1
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Tsissios G, Sallese A, Perez-Estrada JR, Tangeman JA, Chen W, Smucker B, Ratvasky SC, Grajales-Esquivel E, Martinez A, Visser KJ, Joven Araus A, Wang H, Simon A, Yun MH, Del Rio-Tsonis K. Macrophages modulate fibrosis during newt lens regeneration. Stem Cell Res Ther 2024; 15:141. [PMID: 38745238 PMCID: PMC11094960 DOI: 10.1186/s13287-024-03740-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Previous studies have suggested that macrophages are present during lens regeneration in newts, but their role in the process is yet to be elucidated. METHODS Here we generated a transgenic reporter line using the newt, Pleurodeles waltl, that traces macrophages during lens regeneration. Furthermore, we assessed early changes in gene expression during lens regeneration using two newt species, Notophthalmus viridescens and Pleurodeles waltl. Finally, we used clodronate liposomes to deplete macrophages during lens regeneration in both species and tested the effect of a subsequent secondary injury after macrophage recovery. RESULTS Macrophage depletion abrogated lens regeneration, induced the formation of scar-like tissue, led to inflammation, decreased iris pigment epithelial cell (iPEC) proliferation, and increased rates of apoptosis in the eye. Some of these phenotypes persisted throughout the last observation period of 100 days and could be attenuated by exogenous FGF2 administration. A distinct transcript profile encoding acute inflammatory effectors was established for the dorsal iris. Reinjury of the newt eye alleviated the effects of macrophage depletion, including the resolution of scar-like tissue, and re-initiated the regeneration process. CONCLUSIONS Together, our findings highlight the importance of macrophages for facilitating a pro-regenerative environment in the newt eye by regulating fibrotic responses, modulating the overall inflammatory landscape, and maintaining the proper balance of early proliferation and late apoptosis of the iPECs.
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Affiliation(s)
- Georgios Tsissios
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Anthony Sallese
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
| | - J Raul Perez-Estrada
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
| | - Jared A Tangeman
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Weihao Chen
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Byran Smucker
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
- Department of Statistics, Miami University, Oxford, OH, USA
| | - Sophia C Ratvasky
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Erika Grajales-Esquivel
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
| | - Arielle Martinez
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
| | - Kimberly J Visser
- CRTD/ Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Alberto Joven Araus
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Hui Wang
- Center for Visual Sciences at, Miami University, Oxford, OH, USA
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - András Simon
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
| | - Maximina H Yun
- CRTD/ Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Katia Del Rio-Tsonis
- Department of Biology, Miami University, Oxford, OH, USA.
- Center for Visual Sciences at, Miami University, Oxford, OH, USA.
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA.
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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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Tsissios G, Sallese A, Perez-Estrada JR, Tangeman JA, Chen W, Smucker B, Ratvasky SC, Grajales-Esquive EL, Martinez A, Visser KJ, Araus AJ, Wang H, Simon A, Yun MH, Rio-Tsonis KD. Macrophages modulate fibrosis during newt lens regeneration. RESEARCH SQUARE 2023:rs.3.rs-3603645. [PMID: 38045376 PMCID: PMC10690311 DOI: 10.21203/rs.3.rs-3603645/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Background Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Methods Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Results Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Conclusions Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Maximina H Yun
- Dresden University of Technology: Technische Universitat Dresden
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4
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Tsissios G, Sallese A, Perez-Estrada JR, Tangeman JA, Chen W, Smucker B, Ratvasky SC, Grajales-Esquivel E, Martinez A, Visser KJ, Araus AJ, Wang H, Simon A, Yun MH, Rio-Tsonis KD. Macrophages modulate fibrosis during newt lens regeneration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.04.543633. [PMID: 37333184 PMCID: PMC10274724 DOI: 10.1101/2023.06.04.543633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Previous studies indicated that macrophages play a role during lens regeneration in newts, but their function has not been tested experimentally. Here we generated a transgenic newt reporter line in which macrophages can be visualized in vivo. Using this new tool, we analyzed the location of macrophages during lens regeneration. We uncovered early gene expression changes using bulk RNAseq in two newt species, Notophthalmus viridescens and Pleurodeles waltl. Next, we used clodronate liposomes to deplete macrophages, which inhibited lens regeneration in both newt species. Macrophage depletion induced the formation of scar-like tissue, an increased and sustained inflammatory response, an early decrease in iris pigment epithelial cell (iPEC) proliferation and a late increase in apoptosis. Some of these phenotypes persisted for at least 100 days and could be rescued by exogenous FGF2. Re-injury alleviated the effects of macrophage depletion and re-started the regeneration process. Together, our findings highlight the importance of macrophages in facilitating a pro-regenerative environment in the newt eye, helping to resolve fibrosis, modulating the overall inflammatory landscape and maintaining the proper balance of early proliferation and late apoptosis.
