1
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Sugiura N, Agata K. FGF-stimulated tendon cells embrace a chondrogenic fate with BMP7 in newt tissue culture. Dev Growth Differ 2024; 66:182-193. [PMID: 38342985 DOI: 10.1111/dgd.12913] [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: 11/30/2023] [Revised: 01/15/2024] [Accepted: 01/17/2024] [Indexed: 02/13/2024]
Abstract
Newts can regenerate functional elbow joints after amputation at the joint level. Previous studies have suggested the potential contribution of cells from residual tendon tissues to joint cartilage regeneration. A serum-free tissue culture system for tendons was established to explore cell dynamics during joint regeneration. Culturing isolated tendons in this system, stimulated by regeneration-related factors, such as fibroblast growth factor (FGF) and platelet-derived growth factor, led to robust cell migration and proliferation. Moreover, cells proliferating in an FGF-rich environment differentiated into Sox9-positive chondrocytes upon BMP7 introduction. These findings suggest that FGF-stimulated cells from tendons may aid in joint cartilage regeneration during functional elbow joint regeneration in newts.
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Affiliation(s)
- Nao Sugiura
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- Laboratory for Regenerative Biology, National Institute for Basic Biology (NIBB), Okazaki, Japan
| | - Kiyokazu Agata
- Department of Basic Biology, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
- Laboratory for Regenerative Biology, National Institute for Basic Biology (NIBB), Okazaki, Japan
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2
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Kondoh H. Organ Regeneration Without Relying on Regeneration-Dedicated Stem Cells. Results Probl Cell Differ 2024; 72:105-118. [PMID: 38509254 DOI: 10.1007/978-3-031-39027-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
The classic conception of tissue regeneration assumed the existence of tissue-proper regeneration stem cells that are set aside during normal tissue development and reserved as stem cells for regeneration. However, modern studies using cell tracing and other approaches have ruled out the presence of regeneration-proper stem cells in most cases in vertebrate tissue regeneration. The only experimentally validated regeneration-dedicated reserve cells are the satellite cells in skeletal muscle (e.g., Michele 2022) (see Sect. 5.2.3 ). Here, we will first discuss examples of large-scale tissue regeneration, liver regeneration in mammals, and lens and limb regeneration in newts. Then, attempts to widen the tissue regeneration capacity in mammals with exogenous transcription factor genes will be reviewed.
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Affiliation(s)
- Hisato Kondoh
- Osaka University, Suita, Osaka, Japan
- Biohistory Research Hall, Takatsuki, Osaka, Japan
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3
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Aitken KJ, Yadav P, Sidler M, Thanabalasingam T, Ahmed T, Aggarwal P, Yip ST, Jeffrey N, Jiang JX, Siebenaller A, Sotiropoulos C, Huang R, Le DMQ, Delgado-Olguin P, Bagli D. Spontaneous urinary bladder regeneration after subtotal cystectomy increases YAP/WWTR1 signaling and downstream BDNF expression: Implications for smooth muscle injury responses. PLoS One 2023; 18:e0287205. [PMID: 37494380 PMCID: PMC10370683 DOI: 10.1371/journal.pone.0287205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/01/2023] [Indexed: 07/28/2023] Open
Abstract
Rodents have the capacity for spontaneous bladder regeneration and bladder smooth muscle cell (BSMC) migration following a subtotal cystectomy (STC). YAP/WWTR1 and BDNF (Brain-derived neurotrophic factor) play crucial roles in development and regeneration. During partial bladder outlet obstruction (PBO), excessive YAP/WWTR1 signaling and BDNF expression increases BSMC hypertrophy and dysfunction. YAP/WWTR1 and expression of BDNF and CYR61 were examined in models of regeneration and wound repair. Live cell microscopy was utilized in an ex vivo model of STC to visualize cell movement and division. In Sprague-Dawley female rats, STC was performed by resection of the bladder dome sparing the trigone, followed by closure of the bladder. Smooth muscle migration and downstream effects on signaling and expression were also examined after scratch wound of BSMC with inhibitors of YAP and BDNF signaling. Sham, PBO and incision (cystotomy) were comparators for the STC model. Scratch wound in vitro increased SMC migration and expression of BDNF, CTGF and CYR61 in a YAP/WWTR1-dependent manner. Inhibition of YAP/WWTR1 and BDNF signaling reduced scratch-induced migration. BDNF and CYR61 expression was elevated during STC and PBO. STC induces discrete genes associated with endogenous de novo cell regeneration downstream of YAP/WWTR1 activation.
