1
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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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2
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Müller WEG, Neufurth M, Wang S, Schröder HC, Wang X. The Physiological Inorganic Polymers Biosilica and Polyphosphate as Key Drivers for Biomedical Materials in Regenerative Nanomedicine. Int J Nanomedicine 2024; 19:1303-1337. [PMID: 38348175 PMCID: PMC10860874 DOI: 10.2147/ijn.s446405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 02/15/2024] Open
Abstract
There is a need for novel nanomaterials with properties not yet exploited in regenerative nanomedicine. Based on lessons learned from the oldest metazoan phylum, sponges, it has been recognized that two previously ignored or insufficiently recognized principles play an essential role in tissue regeneration, including biomineral formation/repair and wound healing. Firstly, the dependence on enzymes as a driving force and secondly, the availability of metabolic energy. The discovery of enzymatic synthesis and regenerative activity of amorphous biosilica that builds the mineral skeleton of siliceous sponges formed the basis for the development of successful strategies for the treatment of osteochondral impairments in humans. In addition, the elucidation of the functional significance of a second regeneratively active inorganic material, namely inorganic polyphosphate (polyP) and its amorphous nanoparticles, present from sponges to humans, has pushed forward the development of innovative materials for both soft (skin, cartilage) and hard tissue (bone) repair. This energy-rich molecule exhibits a property not shown by any other biopolymer: the delivery of metabolic energy, even extracellularly, necessary for the ATP-dependent tissue regeneration. This review summarizes the latest developments in nanobiomaterials based on these two evolutionarily old, regeneratively active materials, amorphous silica and amorphous polyP, highlighting their specific, partly unique properties and mode of action, and discussing their possible applications in human therapy. The results of initial proof-of-concept studies on patients demonstrating complete healing of chronic wounds are outlined.
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Affiliation(s)
- Werner E G Müller
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Meik Neufurth
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Shunfeng Wang
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Heinz C Schröder
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Xiaohong Wang
- ERC Advanced Investigator Grant Research Group at the Institute for Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, Mainz, Germany
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3
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Girich AS. WntA and Wnt4 during the regeneration of internal organs in the holothurian Eupentacta fraudatrix. Genesis 2024; 62:e23562. [PMID: 37846177 DOI: 10.1002/dvg.23562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023]
Abstract
BACKGROUND Over the past few years, it has been established that wnt genes are involved in the regenerative processes of holothurians. The wnt4 gene was identified as one of the most active genes in Eupentacta fraudatrix regeneration using differential gene expression analysis and qPCR of individual genes. Also, the wntA gene was found in holothurians, which is present only in invertebrates and can perform unique functions. RESULTS In this regard, both these genes and proteins were studied in this work. During regeneration, the Wnt4 protein is found in the cells of the coelomic and ambulacral epithelium, retractor muscles, and radial nerves. Single cells with this protein are also found in the connective tissue of the developing aquapharyngeal bulb and in the hypoderm of the body wall. Cells with WntA are found exclusively in the hypoderm of the body wall. CONCLUSION We assume that both genes are involved in regeneration, but Wnt4 coordinates the formation of the epithelial tissue structure, while WntA maintains the state of the intercellular substance of the body wall.
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Affiliation(s)
- A S Girich
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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4
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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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5
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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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6
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Petersen CP. Wnt signaling in whole-body regeneration. Curr Top Dev Biol 2023; 153:347-380. [PMID: 36967200 DOI: 10.1016/bs.ctdb.2023.01.007] [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] [Indexed: 03/11/2023]
Abstract
Regeneration abilities are widespread among animals and select species can restore any body parts removed by wounds that sever the major body axes. This capability of whole-body regeneration as exemplified in flatworm planarians, Acoels, and Cnidarians involves initial responses to injury, the assessment of wound site polarization, determination of missing tissue and programming of blastema fate, and patterned outgrowth to restore axis content and proportionality. Wnt signaling drives many shared and conserved aspects of the biology of whole-body regeneration in the planarian species Schmidtea mediterranea and Dugesia japonica, in the Acoel Hofstenia miamia, and in Cnidarians Hydra and Nematostella. These overlapping mechanisms suggest whole-body regeneration might be an ancestral property across diverse animal taxa.