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Affiliation(s)
- Georgios Tsissios
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Anthony Sallese
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
| | - J Raul Perez-Estrada
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
| | - Jared A Tangeman
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Weihao Chen
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Byran Smucker
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Department of Statistics, Miami University, Oxford, OH, USA
| | - Sophia C Ratvasky
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
| | - Erika Grajales-Esquivel
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
| | - Arielle Martinez
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
| | - Kimberly J Visser
- CRTD Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Alberto Joven Araus
- Karolinska Institute, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Hui Wang
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Andras Simon
- Karolinska Institute, Department of Cell and Molecular Biology, Stockholm, Sweden
| | - Maximina H Yun
- CRTD Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden, Germany
| | - Katia Del Rio-Tsonis
- Department of Biology, Miami University, Oxford, OH, USA
- Center for Visual Sciences at Miami University, Oxford, OH, USA
- Cellular Molecular and Structural Biology Program, Miami University, Oxford, OH, USA
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5
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Wang X, Hui Q, Jin Z, Rao F, Jin L, Yu B, Banda J, Li X. Roles of growth factors in eye development and ophthalmic diseases. Zhejiang Da Xue Xue Bao Yi Xue Ban 2022; 51:613-625. [PMID: 36581579 PMCID: PMC10264994 DOI: 10.3724/zdxbyxb-2022-0603] [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: 03/01/2022] [Accepted: 07/30/2022] [Indexed: 12/02/2022]
Abstract
Growth factors are active substances secreted by a variety of cells, which act as messengers to regulate cell migration, proliferation and differentiation. Many growth factors are involved in the eye development or the pathophysiological processes of eye diseases. Growth factors such as vascular endothelial growth factor and basic fibroblast growth factor mediate the occurrence and development of diabetic retinopathy, choroidal neovascularization, cataract, diabetic macular edema, and other retinal diseases. On the other hand, growth factors like nerve growth factor, ciliary neurotrophic factor, glial cell line-derived neurotrophic factor, pigment epithelial-derived factor and granulocyte colony-stimulating factor are known to promote optic nerve injury repair. Growth factors are also related to the pathogenesis of myopia. Fibroblast growth factor, transforming growth factor-β, and insulin-like growth factor regulate scleral thickness and influence the occurrence and development of myopia. This article reviews growth factors involved in ocular development and ocular pathophysiology, discusses the relationship between growth factors and ocular diseases, to provide reference for the application of growth factors in ophthalmology.
