how regeneration occurs have been identified. In order to get a better grasp on understanding regeneration as a whole, we must search for new models that are capable of extensive regeneration, as well as those that have been under sampled in the literature. As invertebrate deuterostomes, echinoderms fit both of these requirements. Multiple members regenerate various tissue types at all life stages, including examples of whole-body regeneration. Interrogations in two highly studied echinoderms, the sea urchin and the sea star, have provided knowledge of tissue and whole-body regeneration at various life stages. Work has begun to examine regeneration in echinoderm larvae, a potential new system for understanding regenerative mechanisms in a basal deuterostome. Here, we review the ways these two animals' larvae have been utilized as a model of regeneration.
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Affiliation(s)
- Andrew Wolff
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA;
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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32
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Edgar A, Mitchell DG, Martindale MQ. Whole-Body Regeneration in the Lobate Ctenophore Mnemiopsis leidyi. Genes (Basel) 2021; 12:genes12060867. [PMID: 34198839 PMCID: PMC8228598 DOI: 10.3390/genes12060867] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 01/28/2023] Open
Abstract
Ctenophores (a.k.a. comb jellies) are one of the earliest branching extant metazoan phyla. Adult regenerative ability varies greatly within the group, with platyctenes undergoing both sexual and asexual reproduction by fission while others in the genus Beroe having completely lost the ability to replace missing body parts. We focus on the unique regenerative aspects of the lobate ctenophore, Mnemiopsis leidyi, which has become a popular model for its rapid wound healing and tissue replacement, optical clarity, and sequenced genome. M. leidyi’s highly mosaic, stereotyped development has been leveraged to reveal the polar coordinate system that directs whole-body regeneration as well as lineage restriction of replacement cells in various regenerating organs. Several cell signaling pathways known to function in regeneration in other animals are absent from the ctenophore’s genome. Further research will either reveal ancient principles of the regenerative process common to all animals or reveal novel solutions to the stability of cell fates and whole-body regeneration.
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33
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Rosner A, Armengaud J, Ballarin L, Barnay-Verdier S, Cima F, Coelho AV, Domart-Coulon I, Drobne D, Genevière AM, Jemec Kokalj A, Kotlarska E, Lyons DM, Mass T, Paz G, Pazdro K, Perić L, Ramšak A, Rakers S, Rinkevich B, Spagnuolo A, Sugni M, Cambier S. Stem cells of aquatic invertebrates as an advanced tool for assessing ecotoxicological impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 771:144565. [PMID: 33736145 DOI: 10.1016/j.scitotenv.2020.144565] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/10/2020] [Accepted: 12/13/2020] [Indexed: 06/12/2023]
Abstract
Environmental stressors are assessed through methods that quantify their impacts on a wide range of metrics including species density, growth rates, reproduction, behaviour and physiology, as on host-pathogen interactions and immunocompetence. Environmental stress may induce additional sublethal effects, like mutations and epigenetic signatures affecting offspring via germline mediated transgenerational inheritance, shaping phenotypic plasticity, increasing disease susceptibility, tissue pathologies, changes in social behaviour and biological invasions. The growing diversity of pollutants released into aquatic environments requires the development of a reliable, standardised and 3R (replacement, reduction and refinement of animals in research) compliant in vitro toolbox. The tools have to be in line with REACH regulation 1907/2006/EC, aiming to improve strategies for potential ecotoxicological risks assessment and monitoring of chemicals threatening human health and aquatic environments. Aquatic invertebrates' adult stem cells (ASCs) are numerous and can be pluripotent, as illustrated by high regeneration ability documented in many of these taxa. This is of further importance as in many aquatic invertebrate taxa, ASCs are able to differentiate into germ cells. Here we propose that ASCs from key aquatic invertebrates may be harnessed for applicable and standardised new tests in ecotoxicology. As part of this approach, a battery of modern techniques and endpoints are proposed to be tested for their ability to correctly identify environmental stresses posed by emerging contaminants in aquatic environments. Consequently, we briefly describe the current status of the available toxicity testing and biota-based monitoring strategies in aquatic environmental ecotoxicology and highlight some of the associated open issues such as replicability, consistency and reliability in the outcomes, for understanding and assessing the impacts of various chemicals on organisms and on the entire aquatic environment. Following this, we describe the benefits of aquatic invertebrate ASC-based tools for better addressing ecotoxicological questions, along with the current obstacles and possible overhaul approaches.