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Affiliation(s)
- Christian P Petersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States; Robert Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, United States.
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7
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Foley S, Vlasova A, Marcet-Houben M, Gabaldón T, Hinman VF. Evolutionary analyses of genes in Echinodermata offer insights towards the origin of metazoan phyla. Genomics 2022; 114:110431. [PMID: 35835427 PMCID: PMC9552553 DOI: 10.1016/j.ygeno.2022.110431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 05/10/2022] [Accepted: 07/06/2022] [Indexed: 11/24/2022]
Abstract
Despite recent studies discussing the evolutionary impacts of gene duplications and losses among metazoans, the genomic basis for the evolution of phyla remains enigmatic. Here, we employ phylogenomic approaches to search for orthologous genes without known functions among echinoderms, and subsequently use them to guide the identification of their homologs across other metazoans. Our final set of 14 genes was obtained via a suite of homology prediction tools, gene expression data, gene ontology, and generating the Strongylocentrotus purpuratus phylome. The gene set was subjected to selection pressure analyses, which indicated that they are highly conserved and under negative selection. Their presence across broad taxonomic depths suggests that genes required to form a phylum are ancestral to that phylum. Therefore, rather than de novo gene genesis, we posit that evolutionary forces such as selection on existing genomic elements over large timescales may drive divergence and contribute to the emergence of phyla.
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Affiliation(s)
- Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA; Echinobase #6-46, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA.
| | - Anna Vlasova
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain; Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain; Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Ave, Pittsburgh, PA 15213, USA; Echinobase #6-46, Mellon Institute, 4400 Fifth Ave, Pittsburgh, PA 15213, USA
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8
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Meyer A, Hinman V. The arm of the starfish: The far-reaching applications of Patiria miniata as a model system in evolutionary, developmental, and regenerative biology. Curr Top Dev Biol 2022; 147:523-543. [PMID: 35337461 DOI: 10.1016/bs.ctdb.2022.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Many species of echinoderms have long been considered model research organisms in biology. Historically, much of this research has focused on the embryology of sea urchins and the use of their extensive gene regulatory networks as a tool to understand how the genome controls cell state specification and patterning. The establishment of Patiria miniata, the bat sea star, as a research organism has allowed us to expand on the concepts explored with sea urchins, viewing these genetic networks through a comparative lens, gaining great insight into the evolutionary mechanisms that shape developmental diversity. Extensive molecular tools have been developed in P. miniata, designed to explore gene expression dynamics and build gene regulatory networks. Echinoderms also have a robust set of bioinformatic and computational resources, centered around echinobase.org, an extensive database containing multiomic, developmental, and experimental resources for researchers. In addition to comparative evolutionary development, P. miniata is a promising system in its own right for studying whole body regeneration, metamorphosis and body plan development, as well as marine disease.
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Affiliation(s)
- Anne Meyer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, United States.
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9
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Humphreys T, Weiser K, Arimoto A, Sasaki A, Uenishi G, Fujimoto B, Kawashima T, Taparra K, Molnar J, Satoh N, Marikawa Y, Tagawa K. Ancestral Stem Cell Reprogramming Genes Active in Hemichordate Regeneration. Front Ecol Evol 2022; 10. [PMID: 37008716 PMCID: PMC10065570 DOI: 10.3389/fevo.2022.769433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Hemichordate enteropneust worms regenerate extensively in a manner that resembles the regeneration for which planaria and hydra are well known. Although hemichordates are often classified as an extant phylogenetic group that may hold ancestral deuterostome body plans at the base of the deuterostome evolutionary line leading to chordates, mammals, and humans, extensive regeneration is not known in any of these more advanced groups. Here we investigated whether hemichordates deploy functional homologs of canonical Yamanaka stem cell reprogramming factors, Oct4, Sox2, Nanog, and Klf4, as they regenerate. These reprogramming factors are not expressed during regeneration of limbs, fins, eyes or other structures that represent the best examples of regeneration in chordates. We first examined Ptychodera flava EST libraries and identified Pf-Pou3, Pf-SoxB1, Pf-Msxlx, and Pf-Klf1/2/4 as most closely related to the Yamanaka factors, respectively. In situ hybridization analyses revealed that all these homologs are expressed in a distinct manner during head regeneration. Furthermore, Pf-Pou3 partially rescued the loss of endogenous Oct4 in mouse embryonic stem cells in maintaining the pluripotency gene expression program. Based on these results, we propose that hemichordates may have co-opted these reprogramming factors for their extensive regeneration or that chordates may have lost the ability to mobilize these factors in response to damage. The robustness of these pluripotency gene circuits in the inner cell mass and in formation of induced pluripotent stem cells from mammalian somatic cells shows that these programs are intact in humans and other mammals and that these circuits may respond to as yet unknown gene regulatory signals, mobilizing full regeneration in hemichordates.