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6
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Grigoryan EN. Pigment Epithelia of the Eye: Cell-Type Conversion in Regeneration and Disease. Life (Basel) 2022; 12:life12030382. [PMID: 35330132 PMCID: PMC8955580 DOI: 10.3390/life12030382] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 12/17/2022] Open
Abstract
Pigment epithelial cells (PECs) of the retina (RPE), ciliary body, and iris (IPE) are capable of altering their phenotype. The main pathway of phenotypic switching of eye PECs in vertebrates and humans in vivo and/or in vitro is neural/retinal. Besides, cells of amphibian IPE give rise to the lens and its derivatives, while mammalian and human RPE can be converted along the mesenchymal pathway. The PECs’ capability of conversion in vivo underlies the lens and retinal regeneration in lower vertebrates and retinal diseases such as proliferative vitreoretinopathy and fibrosis in mammals and humans. The present review considers these processes studied in vitro and in vivo in animal models and in humans. The molecular basis of conversion strategies in PECs is elucidated. Being predetermined onto- and phylogenetically, it includes a species-specific molecular context, differential expression of transcription factors, signaling pathways, and epigenomic changes. The accumulated knowledge regarding the mechanisms of PECs phenotypic switching allows the development of approaches to specified conversion for many purposes: obtaining cells for transplantation, creating conditions to stimulate natural regeneration of the retina and the lens, blocking undesirable conversions associated with eye pathology, and finding molecular markers of pathology to be targets of therapy.
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Affiliation(s)
- Eleonora N Grigoryan
- Kol'tsov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
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7
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Demirci Y, Cucun G, Poyraz YK, Mohammed S, Heger G, Papatheodorou I, Ozhan G. Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage. Front Cell Dev Biol 2020; 8:584604. [PMID: 33163496 PMCID: PMC7581945 DOI: 10.3389/fcell.2020.584604] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/11/2020] [Indexed: 01/22/2023] Open
Abstract
Owing to its pronounced regenerative capacity in many tissues and organs, the zebrafish brain represents an ideal platform to understand the endogenous regeneration mechanisms that restore tissue integrity and function upon injury or disease. Although radial glial and neuronal cell populations have been characterized with respect to specific marker genes, comprehensive transcriptomic profiling of the regenerating telencephalon has not been conducted so far. Here, by processing the lesioned and unlesioned hemispheres of the telencephalon separately, we reveal the differentially expressed genes (DEGs) at the early wound healing and early proliferative stages of regeneration, i.e., 20 h post-lesion (hpl) and 3 days post-lesion (dpl), respectively. At 20 hpl, we detect a far higher number of DEGs in the lesioned hemisphere than in the unlesioned half and only 7% of all DEGs in both halves. However, this difference disappears at 3 dpl, where the lesioned and unlesioned hemispheres share 40% of all DEGs. By performing an extensive comparison of the gene expression profiles in these stages, we unravel that the lesioned hemispheres at 20 hpl and 3 dpl exhibit distinct transcriptional profiles. We further unveil a prominent activation of Wnt/β-catenin signaling at 20 hpl, returning to control level in the lesioned site at 3 dpl. Wnt/β-catenin signaling indeed appears to control a large number of genes associated primarily with the p53, apoptosis, forkhead box O (FoxO), mitogen-activated protein kinase (MAPK), and mammalian target of rapamycin (mTOR) signaling pathways specifically at 20 hpl. Based on these results, we propose that the lesioned and unlesioned hemispheres react to injury dynamically during telencephalon regeneration and that the activation of Wnt/β-catenin signaling at the early wound healing stage plays a key role in the regulation of cellular and molecular events.