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Affiliation(s)
- Karen J Aitken
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Priyank Yadav
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Urology and Renal Transplantation, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Martin Sidler
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
- Division Chief, Paediatric and Neonatal Surgeon, University Hospital Ulm, Ulm, Baden-Württemberg, Germany
| | - Thenuka Thanabalasingam
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Human Biology Programme, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Tabina Ahmed
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Human Biology Programme, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Prateek Aggarwal
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Human Biology Programme, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Shing Tai Yip
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nefateri Jeffrey
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jia-Xin Jiang
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Aliza Siebenaller
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Chris Sotiropoulos
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Human Biology Programme, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ryan Huang
- Human Biology Programme, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
| | - David Minh Quynh Le
- Human Biology Programme, Faculty of Arts and Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Paul Delgado-Olguin
- Translational Medicine Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Darius Bagli
- Developmental and Stem Cell Biology, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Urology Division, Department of Surgery, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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4
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Suzuki M, Iida M, Hayashi T, Suzuki KIT. CRISPR-Cas9-Based Functional Analysis in Amphibians: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. Methods Mol Biol 2023; 2637:341-357. [PMID: 36773159 DOI: 10.1007/978-1-0716-3016-7_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Amphibians have made many fundamental contributions to our knowledge, from basic biology to biomedical research on human diseases. Current genome editing tools based on the CRISPR-Cas system enable us to perform gene functional analysis in vivo, even in non-model organisms. We introduce here a highly efficient and easy protocol for gene knockout, which can be used in three different amphibians seamlessly: Xenopus laevis, Xenopus tropicalis, and Pleurodeles waltl. As it utilizes Cas9 ribonucleoprotein complex (RNP) for injection, this cloning-free method enables researchers to obtain founder embryos with a nearly complete knockout phenotype within a week. To evaluate somatic mutation rate and its correlation to the phenotype of a Cas9 RNP-injected embryo (crispant), we also present accurate and cost-effective genotyping methods using pooled amplicon-sequencing and a user-friendly web-based tool.
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Affiliation(s)
- Miyuki Suzuki
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Midori Iida
- Department of Bioscience and Bioinformatics, School of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Fukuoka, Japan
| | - Toshinori Hayashi
- Amphibian Research Center, Hiroshima University, Higashihiroshima, Hiroshima, Japan.,Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Ken-Ichi T Suzuki
- Emerging Model Organisms Facility, Trans-scale Biology Center, National Institute for Basic Biology, Okazaki, Aichi, Japan.
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5
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Seki-Omura R, Hayashi S, Oe S, Koike T, Nakano Y, Hirahara Y, Tanaka S, Kitada M. Establishment of neural stem cell culture from the central nervous system of the Iberian ribbed newt Pleurodeles waltl. Dev Growth Differ 2022; 64:494-500. [PMID: 36308507 DOI: 10.1111/dgd.12820] [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: 05/30/2022] [Revised: 09/06/2022] [Accepted: 09/09/2022] [Indexed: 12/31/2022]
Abstract
Urodele amphibians have exceptional regeneration ability in various organs. Among these, the Iberian ribbed newt (Pleurodeles waltl) has emerged as a useful model organism for investigating the mechanisms underlying regeneration. Neural stem cells (NSCs) are an important source of regeneration in the central nervous system (CNS) and their culture method in vitro has been well established. NSCs form spherical cell aggregates called neurospheres and their formation has been demonstrated in various vertebrates, including some urodele species, but not in P. waltl. In this study, we reported neurosphere formation in brain- and spinal cord-derived cells of post-metamorphic P. waltl. These neurospheres showed proliferative activity and similar expression of marker proteins. However, the surface morphology was found to vary according to their origin, implying that the characteristics of the neurospheres generated from the brain and spinal cord could be similar but not identical. Subsequent in vitro differentiation analysis demonstrated that spinal cord-derived neurospheres gave rise to neurons and glial cells. We also found that cells in neurospheres from P. waltl differentiated to oligodendrocytes, whereas those from axolotls were reported not to differentiate to this cell type under standard culture conditions. Based on our findings, implantation of genetically modified neurospheres together with associated technical advantages in P. waltl could reveal pivotal gene(s) and/or signaling pathway(s) essential for the complete spinal cord regeneration ability in the future.