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Affiliation(s)
- Tom Humphreys
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Keith Weiser
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Asuka Arimoto
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Akane Sasaki
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Gene Uenishi
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Brent Fujimoto
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Takeshi Kawashima
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kekoa Taparra
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Janos Molnar
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yusuke Marikawa
- Institute for Biogenesis Research, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Kuni Tagawa
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Correspondence: Kuni Tagawa
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10
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Wu YC, Franzenburg S, Ribes M, Pita L. Wounding response in Porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer. Sci Rep 2022; 12:1307. [PMID: 35079031 PMCID: PMC8789774 DOI: 10.1038/s41598-022-05230-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/06/2022] [Indexed: 11/24/2022] Open
Abstract
Upon injury, the homeostatic balance that ensures tissue function is disrupted. Wound-induced signaling triggers the recovery of tissue integrity and offers a context to understand the molecular mechanisms for restoring tissue homeostasis upon disturbances. Marine sessile animals are particularly vulnerable to chronic wounds caused by grazers that can compromise prey's health. Yet, in comparison to other stressors like warming or acidification, we know little on how marine animals respond to grazing. Marine sponges (Phylum Porifera) are among the earliest-diverging animals and play key roles in the ecosystem; but they remain largely understudied. Here, we investigated the transcriptomic responses to injury caused by a specialist spongivorous opisthobranch (i.e., grazing treatment) or by clipping with a scalpel (i.e., mechanical damage treatment), in comparison to control sponges. We collected samples 3 h, 1 d, and 6 d post-treatment for differential gene expression analysis on RNA-seq data. Both grazing and mechanical damage activated a similar transcriptomic response, including a clotting-like cascade (e.g., with genes annotated as transglutaminases, metalloproteases, and integrins), calcium signaling, and Wnt and mitogen-activated protein kinase signaling pathways. Wound-induced gene expression signature in sponges resembles the initial steps of whole-body regeneration in other animals. Also, the set of genes responding to wounding in sponges included putative orthologs of cancer-related human genes. Further insights can be gained from taking sponge wound healing as an experimental system to understand how ancient genes and regulatory networks determine healthy animal tissues.
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Affiliation(s)
- Yu-Chen Wu
- Research Unit Marine Microbiology, Department Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Christian-Albrechts University of Kiel, Kiel, Germany
| | - Soeren Franzenburg
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts University of Kiel, Kiel, Germany
| | - Marta Ribes
- Department Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Lucía Pita
- Research Unit Marine Microbiology, Department Marine Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany.
- Department Marine Biology and Oceanography, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain.