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Affiliation(s)
- Yeliz Demirci
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, İzmir, Turkey.,İzmir International Biomedicine and Genome Institute (IBG-İzmir), Dokuz Eylül University, İzmir, Turkey.,European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Gokhan Cucun
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, İzmir, Turkey.,İzmir International Biomedicine and Genome Institute (IBG-İzmir), Dokuz Eylül University, İzmir, Turkey
| | - Yusuf Kaan Poyraz
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, İzmir, Turkey.,İzmir International Biomedicine and Genome Institute (IBG-İzmir), Dokuz Eylül University, İzmir, Turkey
| | - Suhaib Mohammed
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | | | - Irene Papatheodorou
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Cambridge, United Kingdom
| | - Gunes Ozhan
- İzmir Biomedicine and Genome Center (IBG), Dokuz Eylül University Health Campus, İzmir, Turkey.,İzmir International Biomedicine and Genome Institute (IBG-İzmir), Dokuz Eylül University, İzmir, Turkey
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8
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Taira Y, Ikuta Y, Inamori S, Nunome M, Nakano M, Suzuki T, Matsuda Y, Tsudzuki M, Teramoto M, Iida H, Kondoh H. The formation of multiple pituitary pouches from the oral ectoderm causes ectopic lens development in hedgehog signaling-defective avian embryos. Dev Dyn 2020; 249:1425-1439. [PMID: 32633438 DOI: 10.1002/dvdy.222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Hedgehog signaling has various regulatory functions in tissue morphogenesis and differentiation. To investigate its involvement in anterior pituitary precursor development and the lens precursor potential for anterior pituitary precursors, we investigated Talpid mutant Japanese quail embryos, in which hedgehog signaling is defective. RESULTS Talpid mutants develop multiple pituitary precursor-like pouches of variable sizes from the oral ectoderm (OE). The ectopic pituitary pouches initially express the pituitary-associated transcription factor (TF) LHX3 similarly to Rathke's pouch, the genuine pituitary precursor. The pouches coexpress the TFs SOX2 and PAX6, a signature of lens developmental potential. Most Talpid mutant pituitary pouches downregulate LHX3 expression and activate the lens-essential TF PROX1, leading to the development of small lens tissue expressing α-, β-, and δ-crystallins. In contrast, mutant Rathke's pouches express a lower level of LHX3, which is primarily localized in the cytoplasm, and activate the lens developmental pathway. CONCLUSIONS Hedgehog signaling in normal embryos regulates the development of Rathke's pouch in two steps. First, by confining Rathke's pouch development in a low hedgehog signaling region of the OE. Second, by sustaining LHX3 activity to promote anterior pituitary development, while inhibiting ectopic lens development.
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Affiliation(s)
- Yuki Taira
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Yuya Ikuta
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Sachiko Inamori
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Mikiharu Nakano
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takayuki Suzuki
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yoichi Matsuda
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Masaoki Tsudzuki
- Graduate School of Integrated Sciences for Life, and Japanese Avian Bioresources Project Research Center, Hiroshima University, Hiroshima, Japan
| | - Machiko Teramoto
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Hideaki Iida
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan
| | - Hisato Kondoh
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,Institute for Comprehensive Research, Kyoto Sangyo University, Kyoto, Japan
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9
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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: 30] [Impact Index Per Article: 6.0] [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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10
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Grigoryan EN, Radugina EA. Behavior of Stem-Like Cells, Precursors for Tissue Regeneration in Urodela, Under Conditions of Microgravity. Stem Cells Dev 2019; 28:423-437. [PMID: 30696352 DOI: 10.1089/scd.2018.0220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We summarize data from our experiments on stem-like cell-dependent regeneration in amphibians in microgravity. Considering its deleterious effect on many tissues, we asked whether microgravity is compatible with reparative processes, specifically activation and proliferation of source cells. Experiments were conducted using tailed amphibians, which combine profound regenerative capabilities with high robustness, allowing an in vivo study of lens, retina, limb, and tail regeneration in challenging settings of spaceflight. Microgravity promoted stem-like cell proliferation to a varying extent (up to 2-fold), and it seemed to speed up source cell dedifferentiation, as well as sequential differentiation in retina, lens, and limb, leading to formation of bigger and more developed regenerates than in 1g controls. It also promoted proliferation and hypertrophy of Müller glial cells, eliciting a response similar to reactive gliosis. A significant increase in stem-like cell proliferation was mostly beneficial for regeneration and only in rare cases caused moderate tissue growth abnormalities. It is important that microgravity yielded a lasting effect even if applied before operations. We hypothesize on the potential mechanisms of gravity-dependent changes in stem-like cell behavior, including fibroblast growth factor 2 signaling pathway and heat shock proteins, which were affected in our experimental settings. Taken together, our data indicate that microgravity does not disturb the natural regenerative potential of newt stem-like cells, and, depending on the system, even stimulates their dedifferentiation, proliferation, and differentiation. We discuss these data along with publications on mammalian stem cell behavior in vitro and invertebrate regeneration in vivo in microgravity. In vivo data are very scarce and require further research using contemporary methods of cell behavior analysis to elucidate mechanisms of stem cell response to altered gravity. They are relevant for both practical applications, such as managing human reparative responses in spaceflight, and fundamental understanding of stem cell biology.