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Affiliation(s)
- Amalia Rosner
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-30200 Bagnols-sur-Cèze, France.
| | - Loriano Ballarin
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Stéphanie Barnay-Verdier
- Sorbonne Université; CNRS, INSERM, Université Côte d'Azur, Institute for Research on Cancer and Aging Nice, F-06107 Nice, France.
| | - Francesca Cima
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35121 Padova, Italy.
| | - Ana Varela Coelho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal.
| | - Isabelle Domart-Coulon
- Muséum National d'Histoire Naturelle, CNRS, Microorganism Communication and Adaptation Molecules MCAM, Paris F-75005, France.
| | - Damjana Drobne
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Anne-Marie Genevière
- Sorbonne Université, CNRS, Integrative Biology of Marine Organisms, BIOM, F-6650 Banyuls-sur-mer, France.
| | - Anita Jemec Kokalj
- University of Ljubljana, Biotechnical Faculty, Department of Biology, Večna pot 111,D, 1000 Ljubljana, Slovenia.
| | - Ewa Kotlarska
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland.
| | - Daniel Mark Lyons
- Center for Marine Research, Ruđer Bošković Institute, G. Paliaga 5, HR-52210 Rovinj, Croatia.
| | - Tali Mass
- Marine Biology Department, Leon H. Charney School of Marine Sciences, 199 Aba Khoushy Ave, University of Haifa, 3498838, Israel.
| | - Guy Paz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Ksenia Pazdro
- Institute of Oceanology of the Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Lorena Perić
- Rudjer Boskovic Institute, Laboratory for Aquaculture and Pathology of Aquaculture Organisms, Bijenička cesta 54, HR-10000 Zagreb, Croatia.
| | - Andreja Ramšak
- National Institute of Biology, Marine Biology Station, Fornače 41, 6330 Piran, Slovenia.
| | | | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, P.O. Box 8030, Tel Shikmona, Haifa 3108001, Israel.
| | - Antonietta Spagnuolo
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria 2, 20133 Milano, Italy.
| | - Sébastien Cambier
- Luxembourg Institute of Science and Technology, 5, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
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Bideau L, Kerner P, Hui J, Vervoort M, Gazave E. Animal regeneration in the era of transcriptomics. Cell Mol Life Sci 2021; 78:3941-3956. [PMID: 33515282 PMCID: PMC11072743 DOI: 10.1007/s00018-021-03760-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/04/2021] [Accepted: 01/09/2021] [Indexed: 12/27/2022]
Abstract
Animal regeneration, the ability to restore a lost body part, is a process that has fascinated scientists for centuries. In this review, we first present what regeneration is and how it relates to development, as well as the widespread and diverse nature of regeneration in animals. Despite this diversity, animal regeneration includes three common mechanistic steps: initiation, induction and activation of progenitors, and morphogenesis. In this review article, we summarize and discuss, from an evolutionary perspective, the recent data obtained for a variety of regeneration models which have allowed to identify key shared mechanisms that control these main steps of animal regeneration. This review also synthesizes the wealth of high-throughput mRNA sequencing data (bulk mRNA-seq) concerning regeneration which have been obtained in recent years, highlighting the major advances in the regeneration field that these studies have revealed. We stress out that, through a comparative approach, these data provide opportunities to further shed light on the evolution of regeneration in animals. Finally, we point out how the use of single-cell mRNA-seq technology and integration with epigenomic approaches may further help researchers to decipher mechanisms controlling regeneration and their evolution in animals.
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Affiliation(s)
- Loïc Bideau
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Pierre Kerner
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France
| | - Jerome Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, 75006, Paris, France.