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11
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Zheng M, Zueva O, Hinman V. Regeneration of the larval sea star nervous system by wounding induced respecification to the sox2 lineage. eLife 2022; 11:72983. [PMID: 35029145 PMCID: PMC8809897 DOI: 10.7554/elife.72983] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022] Open
Abstract
The ability to restore lost body parts following traumatic injury is a fascinating area of biology that challenges current understanding of the ontogeny of differentiation. The origin of new cells needed to regenerate lost tissue, and whether they are pluripotent or have de- or trans-differentiated, remains one of the most important open questions . Additionally, it is not known whether developmental gene regulatory networks are reused or whether regeneration specific networks are deployed. Echinoderms, including sea stars, have extensive ability for regeneration, however, the technologies for obtaining transgenic echinoderms are limited and tracking cells involved in regeneration, and thus identifying the cellular sources and potencies has proven challenging. In this study, we develop new transgenic tools to follow the fate of populations of cells in the regenerating larva of the sea star Patiria miniata. We show that the larval serotonergic nervous system can regenerate following decapitation. Using a BAC-transgenesis approach we show that expression of the pan ectodermal marker, sox2, is induced in previously sox2 minus cells , even when cell division is inhibited. sox2+ cells give rise to new sox4+ neural precursors that then proceed along an embryonic neurogenesis pathway to reform the anterior nervous systems. sox2+ cells contribute to only neural and ectoderm lineages, indicating that these progenitors maintain their normal, embryonic lineage restriction. This indicates that sea star larval regeneration uses a combination of existing lineage restricted stem cells, as well as respecification of cells into neural lineages, and at least partial reuse of developmental GRNs to regenerate their nervous system.
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Affiliation(s)
- Minyan Zheng
- Department of Genetics, Harvard Medical School, Boston, United States
| | - Olga Zueva
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, United States
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12
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Dieter AC, Vandepas LE, Browne WE. Isolation and Maintenance of In Vitro Cell Cultures from the Ctenophore Mnemiopsis leidyi. Methods Mol Biol 2022; 2450:347-358. [PMID: 35359317 PMCID: PMC9761543 DOI: 10.1007/978-1-0716-2172-1_18] [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] [Indexed: 06/14/2023]
Abstract
The ability to isolate, monitor, and examine specific cells of interest enables targeted experimental manipulations that would otherwise be difficult to perform and interpret in the context of the whole organism. In vitro primary cell cultures derived from ctenophores thus serve as an important tool for understanding complex cellular and molecular interactions that take place both within and between various ctenophore cell types. Here we describe methods for reliably generating and maintaining primary cell cultures derived from the lobate ctenophore Mnemiopsis leidyi that can be used for a wide variety of experimental applications.
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Affiliation(s)
| | - Lauren E Vandepas
- Benaroya Research Institute, Seattle, WA, USA
- National Oceanographic and Atmospheric Administration, Manchester, WA, USA
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13
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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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14
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Medina-Feliciano JG, García-Arrarás JE. Regeneration in Echinoderms: Molecular Advancements. Front Cell Dev Biol 2021; 9:768641. [PMID: 34977019 PMCID: PMC8718600 DOI: 10.3389/fcell.2021.768641] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Which genes and gene signaling pathways mediate regenerative processes? In recent years, multiple studies, using a variety of animal models, have aimed to answer this question. Some answers have been obtained from transcriptomic and genomic studies where possible gene and gene pathway candidates thought to be involved in tissue and organ regeneration have been identified. Several of these studies have been done in echinoderms, an animal group that forms part of the deuterostomes along with vertebrates. Echinoderms, with their outstanding regenerative abilities, can provide important insights into the molecular basis of regeneration. Here we review the available data to determine the genes and signaling pathways that have been proposed to be involved in regenerative processes. Our analyses provide a curated list of genes and gene signaling pathways and match them with the different cellular processes of the regenerative response. In this way, the molecular basis of echinoderm regenerative potential is revealed, and is available for comparisons with other animal taxa.
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15
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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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16
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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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17
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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: 4] [Impact Index Per Article: 1.3] [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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18
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The Tentacular Spectacular: Evolution of Regeneration in Sea Anemones. Genes (Basel) 2021; 12:genes12071072. [PMID: 34356088 PMCID: PMC8306839 DOI: 10.3390/genes12071072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 06/03/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Sea anemones vary immensely in life history strategies, environmental niches and their ability to regenerate. While the sea anemone Nematostella vectensis is the starlet of many key regeneration studies, recent work is emerging on the diverse regeneration strategies employed by other sea anemones. This manuscript will explore current molecular mechanisms of regeneration employed by non-model sea anemones Exaiptasia diaphana (an emerging model species for coral symbiosis studies) and Calliactis polypus (a less well-studied species) and examine how these species compare to the model sea anemone N. vectensis. We summarize the field of regeneration within sea anemones, within the greater context of phylum Cnidaria and in other invertebrate models of regeneration. We also address the current knowledge on two key systems that may be implemented in regeneration: the innate immune system and developmental pathways, including future aspects of work and current limitations.
