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Alibardi L. Progressive modifications during evolution involving epigenetic changes have determined loss of regeneration mainly in terrestrial animals: A hypothesis. Dev Biol 2024; 515:169-177. [PMID: 39029569 DOI: 10.1016/j.ydbio.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 07/21/2024]
Abstract
In order to address a biological explanation for the different regenerative abilities present among animals, a new evolutionary speculation is presented. It is hypothesized that epigenetic mechanisms have lowered or erased regeneration during the evolution of terrestrial invertebrates and vertebrates. The hypothesis indicates that a broad regeneration can only occur in marine or freshwater conditions, and that life on land does not allow for high regeneration. This is due to the physical, chemical and microbial conditions present in the terrestrial environment with respect to those of the aquatic environment. The present speculation provides examples of hypothetic evolutionary animal lineages that colonized the land, such as parasitic annelids, terrestrial mollusks, arthropods and amniotes. These are the animals where regeneration is limited or absent and their injuries are only repaired through limited healing or scarring. It is submitted that this loss derived from changes in the developmental gene pathways sustaining regeneration in the aquatic environment but that cannot be expressed on land. Once regeneration was erased in terrestrial species, re-adaptation to freshwater niches could not reactivate the previously altered gene pathways that determined regeneration. Therefore a broad regeneration was no longer possible or became limited and heteromorphic in the derived, extant animals. Only in few cases extensive healing abilities or regengrow, a healing process where regeneration overlaps with somatic growth, have evolved among arthropods and amniotes. The present paper is an extension of previous speculations trying to explain in biological terms the different regenerative abilities present among metazoans.
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2
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Alibardi L. Regeneration among animals: An evolutionary hypothesis related to aquatic versus terrestrial environment. Dev Biol 2023:S0012-1606(23)00112-4. [PMID: 37353104 DOI: 10.1016/j.ydbio.2023.06.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/31/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023]
Abstract
The present hypothesis tries to explain animal regeneration in relation to the life cycles and environment of different animals. Regeneration is a basic phenomenon present since the origin of life in the sea, as testimonial in lower or more complex extant marine animals. Aquatic animals that evolved an indirect development, forming larvae and transiting into the adult stage through metamorphosis, use gene networks present in their genome for these transformations. In case of injury or organ loss as adults, they can re-utilize most or part of the gene networks previously activated during larval growth and metamorphosis. In contrast, terrestrial animals that evolved life cycles with the elimination of larvae and metamorphosis for the adaptation to land conditions lost some of the genes implicated in these post-developmental processes and consequently also the ability to regenerate. Few arthropods and lizards are capable to form hydrated regenerative blastemas with a similar consistence of embryonic tissues. The present hypothesis submits that regeneration cannot be activated in the dry land environment and consequently was largely or completely abolished in terrestrial animals. After injury or organ loss, nematodes, most arthropods and terrestrial vertebrates can only form scars or a limited healing or regengrow in juveniles. This is a process where somatic growth is superimposed to wound healing so that the apparent regeneration derives from the combination from both processes. When full growth is terminated these terrestrial animals can only heal by scarring.
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3
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Okamura DM, Nguyen ED, Collins SJ, Yoon K, Gere JB, Weiser-Evans MCM, Beier DR, Majesky MW. Mammalian organ regeneration in spiny mice. J Muscle Res Cell Motil 2023; 44:39-52. [PMID: 36131170 DOI: 10.1007/s10974-022-09631-3] [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: 04/07/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022]
Abstract
Fibrosis-driven solid organ failure is a major world-wide health burden with few therapeutic options. Spiny mice (genus: Acomys) are terrestrial mammals that regenerate severe skin wounds without fibrotic scars to evade predators. Recent studies have shown that spiny mice also regenerate acute ischemic and traumatic injuries to kidney, heart, spinal cord, and skeletal muscle. A common feature of this evolved wound healing response is a lack of formation of fibrotic scar tissue that degrades organ function, inhibits regeneration, and leads to organ failure. Complex tissue regeneration is an extremely rare property among mammalian species. In this article, we discuss the evidence that Acomys represents an emerging model organism that offers a unique opportunity for the biomedical community to investigate and clinically translate molecular mechanisms of scarless wound healing and regeneration of organ function in a mammalian species.