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35
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Ereskovsky A, Borisenko IE, Bolshakov FV, Lavrov AI. Whole-Body Regeneration in Sponges: Diversity, Fine Mechanisms, and Future Prospects. Genes (Basel) 2021; 12:506. [PMID: 33805549 PMCID: PMC8066720 DOI: 10.3390/genes12040506] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 02/08/2023] Open
Abstract
While virtually all animals show certain abilities for regeneration after an injury, these abilities vary greatly among metazoans. Porifera (Sponges) is basal metazoans characterized by a wide variety of different regenerative processes, including whole-body regeneration (WBR). Considering phylogenetic position and unique body organization, sponges are highly promising models, as they can shed light on the origin and early evolution of regeneration in general and WBR in particular. The present review summarizes available data on the morphogenetic and cellular mechanisms accompanying different types of WBR in sponges. Sponges show a high diversity of WBR, which principally could be divided into (1) WBR from a body fragment and (2) WBR by aggregation of dissociated cells. Sponges belonging to different phylogenetic clades and even to different species and/or differing in the anatomical structure undergo different morphogeneses after similar operations. A common characteristic feature of WBR in sponges is the instability of the main body axis: a change of the organism polarity is described during all types of WBR. The cellular mechanisms of WBR are different across sponge classes, while cell dedifferentiations and transdifferentiations are involved in regeneration processes in all sponges. Data considering molecular regulation of WBR in sponges are extremely scarce. However, the possibility to achieve various types of WBR ensured by common morphogenetic and cellular basis in a single species makes sponges highly accessible for future comprehensive physiological, biochemical, and molecular studies of regeneration processes.
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Affiliation(s)
- Alexander Ereskovsky
- Institut Méditerranéen de Biodiversité et d’Ecologie Marine et Continentale (IMBE), Aix Marseille University, CNRS, IRD, Station Marine d’Endoume, Rue de la Batterie des Lions, Avignon University, 13007 Marseille, France
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia;
- Evolution of Morphogenesis Laboratory, Koltzov Institute of Developmental Biology of Russian Academy of Sciences, 119334 Moscow, Russia
| | - Ilya E. Borisenko
- Department of Embryology, Faculty of Biology, Saint-Petersburg State University, 199034 Saint-Petersburg, Russia;
| | - Fyodor V. Bolshakov
- Pertsov White Sea Biological Station, Biological Faculty, Lomonosov Moscow State University, 119192 Moscow, Russia; (F.V.B.); (A.I.L.)
| | - Andrey I. Lavrov
- Pertsov White Sea Biological Station, Biological Faculty, Lomonosov Moscow State University, 119192 Moscow, Russia; (F.V.B.); (A.I.L.)
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36
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Elchaninov A, Sukhikh G, Fatkhudinov T. Evolution of Regeneration in Animals: A Tangled Story. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.621686] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The evolution of regenerative capacity in multicellular animals represents one of the most complex and intriguing problems in biology. How could such a seemingly advantageous trait as self-repair become consistently attenuated by the evolution? This review article examines the concept of the origin and nature of regeneration, its connection with the processes of embryonic development and asexual reproduction, as well as with the mechanisms of tissue homeostasis. The article presents a variety of classical and modern hypotheses explaining different trends in the evolution of regenerative capacity which is not always beneficial for the individual and notably for the species. Mechanistically, these trends are driven by the evolution of signaling pathways and progressive restriction of differentiation plasticity with concomitant advances in adaptive immunity. Examples of phylogenetically enhanced regenerative capacity are considered as well, with appropriate evolutionary reasoning for the enhancement and discussion of its molecular mechanisms.
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37
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Pryszlak M, Wiggans M, Chen X, Jaramillo JE, Burns SE, Richards LM, Pugh TJ, Kaplan DR, Huang X, Dirks PB, Pearson BJ. The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells. Cell Rep 2021; 34:108903. [PMID: 33789112 DOI: 10.1016/j.celrep.2021.108903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 10/28/2020] [Accepted: 03/04/2021] [Indexed: 12/12/2022] Open
Abstract
Across the animal kingdom, adult tissue homeostasis is regulated by adult stem cell activity, which is commonly dysregulated in human cancers. However, identifying key regulators of stem cells in the milieu of thousands of genes dysregulated in a given cancer is challenging. Here, using a comparative genomics approach between planarian adult stem cells and patient-derived glioblastoma stem cells (GSCs), we identify and demonstrate the role of DEAD-box helicase DDX56 in regulating aspects of stemness in four stem cell systems: planarians, mouse neural stem cells, human GSCs, and a fly model of glioblastoma. In a human GSC line, DDX56 localizes to the nucleolus, and using planarians, when DDX56 is lost, stem cells dysregulate expression of ribosomal RNAs and lose nucleolar integrity prior to stem cell death. Together, a comparative genomic approach can be used to uncover conserved stemness regulators that are functional in both normal and cancer stem cells.