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Affiliation(s)
- Ryohei Seki-Omura
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Shinichi Hayashi
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Souichi Oe
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Taro Koike
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Yousuke Nakano
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Yukie Hirahara
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Susumu Tanaka
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
| | - Masaaki Kitada
- Department of Anatomy, Faculty of Medicine, Kansai Medical University, Hirakata, Japan
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6
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Shimizu Y, Kiyooka M, Ohshima T. Transcriptome Analyses Reveal IL6/Stat3 Signaling Involvement in Radial Glia Proliferation After Stab Wound Injury in the Adult Zebrafish Optic Tectum. Front Cell Dev Biol 2021; 9:668408. [PMID: 33996824 PMCID: PMC8119998 DOI: 10.3389/fcell.2021.668408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/30/2021] [Indexed: 01/09/2023] Open
Abstract
Adult zebrafish have many neurogenic niches and a high capacity for central nervous system regeneration compared to mammals, including humans and rodents. The majority of radial glia (RG) in the zebrafish optic tectum are quiescent under physiological conditions; however, stab wound injury induces their proliferation and differentiation into newborn neurons. Although previous studies have functionally analyzed the molecular mechanisms of RG proliferation and differentiation and have performed single-cell transcriptomic analyses around the peak of RG proliferation, the cellular response and changes in global gene expression during the early stages of tectum regeneration remain poorly understood. In this study, we performed histological analyses which revealed an increase in isolectin B4+ macrophages prior to the induction of RG proliferation. Moreover, transcriptome and pathway analyses based on differentially expressed genes identified various enriched pathways, including apoptosis, the innate immune system, cell proliferation, cytokine signaling, p53 signaling, and IL6/Jak-Stat signaling. In particular, we found that Stat3 inhibition suppressed RG proliferation after stab wound injury and that IL6 administration into cerebroventricular fluid activates RG proliferation without causing injury. Together, the findings of these transcriptomic and functional analyses reveal that IL6/Stat3 signaling is an initial trigger of RG activation during optic tectum regeneration.
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Affiliation(s)
- Yuki Shimizu
- Functional Biomolecular Research Group, Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Osaka, Japan.,DBT-AIST International Laboratory for Advanced Biomedicine, National Institute of Advanced Industrial Science and Technology, Osaka, Japan
| | - Mariko Kiyooka
- Department of Life Science and Medical Bio-Science, Waseda University, Tokyo, Japan
| | - Toshio Ohshima
- Department of Life Science and Medical Bio-Science, Waseda University, Tokyo, Japan.,Graduate School of Advanced Science and Engineering, Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
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7
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Arenas Gómez CM, Echeverri K. Salamanders: The molecular basis of tissue regeneration and its relevance to human disease. Curr Top Dev Biol 2021; 145:235-275. [PMID: 34074531 PMCID: PMC8186737 DOI: 10.1016/bs.ctdb.2020.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Salamanders are recognized for their ability to regenerate a broad range of tissues. They have also have been used for hundreds of years for classical developmental biology studies because of their large accessible embryos. The range of tissues these animals can regenerate is fascinating, from full limbs to parts of the brain or heart, a potential that is missing in humans. Many promising research efforts are working to decipher the molecular blueprints shared across the organisms that naturally have the capacity to regenerate different tissues and organs. Salamanders are an excellent example of a vertebrate that can functionally regenerate a wide range of tissue types. In this review, we outline some of the significant insights that have been made that are aiding in understanding the cellular and molecular mechanisms of tissue regeneration in salamanders and discuss why salamanders are a worthy model in which to study regenerative biology and how this may benefit research fields like regenerative medicine to develop therapies for humans in the future.