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19
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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:genes12071063. [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
- Correspondence: ; Tel.: +1-412-268-9348
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20
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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: 2] [Impact Index Per Article: 0.7] [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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21
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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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22
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Foley S, Ku C, Arshinoff B, Lotay V, Karimi K, Vize PD, Hinman V. Integration of 1:1 orthology maps and updated datasets into Echinobase. Database (Oxford) 2021; 2021:baab030. [PMID: 34010390 PMCID: PMC8132956 DOI: 10.1093/database/baab030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/23/2021] [Accepted: 04/30/2021] [Indexed: 12/24/2022]
Abstract
Echinobase (https://echinobase.org) is a central online platform that generates, manages and hosts genomic data relevant to echinoderm research. While the resource primarily serves the echinoderm research community, the recent release of an excellent quality genome for the frequently studied purple sea urchin (Strongylocentrotus purpuratus genome, v5.0) has provided an opportunity to adapt to the needs of a broader research community across other model systems. To this end, establishing pipelines to identify orthologous genes between echinoderms and other species has become a priority in many contexts including nomenclature, linking to data in other model organisms, and in internal functionality where data gathered in one hosted species can be associated with genes in other hosted echinoderms. This paper describes the orthology pipelines currently employed by Echinobase and how orthology data are processed to yield 1:1 ortholog mappings between a variety of echinoderms and other model taxa. We also describe functions of interest that have recently been included on the resource, including an updated developmental time course for S.purpuratus, and additional tracks for genome browsing. These data enhancements will increase the accessibility of the resource to non-echinoderm researchers and simultaneously expand the data quality and quantity available to core Echinobase users. Database URL: https://echinobase.org.
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Affiliation(s)
- Saoirse Foley
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
- Echinobase #6-46, Mellon Institute, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Carolyn Ku
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
- Echinobase #6-46, Mellon Institute, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
| | - Brad Arshinoff
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta TN2 1N4, Canada
| | - Veronica Hinman
- Department of Biological Sciences, Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA
- Echinobase #6-46, Mellon Institute, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
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23
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Kraus A, Buckley KM, Salinas I. Sensing the world and its dangers: An evolutionary perspective in neuroimmunology. eLife 2021; 10:66706. [PMID: 33900197 PMCID: PMC8075586 DOI: 10.7554/elife.66706] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Detecting danger is key to the survival and success of all species. Animal nervous and immune systems cooperate to optimize danger detection. Preceding studies have highlighted the benefits of bringing neurons into the defense game, including regulation of immune responses, wound healing, pathogen control, and survival. Here, we summarize the body of knowledge in neuroimmune communication and assert that neuronal participation in the immune response is deeply beneficial in each step of combating infection, from inception to resolution. Despite the documented tight association between the immune and nervous systems in mammals or invertebrate model organisms, interdependence of these two systems is largely unexplored across metazoans. This review brings a phylogenetic perspective of the nervous and immune systems in the context of danger detection and advocates for the use of non-model organisms to diversify the field of neuroimmunology. We identify key taxa that are ripe for investigation due to the emergence of key evolutionary innovations in their immune and nervous systems. This novel perspective will help define the primordial principles that govern neuroimmune communication across taxa.