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Affiliation(s)
- Michael Pryszlak
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada
| | - Mallory Wiggans
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada
| | - Xin Chen
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada
| | - Julia E Jaramillo
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada
| | - Sarah E Burns
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada
| | - Laura M Richards
- Department of Medical Biophysics, University of Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Trevor J Pugh
- Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; Department of Medical Biophysics, University of Toronto, ON M5G 1L7, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - David R Kaplan
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada
| | - Xi Huang
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Toronto, ON M5G 0A4, Canada
| | - Peter B Dirks
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada; The Hospital for Sick Children, Arthur and Sonia Labatt Brain Tumor Research Centre, Toronto, ON M5G 0A4, Canada
| | - Bret J Pearson
- The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON M5G 0A4, Canada; University of Toronto, Department of Molecular Genetics, Toronto, ON M5S 1A8, Canada; Ontario Institute for Cancer Research, Toronto, ON M5G 0A3, Canada.
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38
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Luz BLP, Miller DJ, Kitahara MV. High regenerative capacity is a general feature within colonial dendrophylliid corals (Anthozoa, Scleractinia). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 336:281-292. [PMID: 33503321 DOI: 10.1002/jez.b.23021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/21/2022]
Abstract
The regenerative capacity of cnidarians plays an essential role in the maintenance and restoration of coral reef ecosystems by allowing faster recovery from disturbances and more efficient small-scale dispersal. However, in the case of invasive species, this property may contribute to their dispersal and success in nonnative habitats. Given that four Indo-Pacific members of the coral genus Tubastraea have invaded the Atlantic, here we evaluated the ability of three of these species (Tubastraea coccinea, Tubastraea diaphana, and Tubastraea micranthus) to regenerate from fragments of undifferentiated coral tissue to fully functional polyps in response to differences in food supply and fragment size. For comparative purposes, another colonial dendrophylliid (Dendrophyllia sp.) was included in the analyses. All dendrophylliids displayed regenerative ability and high survival rates that were independent of whether or not food was supplied or fragment size. However, regeneration rates varied between species and were influenced by fragment size. Temporal expression of key genes of the regenerative process (Wnt and FGF) was profiled during whole-body regeneration of T. coccinea, suggesting a remarkable regenerative ability of T. coccinea that points to its potential use as a laboratory model for the investigation of regeneration in colonial calcified anthozoans.
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Affiliation(s)
- Bruna Louise Pereira Luz
- Coastal and Ocean Systems Graduate Program, Federal University of Paraná, Pontal do Sul, Pontal do Paraná, Paraná, Brazil.,Center for Marine Biology, University of São Paulo, Praia do Cabelo Gordo, São Sebastião, Brazil.,ARC Centre of Excellence for Coral Reef Studies and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - David John Miller
- ARC Centre of Excellence for Coral Reef Studies and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia
| | - Marcelo Visentini Kitahara
- Coastal and Ocean Systems Graduate Program, Federal University of Paraná, Pontal do Sul, Pontal do Paraná, Paraná, Brazil.,Center for Marine Biology, University of São Paulo, Praia do Cabelo Gordo, São Sebastião, Brazil.,Department of Marine Sciences, Federal University of São Paulo, Santos, São Paulo, Brazil
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39
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Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. Sci Rep 2021; 11:346. [PMID: 33431961 PMCID: PMC7801731 DOI: 10.1038/s41598-020-79436-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians or sea cucumbers, cellular processes of intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Comparisons of differential expression were made using the mesentery as a reference against 24 h and 3 days regenerating intestine, revealing a large number of differentially expressed transcripts. Gene ontology and pathway enrichment analysis showed evidence of increasing transcriptional activity. Further analysis of transcripts associated with transcription factors revealed diverse expression patterns with mechanisms involving developmental and cancer-related activity that could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
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40
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Fields C, Levin M. Why isn't sex optional? Stem-cell competition, loss of regenerative capacity, and cancer in metazoan evolution. Commun Integr Biol 2020; 13:170-183. [PMID: 33403054 PMCID: PMC7746248 DOI: 10.1080/19420889.2020.1838809] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/15/2022] Open
Abstract
Animals that can reproduce vegetatively by fission or budding and also sexually via specialized gametes are found in all five primary animal lineages (Bilateria, Cnidaria, Ctenophora, Placozoa, Porifera). Many bilaterian lineages, including roundworms, insects, and most chordates, have lost the capability of vegetative reproduction and are obligately gametic. We suggest a developmental explanation for this evolutionary phenomenon: obligate gametic reproduction is the result of germline stem cells winning a winner-take-all competition with non-germline stem cells for control of reproduction and hence lineage survival. We develop this suggestion by extending Hamilton's rule, which factors the relatedness between parties into the cost/benefit analysis that underpins cooperative behaviors, to include similarity of cellular state. We show how coercive or deceptive cell-cell signaling can be used to make costly cooperative behaviors appear less costly to the cooperating party. We then show how competition between stem-cell lineages can render an ancestral combination of vegetative reproduction with facultative sex unstable, with one or the other process driven to extinction. The increased susceptibility to cancer observed in obligately-sexual lineages is, we suggest, a side-effect of deceptive signaling that is exacerbated by the loss of whole-body regenerative abilities. We suggest a variety of experimental approaches for testing our predictions.