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Affiliation(s)
- Eleonora N Grigoryan
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
| | - Elena A Radugina
- Koltzov Institute of Developmental Biology of Russian Academy of Sciences, Moscow, Russia
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Zondag LE, Rutherford K, Gemmell NJ, Wilson MJ. Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis. BMC Genomics 2016; 17:114. [PMID: 26879048 PMCID: PMC4755014 DOI: 10.1186/s12864-016-2435-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/05/2016] [Indexed: 01/16/2023] Open
Abstract
Background Regenerative capacity differs greatly between animals. In vertebrates regenerative abilities are highly limited and tissue or organ specific. However the closest related chordate to the vertebrate clade, Botrylloides leachi, can undergo whole body regeneration (WBR). Therefore, research on WBR in B. leachi has focused on pathways known to be important for regeneration in vertebrates. To obtain a comprehensive vision of this unique process we have carried out the first de novo transcriptome sequencing for multiple stages of WBR occurring in B. leachi. The identified changes in gene expression during B. leachi WBR offer novel insights into this remarkable ability to regenerate. Results The transcriptome of B. leachi tissue undergoing WBR were analysed using differential gene expression, gene ontology and pathway analyses. We observed up-regulation in the expression of genes involved in wound healing and known developmental pathways including WNT, TGF-β and Notch, during the earliest stages of WBR. Later in WBR, the expression patterns in several pathways required for protein synthesis, biogenesis and the organisation of cellular components were up-regulated. Conclusions While the genes expressed early on are characteristic of a necessary wound healing response to an otherwise lethal injury, the subsequent vast increase in protein synthesis conceivably sustains the reestablishment of the tissue complexity and body axis polarity within the regenerating zooid. We have, for the first time, provided a global overview of the genes and their corresponding pathways that are modulated during WBR in B. leachi. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2435-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisa E Zondag
- Department of Anatomy, Otago School of Medical Sciences, Developmental Biology and Genomics Laboratory, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
| | - Kim Rutherford
- Department of Anatomy, Centre for Reproduction and Genomics and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand.
| | - Neil J Gemmell
- Department of Anatomy, Centre for Reproduction and Genomics and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand.
| | - Megan J Wilson
- Department of Anatomy, Otago School of Medical Sciences, Developmental Biology and Genomics Laboratory, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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Li Q, Yang H, Zhong TP. Regeneration across metazoan phylogeny: lessons from model organisms. J Genet Genomics 2015; 42:57-70. [PMID: 25697100 DOI: 10.1016/j.jgg.2014.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/18/2014] [Accepted: 12/21/2014] [Indexed: 01/09/2023]
Abstract
Comprehending the diversity of the regenerative potential across metazoan phylogeny represents a fundamental challenge in biology. Invertebrates like Hydra and planarians exhibit amazing feats of regeneration, in which an entire organism can be restored from minute body segments. Vertebrates like teleost fish and amphibians can also regrow large sections of the body. While this regenerative capacity is greatly attenuated in mammals, there are portions of major organs that remain regenerative. Regardless of the extent, there are common basic strategies to regeneration, including activation of adult stem cells and proliferation of differentiated cells. Here, we discuss the cellular features and molecular mechanisms that are involved in regeneration in different model organisms, including Hydra, planarians, zebrafish and newts as well as in several mammalian organs.