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Affiliation(s)
- Aurora Kraus
- Department of Biology, University of New Mexico, Albuquerque, United States
| | | | - Irene Salinas
- Department of Biology, University of New Mexico, Albuquerque, United States
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24
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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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25
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Cazet JF, Cho A, Juliano CE. Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra. eLife 2021; 10:60562. [PMID: 33779545 PMCID: PMC8049744 DOI: 10.7554/elife.60562] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 03/28/2021] [Indexed: 12/13/2022] Open
Abstract
During whole-body regeneration, a bisection injury can trigger two different types of regeneration. To understand the transcriptional regulation underlying this adaptive response, we characterized transcript abundance and chromatin accessibility during oral and aboral regeneration in the cnidarian Hydra vulgaris. We found that the initial response to amputation at both wound sites is identical and includes widespread apoptosis and the activation of the oral-specifying Wnt signaling pathway. By 8 hr post amputation, Wnt signaling became restricted to oral regeneration. Wnt pathway genes were also upregulated in puncture wounds, and these wounds induced the formation of ectopic oral structures if pre-existing organizers were simultaneously amputated. Our work suggests that oral patterning is activated as part of a generic injury response in Hydra, and that alternative injury outcomes are dependent on signals from the surrounding tissue. Furthermore, Wnt signaling is likely part of a conserved wound response predating the split of cnidarians and bilaterians.
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Affiliation(s)
- Jack F Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Adrienne Cho
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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26
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Safian D, Wiegertjes GF, Pollux BJA. The Fish Family Poeciliidae as a Model to Study the Evolution and Diversification of Regenerative Capacity in Vertebrates. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.613157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The capacity of regenerating a new structure after losing an old one is a major challenge in the animal kingdom. Fish have emerged as an interesting model to study regeneration due to their high and diverse regenerative capacity. To date, most efforts have focused on revealing the mechanisms underlying fin regeneration, but information on why and how this capacity evolves remains incomplete. Here, we propose the livebearing fish family Poeciliidae as a promising new model system to study the evolution of fin regeneration. First, we review the current state of knowledge on the evolution of regeneration in the animal kingdom, with a special emphasis on fish fins. Second, we summarize recent advances in our understanding of the mechanisms behind fin regeneration in fish. Third, we discuss potential evolutionary pressures that may modulate the regenerative capacity of fish fins and propose three new theories for how natural and sexual selection can lead to the evolution of fin regeneration: (1) signaling-driven fin regeneration, (2) predation-driven fin regeneration, and (3) matrotrophy-suppressed fin regeneration. Finally, we argue that fish from the family Poeciliidae are an excellent model system to test these theories, because they comprise of a large variety of species in a well-defined phylogenetic framework that inhabit very different environments and display remarkable variation in reproductive traits, allowing for comparative studies of fin regeneration among closely related species, among populations within species or among individuals within populations. This new model system has the potential to shed new light on the underlying genetic and molecular mechanisms driving the evolution and diversification of regeneration in vertebrates.
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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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Piovani L, Czarkwiani A, Ferrario C, Sugni M, Oliveri P. Ultrastructural and molecular analysis of the origin and differentiation of cells mediating brittle star skeletal regeneration. BMC Biol 2021; 19:9. [PMID: 33461552 PMCID: PMC7814545 DOI: 10.1186/s12915-020-00937-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 12/02/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Regeneration is the ability to re-grow body parts or tissues after trauma, and it is widespread across metazoans. Cells involved in regeneration can arise from a pool of undifferentiated proliferative cells or be recruited from pre-existing differentiated tissues. Both mechanisms have been described in different phyla; however, the cellular and molecular mechanisms employed by different animals to restore lost tissues as well as the source of cells involved in regeneration remain largely unknown. Echinoderms are a clade of deuterostome invertebrates that show striking larval and adult regenerative abilities in all extant classes. Here, we use the brittle star Amphiura filiformis to investigate the origin and differentiation of cells involved in skeletal regeneration using a combination of microscopy techniques and molecular markers. RESULTS Our ultrastructural analyses at different regenerative stages identify a population of morphologically undifferentiated cells which appear in close contact with the proliferating epithelium of the regenerating aboral coelomic cavity. These cells express skeletogenic marker genes, such as the transcription factor alx1 and the differentiation genes c-lectin and msp130L, and display a gradient of morphological differentiation from the aboral coelomic cavity towards the epidermis. Cells closer to the epidermis, which are in contact with developing spicules, have the morphology of mature skeletal cells (sclerocytes), and express several skeletogenic transcription factors and differentiation genes. Moreover, as regeneration progresses, sclerocytes show a different combinatorial expression of genes in various skeletal elements. CONCLUSIONS We hypothesize that sclerocyte precursors originate from the epithelium of the proliferating aboral coelomic cavity. As these cells migrate towards the epidermis, they differentiate and start secreting spicules. Moreover, our study shows that molecular and cellular processes involved in skeletal regeneration resemble those used during skeletal development, hinting at a possible conservation of developmental programmes during adult regeneration. Finally, we highlight that many genes involved in echinoderm skeletogenesis also play a role in vertebrate skeleton formation, suggesting a possible common origin of the deuterostome endoskeleton pathway.