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Affiliation(s)
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, USA
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41
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Wiggans M, Pearson BJ. One stem cell program to rule them all? FEBS J 2020; 288:3394-3406. [PMID: 33063917 DOI: 10.1111/febs.15598] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/17/2020] [Accepted: 10/12/2020] [Indexed: 12/23/2022]
Abstract
Many species of animals have stem cells that they maintain throughout their lives, which suggests that stem cells are an ancestral feature of all animals. From this, we take the viewpoint that cells with the biological properties of 'stemness'-self-renewal and multipotency-may share ancestral genetic circuitry. However, in practice is it very difficult to identify and compare stemness gene signatures across diverse animals and large evolutionary distances? First, it is critical to experimentally demonstrate self-renewal and potency. Second, genomic methods must be used to determine specific gene expression in stem cell types compared with non-stem cell types to determine stem cell gene enrichment. Third, gene homology must be mapped between diverse animals across large evolutionary distances. Finally, conserved genes that fulfill these criteria must be tested for role in stem cell function. It is our viewpoint that by comparing stem cell-specific gene signatures across evolution, ancestral programs of stemness can be uncovered, and ultimately, the dysregulation of stemness programs drives the state of cancer stem cells.
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Affiliation(s)
- Mallory Wiggans
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, ON, Canada
| | - Bret J Pearson
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, ON, Canada.,Ontario Institute for Cancer Research, Toronto, ON, Canada
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42
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Ferrario C, Sugni M, Somorjai IML, Ballarin L. Beyond Adult Stem Cells: Dedifferentiation as a Unifying Mechanism Underlying Regeneration in Invertebrate Deuterostomes. Front Cell Dev Biol 2020; 8:587320. [PMID: 33195242 PMCID: PMC7606891 DOI: 10.3389/fcell.2020.587320] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/25/2020] [Indexed: 12/15/2022] Open
Abstract
The diversity of regenerative phenomena seen in adult metazoans, as well as their underlying mechanistic bases, are still far from being comprehensively understood. Reviewing both ultrastructural and molecular data, the present work aims to showcase the increasing relevance of invertebrate deuterostomes, i.e., echinoderms, hemichordates, cephalochordates and tunicates, as invaluable models to study cellular aspects of adult regeneration. Our comparative approach suggests a fundamental contribution of local dedifferentiation -rather than mobilization of resident undifferentiated stem cells- as an important cellular mechanism contributing to regeneration in these groups. Thus, elucidating the cellular origins, recruitment and fate of cells, as well as the molecular signals underpinning tissue regrowth in regeneration-competent deuterostomes, will provide the foundation for future research in tackling the relatively limited regenerative abilities of vertebrates, with clear applications in regenerative medicine.