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Affiliation(s)
- Claudia Marcela Arenas Gómez
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, University of Chicago, Woods Hole, MA, United States
| | - Karen Echeverri
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, University of Chicago, Woods Hole, MA, United States.
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8
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Insights regarding skin regeneration in non-amniote vertebrates: Skin regeneration without scar formation and potential step-up to a higher level of regeneration. Semin Cell Dev Biol 2019; 100:109-121. [PMID: 31831357 DOI: 10.1016/j.semcdb.2019.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/17/2022]
Abstract
Skin wounds are among the most common injuries in animals and humans. Vertebrate skin is composed of an epidermis and dermis. After a deep skin injury in mammals, the wound heals, but the dermis cannot regenerate. Instead, collagenous scar tissue forms to fill the gap in the dermis, but the scar does not function like the dermis and often causes disfiguration. In contrast, in non-amniote vertebrates, including fish and amphibians, the dermis and skin derivatives are regenerated after a deep skin injury, without a recognizable scar remaining. Furthermore, skin regeneration can be compared with a higher level of organ regeneration represented by limb regeneration in these non-amniotes, as fish, anuran amphibians (frogs and toads), and urodele amphibians (newts and salamanders) have a high capacity for organ regeneration. Comparative studies of skin regeneration together with limb or other organ regeneration could reveal how skin regeneration is stepped up to a higher level of regeneration. The long history of regenerative biology research has revealed that fish, anurans, and urodeles have their own strengths as models for regeneration studies, and excellent model organisms of these non-amniote vertebrates that are suitable for molecular genetic studies are now available. Here, we summarize the advantages of fish, anurans, and urodeles for skin regeneration studies with special reference to three model organisms: zebrafish (Danio rerio), African clawed frog (Xenopus laevis), and Iberian ribbed newt (Pleurodele waltl). All three of these animals quickly cover skin wounds with the epidermis (wound epidermis formation) and regenerate the dermis and skin derivatives as adults. The availability of whole genome sequences, transgenesis, and genome editing with these models enables cell lineage tracing and the use of human disease models in skin regeneration phenomena, for example. Zebrafish present particular advantages in genetics research (e.g., human disease model and Cre-loxP system). Amphibians (X. laevis and P. waltl) have a skin structure (keratinized epidermis) common with humans, and skin regeneration in these animals can be stepped up to limb regeneration, a higher level of regeneration.
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9
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Abstract
Brain tissue lost after a stroke is not regenerated, although a repair response associated with neurogenesis does occur. A failure to regenerate functional brain tissue is not caused by the lack of available neural cells, but rather the absence of structural support to permit a repopulation of the lesion cavity. Inductive bioscaffolds can provide this support and promote the invasion of host cells into the tissue void. The putative mechanisms of bioscaffold degradation and its pivotal role to permit invasion of neural cells are reviewed and discussed in comparison to peripheral wound healing. Key differences between regenerating and non-regenerating tissues are contrasted in an evolutionary context, with a special focus on the neurogenic response as a conditio sine qua non for brain regeneration. The pivotal role of the immune system in biodegradation and the formation of a neovasculature are contextualized with regeneration of peripheral soft tissues. The application of rehabilitation to integrate newly forming brain tissue is suggested as necessary to develop functional tissue that can alleviate behavioral impairments. Pertinent aspects of brain tissue development are considered to provide guidance to produce a metabolically and functionally integrated de novo tissue. Although little is currently known about mechanisms involved in brain tissue regeneration, this review outlines the various components and their interplay to provide a framework for ongoing and future studies. It is envisaged that a better understanding of the mechanisms involved in brain tissue regeneration will improve the design of biomaterials and the methods used for implantation, as well as rehabilitation strategies that support the restoration of behavioral functions.