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Affiliation(s)
- Qiao Li
- State Key Laboratory of Genetic Engineering, Department of Genetics, Fudan University School of Life Science, Shanghai 200433, China
| | - Hao Yang
- State Key Laboratory of Genetic Engineering, Department of Genetics, Fudan University School of Life Science, Shanghai 200433, China
| | - Tao P Zhong
- State Key Laboratory of Genetic Engineering, Department of Genetics, Fudan University School of Life Science, Shanghai 200433, China; Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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Markitantova YV, Avdonin PP, Grigoryan EN. FGF2 signaling pathway components in tissues of the posterior eye sector in the adult newt Pleurodeles waltl. BIOL BULL+ 2014. [DOI: 10.1134/s1062359014040074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Grigoryan EN, Markitantova YV, Avdonin PP, Radugina EA. Study of regeneration in amphibians in age of molecular-genetic approaches and methods. RUSS J GENET+ 2013. [DOI: 10.1134/s1022795413010043] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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15
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Abstract
Comparative studies of lens and retina regeneration have been conducted within a wide variety of animals over the last 100 years. Although amphibians, fish, birds and mammals have all been noted to possess lens- or retina-regenerative properties at specific developmental stages, lens or retina regeneration in adult animals is limited to lower vertebrates. The present review covers the newest perspectives on lens and retina regeneration from these different model organisms with a focus on future trends in regeneration research.
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King MW, Neff AW, Mescher AL. The developing Xenopus limb as a model for studies on the balance between inflammation and regeneration. Anat Rec (Hoboken) 2012; 295:1552-61. [PMID: 22933418 DOI: 10.1002/ar.22443] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 12/16/2011] [Indexed: 01/21/2023]
Abstract
The roles of inflammation and immune cell reactivity triggered by amputation have only recently begun to be addressed in investigations of epimorphic regeneration, although studies of tissue repair in mammals clearly show the importance of the immune system in determining the quality of the repair process. Here, we first review inflammation-related work in non-mammalian systems of epimorphic regeneration which suggests that regeneration of an amputated appendage requires continuous modulation of the local immune response, from the first hours after amputation through the period of blastema patterning. We then present data on the effects of anti-inflammatory and proinflammatory agents on regeneration of larval Xenopus hindlimbs. Treatment with the glucocorticoid beclomethasone immediately after amputation inhibits regeneration in regeneration-complete stage 53 limbs. Other anti-inflammatory agents, including the inhibitors of cyclooxygenase-2 (COX-2) activity celecoxib and diclofenac, applied similarly to larvae amputated at stage 55, when the capacity for limb regeneration is normally being lost, restore regenerative capacity. This suggests that although injury-related events sensitive to glucocorticoids are necessary for regeneration, resolution of the inflammatory response may also be required to allow the complete regenerative response and normal blastema patterning. Conversely, if resolution of inflammation is prevented by local treatment of amputated limbs with beryllium, a strong immunoadjuvant, regeneration is inhibited, and gene expression data suggest that this inhibition results from a failure of normal blastema patterning. Both positive and negative effects of immune- or inflammation-related activities occur during anuran limb regeneration and this underscores the importance of considering immune cells in studies of epimorphic regeneration.
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Affiliation(s)
- Michael W King
- Indiana University Center for Regenerative Biology and Medicine, Indiana University School of Medicine, Terre Haute, Indiana, USA
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Day RC, Beck CW. Transdifferentiation from cornea to lens in Xenopus laevis depends on BMP signalling and involves upregulation of Wnt signalling. BMC DEVELOPMENTAL BIOLOGY 2011; 11:54. [PMID: 21896182 PMCID: PMC3184090 DOI: 10.1186/1471-213x-11-54] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Accepted: 09/06/2011] [Indexed: 11/30/2022]
Abstract
Background Surgical removal of the lens from larval Xenopus laevis results in a rapid transdifferention of central corneal cells to form a new lens. The trigger for this process is understood to be an induction event arising from the unprecedented exposure of the cornea to the vitreous humour that occurs following lens removal. The molecular identity of this trigger is unknown. Results Here, we have used a functional transgenic approach to show that BMP signalling is required for lens regeneration and a microarray approach to identify genes that are upregulated specifically during this process. Analysis of the array data strongly implicates Wnt signalling and the Pitx family of transcription factors in the process of cornea to lens transdifferentiation. Our analysis also captured several genes associated with congenital cataract in humans. Pluripotency genes, in contrast, were not upregulated, supporting the idea that corneal cells transdifferentiate without returning to a stem cell state. Several genes from the array were expressed in the forming lens during embryogenesis. One of these, Nipsnap1, is a known direct target of BMP signalling. Conclusions Our results strongly implicate the developmental Wnt and BMP signalling pathways in the process of cornea to lens transdifferentiation (CLT) in Xenopus, and suggest direct transdifferentiation between these two anterior eye tissues.