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Affiliation(s)
- Cinzia Ferrario
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Milan, Italy
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Milan, Italy
| | - Ildiko M. L. Somorjai
- The Willie Russel Laboratories, Biomedical Sciences Research Complex, North Haugh, University of St Andrews, St Andrews, United Kingdom
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43
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Holland ND, Somorjai IML. Serial blockface SEM suggests that stem cells may participate in adult notochord growth in an invertebrate chordate, the Bahamas lancelet. EvoDevo 2020; 11:22. [PMID: 33088474 PMCID: PMC7568382 DOI: 10.1186/s13227-020-00167-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 10/07/2020] [Indexed: 01/07/2023] Open
Abstract
Background The cellular basis of adult growth in cephalochordates (lancelets or amphioxus) has received little attention. Lancelets and their constituent organs grow slowly but continuously during adult life. Here, we consider whether this slow organ growth involves tissue-specific stem cells. Specifically, we focus on the cell populations in the notochord of an adult lancelet and use serial blockface scanning electron microscopy (SBSEM) to reconstruct the three-dimensional fine structure of all the cells in a tissue volume considerably larger than normally imaged with this technique. Results In the notochordal region studied, we identified 10 cells with stem cell-like morphology at the posterior tip of the organ, 160 progenitor (Müller) cells arranged along its surface, and 385 highly differentiated lamellar cells constituting its core. Each cell type could clearly be distinguished on the basis of cytoplasmic density and overall cell shape. Moreover, because of the large sample size, transitions between cell types were obvious. Conclusions For the notochord of adult lancelets, a reasonable interpretation of our data indicates growth of the organ is based on stem cells that self-renew and also give rise to progenitor cells that, in turn, differentiate into lamellar cells. Our discussion compares the cellular basis of adult notochord growth among chordates in general. In the vertebrates, several studies implied that proliferating cells (chordoblasts) in the cortex of the organ might be stem cells. However, we think it is more likely that such cells actually constitute a progenitor population downstream from and maintained by inconspicuous stem cells. We venture to suggest that careful searches should find stem cells in the adult notochords of many vertebrates, although possibly not in the notochordal vestiges (nucleus pulposus regions) of mammals, where the presence of endogenous proliferating cells remains controversial.
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Affiliation(s)
- Nicholas D Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California At San Diego, La Jolla, CA 92093 USA
| | - Ildiko M L Somorjai
- School of Biology, University of Saint Andrews, St. Andrews, KY16 9ST Scotland
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44
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Kim IV, Riedelbauch S, Kuhn CD. The piRNA pathway in planarian flatworms: new model, new insights. Biol Chem 2020; 401:1123-1141. [DOI: 10.1515/hsz-2019-0445] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/12/2020] [Indexed: 12/22/2022]
Abstract
AbstractPIWI-interacting RNAs (piRNAs) are small regulatory RNAs that associate with members of the PIWI clade of the Argonaute superfamily of proteins. piRNAs are predominantly found in animal gonads. There they silence transposable elements (TEs), regulate gene expression and participate in DNA methylation, thus orchestrating proper germline development. Furthermore, PIWI proteins are also indispensable for the maintenance and differentiation capabilities of pluripotent stem cells in free-living invertebrate species with regenerative potential. Thus, PIWI proteins and piRNAs seem to constitute an essential molecular feature of somatic pluripotent stem cells and the germline. In keeping with this hypothesis, both PIWI proteins and piRNAs are enriched in neoblasts, the adult stem cells of planarian flatworms, and their presence is a prerequisite for the proper regeneration and perpetual tissue homeostasis of these animals. The piRNA pathway is required to maintain the unique biology of planarians because, in analogy to the animal germline, planarian piRNAs silence TEs and ensure stable genome inheritance. Moreover, planarian piRNAs also contribute to the degradation of numerous protein-coding transcripts, a function that may be critical for neoblast differentiation. This review gives an overview of the planarian piRNA pathway and of its crucial function in neoblast biology.