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Affiliation(s)
- Daryl M Okamura
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Elizabeth D Nguyen
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Kevin Yoon
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Joshua B Gere
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Mary C M Weiser-Evans
- Department of Medicine, Division of Renal Diseases & Hypertension, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David R Beier
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Mark W Majesky
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98195, USA.
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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4
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Alibardi L. Regeneration or Scarring Derive from Specific Evolutionary Environmental Adaptations of the Life Cycles in Different Animals. BIOLOGY 2023; 12:biology12050733. [PMID: 37237545 DOI: 10.3390/biology12050733] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023]
Abstract
The ability to heal or even regenerate large injuries in different animals derives from the evolution of their specific life cycles during geological times. The present, new hypothesis tries to explain the distribution of organ regeneration among animals. Only invertebrates and vertebrates that include larval and intense metamorphic transformations can broadly regenerate as adults. Basically, regeneration competent animals are aquatic while terrestrial species have largely or completely lost most of the regeneration ability. Although genomes of terrestrial species still contain numerous genes that in aquatic species allow a broad regeneration ("regenerative genes"), the evolution of terrestrial species has variably modified the genetic networks linking these genes to the others that evolved during land adaptation, resulting in the inhibition of regeneration. Loss of regeneration took place by the elimination of intermediate larval phases and metamorphic transformations in the life cycles of land invertebrates and vertebrates. Once the evolution along a specific lineage generated species that could no longer regenerate, this outcome could not change anymore. It is therefore likely that what we learn from regenerative species will explain their mechanisms of regeneration but cannot or only partly be applied to non-regenerative species. Attempts to introduce "regenerative genes" in non-regenerative species most likely would disorder the entire genetic networks of the latter, determining death, teratomas and cancer. This awareness indicates the difficulty to introduce regenerative genes and their activation pathways in species that evolved genetic networks suppressing organ regeneration. Organ regeneration in non-regenerating animals such as humans should move to bio-engineering interventions in addition to "localized regenerative gene therapies" in order to replace lost tissues or organs.
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Affiliation(s)
- Lorenzo Alibardi
- Comparative Histolab Padova and Department of Biology, University of Bologna, 40126 Bologna, Italy
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5
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Gattupalli M, Dey P, Poovizhi S, Patel RB, Mishra D, Banerjee S. The Prospects of RNAs and Common Significant Pathways in Cancer Therapy and Regenerative Medicine. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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6
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Wang J, Chen X, Hou X, Wang J, Yue W, Huang S, Xu G, Yan J, Lu G, Hofreiter M, Li C, Wang C. "Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis. SCIENCE ADVANCES 2022; 8:eabl4642. [PMID: 36112682 PMCID: PMC9481118 DOI: 10.1126/sciadv.abl4642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/01/2022] [Indexed: 05/22/2023]
Abstract
Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod-specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective.
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Affiliation(s)
- Jun Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xiaowen Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xin Hou
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Jingan Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Wucheng Yue
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Shu Huang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Gangchun Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization certified by the Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jizhou Yan
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Guoqing Lu
- Department of Biology, University of Nebraska at Omaha, Omaha, NE 68182, USA
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Faculty of Science, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
| | - Chenhong Li
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
| | - Chenghui Wang
- Key Laboratory of Freshwater Aquatic Genetic Resources certified by the Ministry of Agriculture and Rural Affairs/National Demonstration Center for Experimental Fisheries Science Education/Shanghai Engineering Research Center of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Corresponding author. Email (M.H.); (C.L.); (C.W.)