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Affiliation(s)
- Laura Piovani
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Center for Life Origins and Evolution, University College London, London, UK
| | - Anna Czarkwiani
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Present Address: DFG-Center for Regenerative Therapies Technische Universität Dresden (CRTD), Dresden, Germany
| | - Cinzia Ferrario
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria, 16, 20133, Milan, Italy
| | - Michela Sugni
- Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy.
- Center for Complexity and Biosystems, Department of Physics, University of Milan, Via Celoria, 16, 20133, Milan, Italy.
- GAIA 2050 Center, Department of Environmental Science and Policy, University of Milan, Via Celoria, 2, 20133, Milan, Italy.
| | - Paola Oliveri
- Department of Genetics, Evolution and Environment, University College London, London, UK.
- Center for Life Origins and Evolution, University College London, London, UK.
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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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Abstract
Regeneration is the process by which organisms replace lost or damaged tissue, and regenerative capacity can vary greatly among species, tissues and life stages. Tissue regeneration shares certain hallmarks of embryonic development, in that lineage-specific factors can be repurposed upon injury to initiate morphogenesis; however, many differences exist between regeneration and embryogenesis. Recent studies of regenerating tissues in laboratory model organisms - such as acoel worms, frogs, fish and mice - have revealed that chromatin structure, dedicated enhancers and transcriptional networks are regulated in a context-specific manner to control key gene expression programmes. A deeper mechanistic understanding of the gene regulatory networks of regeneration pathways might ultimately enable their targeted reactivation as a means to treat human injuries and degenerative diseases. In this Review, we consider the regeneration of body parts across a range of tissues and species to explore common themes and potentially exploitable elements.
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Affiliation(s)
- Joseph A Goldman
- Department of Biological Chemistry and Pharmacology, Ohio State University, Columbus, OH, USA.
| | - Kenneth D Poss
- Regeneration Next, Duke University, Durham, NC, USA.
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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Gehrke AR, Neverett E, Luo YJ, Brandt A, Ricci L, Hulett RE, Gompers A, Ruby JG, Rokhsar DS, Reddien PW, Srivastava M. Acoel genome reveals the regulatory landscape of whole-body regeneration. Science 2019; 363:363/6432/eaau6173. [PMID: 30872491 DOI: 10.1126/science.aau6173] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/08/2018] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Whole-body regeneration is accompanied by complex transcriptomic changes, yet the chromatin regulatory landscapes that mediate this dynamic response remain unexplored. To decipher the regulatory logic that orchestrates regeneration, we sequenced the genome of the acoel worm Hofstenia miamia, a highly regenerative member of the sister lineage of other bilaterians. Epigenomic profiling revealed thousands of regeneration-responsive chromatin regions and identified dynamically bound transcription factor motifs, with the early growth response (EGR) binding site as the most variably accessible during Hofstenia regeneration. Combining egr inhibition with chromatin profiling suggests that Egr functions as a pioneer factor to directly regulate early wound-induced genes. The genetic connections inferred by this approach allowed the construction of a gene regulatory network for whole-body regeneration, enabling genomics-based comparisons of regeneration across species.
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Affiliation(s)
- Andrew R Gehrke
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Emily Neverett
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yi-Jyun Luo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Alexander Brandt
- Department of Chemistry, University of California, Berkeley, CA 94703, USA
| | - Lorenzo Ricci
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ryan E Hulett
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Annika Gompers
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - J Graham Ruby
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA
| | - Daniel S Rokhsar
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94703, USA
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Howard Hughes Medical Institute, and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02138, USA
| | - Mansi Srivastava
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. .,Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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