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Affiliation(s)
- Iana V. Kim
- Gene regulation by Non-coding RNA, Elite Network of Bavaria and University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Sebastian Riedelbauch
- Gene regulation by Non-coding RNA, Elite Network of Bavaria and University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | - Claus-D. Kuhn
- Gene regulation by Non-coding RNA, Elite Network of Bavaria and University of Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
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45
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Dunoyer LA, Seifert AW, Van Cleve J. Evolutionary bedfellows: Reconstructing the ancestral state of autotomy and regeneration. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 336:94-115. [PMID: 32558244 DOI: 10.1002/jez.b.22974] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 05/18/2020] [Accepted: 05/24/2020] [Indexed: 11/11/2022]
Abstract
Some form of regeneration occurs in all lifeforms and extends from single-cell organisms to humans. The degree to which regenerative ability is distributed across different taxa, however, is harder to ascertain given the potential for phylogenetic constraint or inertia, and adaptive processes to shape this pattern. Here, we examine the phylogenetic history of regeneration in two groups where the trait has been well-studied: arthropods and reptiles. Because autotomy is often present alongside regeneration in these groups, we performed ancestral state reconstructions for both traits to more precisely assess the timing of their origins and the degree to which these traits coevolve. Using an ancestral trait reconstruction, we find that autotomy and regeneration were present at the base of the arthropod and reptile trees. We also find that when autotomy is lost it does not re-evolve easily. Lastly, we find that the distribution of regeneration is intimately connected to autotomy with the association being stronger in reptiles than in arthropods. Although these patterns suggest that decoupling autotomy and regeneration at a broad phylogenetic scale may be difficult, the available data provides useful insight into their entanglement. Ultimately, our reconstructions provide the important groundwork to explore how selection may have played a role during the loss of regeneration in specific lineages.
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Affiliation(s)
- Luc A Dunoyer
- Department of Biology, University of Kentucky, Lexington, Kentucky.,Department of Life Sciences, Wake Technical Community College, Raleigh, North Carolina
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, Kentucky
| | - Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, Kentucky
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46
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Cell-based therapies for the treatment of myocardial infarction: lessons from cardiac regeneration and repair mechanisms in non-human vertebrates. Heart Fail Rev 2020; 24:133-142. [PMID: 30421074 DOI: 10.1007/s10741-018-9750-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ischemic cardiomyopathy is the cardiovascular condition with the highest impact on the Western population. In mammals (humans included), prolonged ischemia in the ventricular walls causes the death of cardiomyocytes (myocardial infarction, MI). The loss of myocardial mass is soon compensated by the formation of a reparative, non-contractile fibrotic scar that ultimately affects heart performance. Despite the enormous clinical relevance of MI, no effective therapy is available for the long-term treatment of this condition. Moreover, since the human heart is not able to undergo spontaneous regeneration, many researchers aim at designing cell-based therapies that allow for the substitution of dead cardiomyocytes by new, functional ones. So far, the majority of such strategies rely on the injection of different progenitor/stem cells to the infarcted heart. These cardiovascular progenitors, which are expected to differentiate into cardiomyocytes de novo, seldom give rise to new cardiac muscle. In this context, the most important challenge in the field is to fully disclose the molecular and cellular mechanisms that could promote active myocardial regeneration after cardiac damage. Accordingly, we suggest that such strategy should be inspired by the unique regenerative and reparative responses displayed by non-human animal models, from the restricted postnatal myocardial regeneration abilities of the murine heart to the full ventricular regeneration of some bony fishes (e.g., zebrafish). In this review article, we will discuss about current scientific approaches to study cardiac reparative and regenerative phenomena using animal models.
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47
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Planarian EGF repeat-containing genes megf6 and hemicentin are required to restrict the stem cell compartment. PLoS Genet 2020; 16:e1008613. [PMID: 32078629 PMCID: PMC7059952 DOI: 10.1371/journal.pgen.1008613] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/06/2020] [Accepted: 01/16/2020] [Indexed: 12/17/2022] Open
Abstract
The extracellular matrix (ECM) is important for maintaining the boundaries between tissues. This role is particularly critical in the stem cell niche, as pre-neoplastic or cancerous stem cells must pass these boundaries in order to invade into the surrounding tissue. Here, we examine the role of the ECM as a regulator of the stem cell compartment in the planarian Schmidtea mediterranea, a highly regenerative, long-lived organism with a large population of adult stem cells. We identify two EGF repeat-containing genes, megf6 and hemicentin, with identical knockdown phenotypes. We find that megf6 and hemicentin are needed to maintain the structure of the basal lamina, and in the absence of either gene, pluripotent stem cells migrate ectopically outside of their compartment and hyper-proliferate, causing lesions in the body wall muscle. These muscle lesions and ectopic stem cells are also associated with ectopic gut branches, which protrude from the normal gut towards the dorsal side of the animal. Interestingly, both megf6 and hemicentin knockdown worms are capable of regenerating tissue free of both muscle lesions and ectopic cells, indicating that these genes are dispensable for regeneration. These results provide insight into the role of planarian ECM in restricting the stem cell compartment, and suggest that signals within the compartment may act to suppress stem cell hyperproliferation. The freshwater planarian maintains a large population of adult stem cells throughout its long lifespan. Although these stem cells are constantly dividing, the rate of division is tightly controlled to such a degree that planarians almost never develop neoplastic growths. In addition, the stem cells are located in a specific spatial compartment within the animal, although no known physical boundary keeps them in place. What mechanisms do planarians use to control the number, rate of division, and location of their stem cells? Here, we find that two EGF repeat-containing genes, megf6 and hemicentin, are required to keep stem cells within their compartment. Although these two genes are expressed in different cell populations, we find that both are required to maintain the epithelial basal lamina. In the absence of either gene, stem cells can escape their compartment and migrate towards the skin of the animal, where they divide at an accelerated rate and cause lesions in the muscle. These results show that the extracellular matrix plays a role in limiting the boundaries of the stem cell compartment.