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7
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Osorio-Méndez D, Miller A, Begeman IJ, Kurth A, Hagle R, Rolph D, Dickson AL, Chen CH, Halloran M, Poss KD, Kang J. Voltage-gated sodium channel scn8a is required for innervation and regeneration of amputated adult zebrafish fins. Proc Natl Acad Sci U S A 2022; 119:e2200342119. [PMID: 35867745 PMCID: PMC9282381 DOI: 10.1073/pnas.2200342119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/10/2022] [Indexed: 01/09/2023] Open
Abstract
Teleost fishes and urodele amphibians can regenerate amputated appendages, whereas this ability is restricted to digit tips in adult mammals. One key component of appendage regeneration is reinnervation of the wound area. However, how innervation is regulated in injured appendages of adult vertebrates has seen limited research attention. From a forward genetics screen for temperature-sensitive defects in zebrafish fin regeneration, we identified a mutation that disrupted regeneration while also inducing paralysis at the restrictive temperature. Genetic mapping and complementation tests identify a mutation in the major neuronal voltage-gated sodium channel (VGSC) gene scn8ab. Conditional disruption of scn8ab impairs early regenerative events, including blastema formation, but does not affect morphogenesis of established regenerates. Whereas scn8ab mutations reduced neural activity as expected, they also disrupted axon regrowth and patterning in fin regenerates, resulting in hypoinnervation. Our findings indicate that the activity of VGSCs plays a proregenerative role by promoting innervation of appendage stumps.
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Affiliation(s)
- Daniel Osorio-Méndez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Miller
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Ian J. Begeman
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Andrew Kurth
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Ryan Hagle
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Daniela Rolph
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
| | - Amy L. Dickson
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Mary Halloran
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53705
| | - Kenneth D. Poss
- Duke Regeneration Center, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin–Madison, Madison, WI 53705
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8
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Yue Z, Lei M, Paus R, Chuong CM. The global regulatory logic of organ regeneration: circuitry lessons from skin and its appendages. Biol Rev Camb Philos Soc 2021; 96:2573-2583. [PMID: 34145718 PMCID: PMC10874616 DOI: 10.1111/brv.12767] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022]
Abstract
In organ regeneration, the regulatory logic at a systems level remains largely unclear. For example, what defines the quantitative threshold to initiate regeneration, and when does the regeneration process come to an end? What leads to the qualitatively different responses of regeneration, which restore the original structure, or to repair which only heals a wound? Here we discuss three examples in skin regeneration: epidermal recovery after radiation damage, hair follicle fate choice after chemotherapy damage, and wound-induced feather regeneration. We propose that the molecular regulatory circuitry is of paramount significance in organ regeneration. It is conceivable that defects in these controlling pathways may lead to failed regeneration and/or organ renewal, and understanding the underlying logic could help to identify novel therapeutic strategies.
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Affiliation(s)
- ZhiCao Yue
- Department of Cell Biology and Medical Genetics, Carson International Cancer Center, Guangdong Key Laboratory for Genome Stability and Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Mingxing Lei
- 111 Project Laboratory of Biomechanics and Tissue Repair, College of Bioengineering, Chongqing University, Chongqing, 400038, China
| | - Ralf Paus
- Department of Dermatology & Cutaneous Surgery, University of Miami Miller School of Medicine, Miami, FL, 33136, U.S.A
| | - Cheng-Ming Chuong
- Department of Pathology, University of Southern California, Los Angeles, CA, 90033, U.S.A
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9
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Lin YF, Sam J, Evans T. Sirt1 promotes tissue regeneration in zebrafish through regulating the mitochondrial unfolded protein response. iScience 2021; 24:103118. [PMID: 34622167 PMCID: PMC8479786 DOI: 10.1016/j.isci.2021.103118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 08/12/2021] [Accepted: 09/09/2021] [Indexed: 11/16/2022] Open
Abstract
The mitochondrial unfolded protein response (UPRmt) is an organellar stress signaling pathway that functions to detect and restore disruption of mitochondrial proteostasis. The UPRmt is involved in a wide range of physiological and disease conditions, including aging, stem cell maintenance, innate immunity, neurodegeneration, and cancer. Here we report that the UPRmt is integral to zebrafish fin regeneration. Taking advantage of a novel zebrafish UPRmt reporter, we observed that UPRmt activation occurs in regenerating fin tissue shortly after injury. Through chemical and genetic approaches, we discovered that the Sirt1-UPRmt pathway, best known for its role in promoting lifespan extension, is crucial for fin regeneration. The metabolism of NAD+ is an important contributor to Sirt1 activity in this context. We propose that Sirt1 activation induces mitochondrial biogenesis in injured fin tissue, which leads to UPRmt activation and promotes tissue regeneration.