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Affiliation(s)
- Robert C Day
- Genetics Otago, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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Curado S, Ober EA, Walsh S, Cortes-Hernandez P, Verkade H, Koehler CM, Stainier DYR. The mitochondrial import gene tomm22 is specifically required for hepatocyte survival and provides a liver regeneration model. Dis Model Mech 2010; 3:486-95. [PMID: 20483998 DOI: 10.1242/dmm.004390] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Understanding liver development should lead to greater insights into liver diseases and improve therapeutic strategies. In a forward genetic screen for genes regulating liver development in zebrafish, we identified a mutant--oliver--that exhibits liver-specific defects. In oliver mutants, the liver is specified, bile ducts form and hepatocytes differentiate. However, the hepatocytes die shortly after their differentiation, and thus the resulting mutant liver consists mainly of biliary tissue. We identified a mutation in the gene encoding translocase of the outer mitochondrial membrane 22 (Tomm22) as responsible for this phenotype. Mutations in tomm genes have been associated with mitochondrial dysfunction, but most studies on the effect of defective mitochondrial protein translocation have been carried out in cultured cells or unicellular organisms. Therefore, the tomm22 mutant represents an important vertebrate genetic model to study mitochondrial biology and hepatic mitochondrial diseases. We further found that the temporary knockdown of Tomm22 levels by morpholino antisense oligonucleotides causes a specific hepatocyte degeneration phenotype that is reversible: new hepatocytes repopulate the liver as Tomm22 recovers to wild-type levels. The specificity and reversibility of hepatocyte ablation after temporary knockdown of Tomm22 provides an additional model to study liver regeneration, under conditions where most hepatocytes have died. We used this regeneration model to analyze the signaling commonalities between hepatocyte development and regeneration.
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Affiliation(s)
- Silvia Curado
- Department of Biochemistry and Biophysics, Programs in Developmental Biology, Genetics and Human Genetics, University of California-San Francisco, 1550 Fourth Street, San Francisco, CA 94158-2324, USA.
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Godwin JW, Liem KF, Brockes JP. Tissue factor expression in newt iris coincides with thrombin activation and lens regeneration. Mech Dev 2010; 127:321-8. [PMID: 20420902 DOI: 10.1016/j.mod.2010.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Revised: 04/12/2010] [Accepted: 04/16/2010] [Indexed: 12/17/2022]
Abstract
Lens regeneration in adult salamanders occurs at the pupillary margin of the mid-dorsal iris where pigmented epithelial cells (PEC) re-enter the cell cycle and transdifferentiate into lens. It is not understood how the injury caused by removal of the lens (lentectomy) in one location is linked to initiating the response in a different spatial location (dorsal iris) and to this particular sector. We propose that the blood provides a link between the localised coagulation and signal transduction pathways that lead to regeneration. A transmembrane protein (tissue factor) is expressed in a striking patch-like domain in the dorsal iris of the newt that localises coagulation specifically to this location, but is not expressed in the axolotl, a related species that does not show thrombin activation after lentectomy and cannot regenerate its lens. Our hypothesis is that tissue factor expression localises the initiation of regeneration through the activation of thrombin and the recruitment of blood cells, leading to local growth factor release. This is the first example of gene expression in a patch of cells that prefigures the location of a regenerative response, and links the immune system with the initiation of a regenerative program.
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Affiliation(s)
- James W Godwin
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.
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