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48
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Fields C, Levin M. Does regeneration recapitulate phylogeny? Planaria as a model of body-axis specification in ancestral eumetazoa. Commun Integr Biol 2020; 13:27-38. [PMID: 32128026 PMCID: PMC7039665 DOI: 10.1080/19420889.2020.1729601] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/07/2020] [Accepted: 02/09/2020] [Indexed: 12/31/2022] Open
Abstract
Metazoan body plans combine well-defined primary, secondary, and in many bilaterians, tertiary body axes with structural asymmetries at multiple scales. Despite decades of study, how axis-defining symmetries and system-defining asymmetries co-emerge during both evolution and development remain open questions. Regeneration studies in asexual planaria have demonstrated an array of viable forms with symmetrized and, in some cases, duplicated body axes. We suggest that such forms may point toward an ancestral eumetazoan form with characteristics of both cnidarians and placazoa.
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Affiliation(s)
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA, USA
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49
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The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. Sci Rep 2020; 10:1522. [PMID: 32001787 PMCID: PMC6992634 DOI: 10.1038/s41598-020-58470-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/15/2020] [Indexed: 12/11/2022] Open
Abstract
The holothurian Eupentacta fraudatrix is a unique organism for studying regeneration mechanisms. Moreover, E. fraudatrix can quickly restore parts of its body and entire organ systems, yet at the moment, there is no data on the participation of stem cells in the process. To the contrary, it has been repeatedly confirmed that this process is only due to the transformation of terminally differentiated cells. In this study, we examine changes in gene expression during gut regeneration of the holothurian E. fraudatrix. Transcriptomes of intestinal anlage of the three stages of regeneration, as well as the normal gut, were sequenced with an Illumina sequencer (San Diego, CA, USA). We identified 14,617 sea urchin protein homologs, of which 308 were transcription factors. After analysing the dynamics of gene expression during regeneration and the map of biological processes in which they participate, we identified 11 factors: Ef-EGR1, Ef-ELF, Ef-GATA3, Ef-ID2, Ef-KLF1/2/4, Ef-MSC, Ef-PCGF2, Ef-PRDM9, Ef-SNAI2, Ef-TBX20, and Ef-TCF24. With the exception of TCF24, they are all involved in the regeneration, development, epithelial-mesenchymal transition, and immune response in other animals. We suggest that these transcription factors may also be involved in the transdifferentiation of coelomic epithelial cells into enterocytes in holothurians.
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50
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Ivankovic M, Haneckova R, Thommen A, Grohme MA, Vila-Farré M, Werner S, Rink JC. Model systems for regeneration: planarians. Development 2019; 146:146/17/dev167684. [PMID: 31511248 DOI: 10.1242/dev.167684] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Planarians are a group of flatworms. Some planarian species have remarkable regenerative abilities, which involve abundant pluripotent adult stem cells. This makes these worms a powerful model system for understanding the molecular and evolutionary underpinnings of regeneration. By providing a succinct overview of planarian taxonomy, anatomy, available tools and the molecular orchestration of regeneration, this Primer aims to showcase both the unique assets and the questions that can be addressed with this model system.
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Affiliation(s)
- Mario Ivankovic
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Radmila Haneckova
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Albert Thommen
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Markus A Grohme
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Miquel Vila-Farré
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Steffen Werner
- FOM Institute AMOLF, Department of Systems Biology, Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Jochen C Rink
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany .,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
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