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Affiliation(s)
- Yi-Fan Lin
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, LC-708, New York, NY 10065, USA
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
- Department of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jessica Sam
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, LC-708, New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, LC-708, New York, NY 10065, USA
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10
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Abstract
Plants exhibit remarkable lineage plasticity, allowing them to regenerate organs that differ from their respective origins. Such developmental plasticity is dependent on the activity of pluripotent founder cells or stem cells residing in meristems. At the shoot apical meristem (SAM), the constant flow of cells requires continuing cell specification governed by a complex genetic network, with the WUSCHEL transcription factor and phytohormone cytokinin at its core. In this review, I discuss some intriguing recent discoveries that expose new principles and mechanisms of patterning and cell specification acting both at the SAM and, prior to meristem organogenesis during shoot regeneration. I also highlight unanswered questions and future challenges in the study of SAM and meristem regeneration. Finally, I put forward a model describing stochastic events mediated by epigenetic factors to explain how the gene regulatory network might be initiated at the onset of shoot regeneration. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 76100, Israel;
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11
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Function and regulation of muscle stem cells in skeletal muscle development and regeneration: a narrative review. JOURNAL OF BIO-X RESEARCH 2021. [DOI: 10.1097/jbr.0000000000000105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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12
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Tseng TL, Wang YT, Tsao CY, Ke YT, Lee YC, Hsu HJ, Poss KD, Chen CH. The RNA helicase Ddx52 functions as a growth switch in juvenile zebrafish. Development 2021; 148:271093. [PMID: 34323273 DOI: 10.1242/dev.199578] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/30/2021] [Indexed: 12/18/2022]
Abstract
Vertebrate animals usually display robust growth trajectories during juvenile stages, and reversible suspension of this growth momentum by a single genetic determinant has not been reported. Here, we report a single genetic factor that is essential for juvenile growth in zebrafish. Using a forward genetic screen, we recovered a temperature-sensitive allele, pan (after Peter Pan), that suspends whole-organism growth at juvenile stages. Remarkably, even after growth is halted for a full 8-week period, pan mutants are able to resume a robust growth trajectory after release from the restrictive temperature, eventually growing into fertile adults without apparent adverse phenotypes. Positional cloning and complementation assays revealed that pan encodes a probable ATP-dependent RNA helicase (DEAD-Box Helicase 52; ddx52) that maintains the level of 47S precursor ribosomal RNA. Furthermore, genetic silencing of ddx52 and pharmacological inhibition of bulk RNA transcription similarly suspend the growth of flies, zebrafish and mice. Our findings reveal evidence that safe, reversible pauses of juvenile growth can be mediated by targeting the activity of a single gene, and that its pausing mechanism has high evolutionary conservation.
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Affiliation(s)
- Tzu-Lun Tseng
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Ying-Ting Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chang-Yu Tsao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Teng Ke
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yi-Ching Lee
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Hwei-Jan Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Kenneth D Poss
- Department of Cell Biology, Regeneration Next, Duke University Medical Center, Durham, NC 27710, USA
| | - Chen-Hui Chen
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan
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13
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Feleke M, Bennett S, Chen J, Chandler D, Hu X, Xu J. Biological insights into the rapid tissue regeneration of freshwater crayfish and crustaceans. Cell Biochem Funct 2021; 39:740-753. [PMID: 34165197 DOI: 10.1002/cbf.3653] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/03/2021] [Indexed: 11/12/2022]
Abstract
The freshwater crayfish is capable of regenerating limbs, following autotomy, injury and predation. In arthropod species, regeneration and moulting are two processes linked and strongly regulated by ecdysone. The regeneration of crayfish limbs is divided into wound healing, blastema formation, cellular reprogramming and tissue patterning. Limb blastema cells undergo proliferation, dedifferentiation and redifferentiation. A limb bud, containing folded segments of the regenerating limb, is encased within a cuticular sheath. The functional limb regenerates, in proecdysis, in two to three consecutive moults. Rapid tissue growth is regulated by hormones, limb nerves and local cells. The TGF-β/activin signalling pathway has been determined in the crayfish, P. fallax f. virginalis, and is suggested as a potential regulator of tissue regeneration. In this review article, we discuss current understanding of tissue regeneration in the crayfish and various crustaceans. A thorough understanding of the cellular, genetic and molecular pathways of these biological processes is promising for the development of therapeutic applications for a wide array of diseases in regenerative medicine.