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Affiliation(s)
- Michel Modo
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States,Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, United States,Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, United States,Department of Radiology, University of Pittsburgh, Pittsburgh, PA, United States,*Correspondence: Michel Modo,
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10
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Joven A, Elewa A, Simon A. Model systems for regeneration: salamanders. Development 2019; 146:146/14/dev167700. [PMID: 31332037 DOI: 10.1242/dev.167700] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 05/28/2019] [Indexed: 02/03/2023]
Abstract
Salamanders have been hailed as champions of regeneration, exhibiting a remarkable ability to regrow tissues, organs and even whole body parts, e.g. their limbs. As such, salamanders have provided key insights into the mechanisms by which cells, tissues and organs sense and regenerate missing or damaged parts. In this Primer, we cover the evolutionary context in which salamanders emerged. We outline the varieties of mechanisms deployed during salamander regeneration, and discuss how these mechanisms are currently being explored and how they have advanced our understanding of animal regeneration. We also present arguments about why it is important to study closely related species in regeneration research.
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Affiliation(s)
- Alberto Joven
- Karolinska Institute, Department of Cell and Molecular Biology, Biomedicum, Solnavägen 9, 17163 Stockolm, Sweden
| | - Ahmed Elewa
- Karolinska Institute, Department of Cell and Molecular Biology, Biomedicum, Solnavägen 9, 17163 Stockolm, Sweden
| | - András Simon
- Karolinska Institute, Department of Cell and Molecular Biology, Biomedicum, Solnavägen 9, 17163 Stockolm, Sweden
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11
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Matsunami M, Suzuki M, Haramoto Y, Fukui A, Inoue T, Yamaguchi K, Uchiyama I, Mori K, Tashiro K, Ito Y, Takeuchi T, Suzuki KIT, Agata K, Shigenobu S, Hayashi T. A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology. DNA Res 2019; 26:217-229. [PMID: 31006799 PMCID: PMC6589553 DOI: 10.1093/dnares/dsz003] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/28/2019] [Indexed: 12/14/2022] Open
Abstract
Urodele newts have unique biological properties, notably including prominent regeneration ability. The Iberian ribbed newt, Pleurodeles waltl, is a promising model amphibian distinguished by ease of breeding and efficient transgenic and genome editing methods. However, limited genetic information is available for P. waltl. We conducted an intensive transcriptome analysis of P. waltl using RNA-sequencing to build and annotate gene models. We generated 1.2 billion Illumina reads from a wide variety of samples across 12 different tissues/organs, unfertilized egg, and embryos at eight different developmental stages. These reads were assembled into 1,395,387 contigs, from which 202,788 non-redundant ORF models were constructed. The set is expected to cover a large fraction of P. waltl protein-coding genes, as confirmed by BUSCO analysis, where 98% of universal single-copy orthologs were identified. Ortholog analyses revealed the gene repertoire evolution of urodele amphibians. Using the gene set as a reference, gene network analysis identified regeneration-, developmental-stage-, and tissue-specific co-expressed gene modules. Our transcriptome resource is expected to enhance future research employing this emerging model animal for regeneration research as well as for investigations in other areas including developmental biology, stem cell biology, and cancer research. These data are available via our portal website, iNewt (http://www.nibb.ac.jp/imori/main/).
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Affiliation(s)
- Masatoshi Matsunami
- Department of Advanced Genomics and Laboratory Medicine, Graduate School of Medicine, University of the Ryukyus, Nishihara-Cho, Okinawa, Japan
| | - Miyuki Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
| | - Yoshikazu Haramoto
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Akimasa Fukui
- Department of Biological Sciences, Faculty of Science and Engineering, Chuo University, Bunkyo-Ku, Tokyo, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Ikuo Uchiyama
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kazuki Mori
- Computational Bio Big-Data Open Innovation Lab. (CBBD-OIL), Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Shinjuku-Ku, Tokyo, Japan
| | - Kosuke Tashiro
- Laboratory of Molecular Gene Technology, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Fukuoka, Japan
| | - Yuzuru Ito
- Biotechnology Research Institute for Drug Discovery, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Takeuchi
- Department of Biomedical Sciences, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
| | - Ken-ichi T Suzuki
- Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Higashihiroshima, Hiroshima, Japan
- Center for the Development of New Model Organisms, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Gakushuin University, Toshima-Ku, Tokyo, Japan
| | - Shuji Shigenobu
- NIBB Core Research Facilities, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Toshinori Hayashi
- Department of Biomedical Sciences, School of Life Science, Faculty of Medicine, Tottori University, Yonago, Tottori, Japan
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