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Affiliation(s)
- Mesalie Feleke
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Samuel Bennett
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
| | - Jiazhi Chen
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia.,Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - David Chandler
- Australian Genome Research Facility, Medical Research Foundation, Royal Perth Hospital, Perth, Western Australia, Australia
| | - Xiaoyong Hu
- Guangdong Provincial Key Laboratory of Industrial Surfactant, Guangdong Research Institute of Petrochemical and Fine Chemical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Jiake Xu
- Division of Regenerative Biology, School of Biomedical Sciences, University of Western Australia, Perth, Western Australia, Australia
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14
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Stewart S, Le Bleu HK, Yette GA, Henner AL, Robbins AE, Braunstein JA, Stankunas K. longfin causes cis-ectopic expression of the kcnh2a ether-a-go-go K+ channel to autonomously prolong fin outgrowth. Development 2021; 148:dev199384. [PMID: 34061172 PMCID: PMC8217709 DOI: 10.1242/dev.199384] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/19/2021] [Indexed: 12/11/2022]
Abstract
Organs stop growing to achieve a characteristic size and shape in scale with the body of an animal. Likewise, regenerating organs sense injury extents to instruct appropriate replacement growth. Fish fins exemplify both phenomena through their tremendous diversity of form and remarkably robust regeneration. The classic zebrafish mutant longfint2 develops and regenerates dramatically elongated fins and underlying ray skeleton. We show longfint2 chromosome 2 overexpresses the ether-a-go-go-related voltage-gated potassium channel kcnh2a. Genetic disruption of kcnh2a in cis rescues longfint2, indicating longfint2 is a regulatory kcnh2a allele. We find longfint2 fin overgrowth originates from prolonged outgrowth periods by showing Kcnh2a chemical inhibition during late stage regeneration fully suppresses overgrowth. Cell transplantations demonstrate longfint2-ectopic kcnh2a acts tissue autonomously within the fin intra-ray mesenchymal lineage. Temporal inhibition of the Ca2+-dependent phosphatase calcineurin indicates it likewise entirely acts late in regeneration to attenuate fin outgrowth. Epistasis experiments suggest longfint2-expressed Kcnh2a inhibits calcineurin output to supersede growth cessation signals. We conclude ion signaling within the growth-determining mesenchyme lineage controls fin size by tuning outgrowth periods rather than altering positional information or cell-level growth potency.
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Affiliation(s)
- Scott Stewart
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Heather K. Le Bleu
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Gabriel A. Yette
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Astra L. Henner
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Amy E. Robbins
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
| | - Joshua A. Braunstein
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
| | - Kryn Stankunas
- Institute of Molecular Biology, University of Oregon, 273 Onyx Bridge, 1318 Franklin Blvd, Eugene, OR 97403-1229, USA
- Department of Biology, University of Oregon, 77 Klamath Hall, Eugene, OR 97403-1210, USA
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15
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Vullien A, Röttinger É, Vervoort M, Gazave E. [A trio of mechanisms involved in regeneration initiation in animals]. Med Sci (Paris) 2021; 37:349-358. [PMID: 33908852 DOI: 10.1051/medsci/2021037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Whole-body and complex structure regeneration is a widespread phenomenon in animals. While regenerative abilities vary greatly from one species to another, a number of mechanisms appear essential for regeneration in distantly related phylogenetic groups. In this review, we synthetize the knowledge gathered on the implication of three mechanisms that appear to be important for the initiation of regeneration in animals. Reactive Oxygen Species (ROS) are metabolic by-products involved in cell signalling, which are produced shortly after amputation in several species. ROS production may be responsible for triggering apoptosis, another recurring mechanism involved in regeneration initiation. In turn, apoptosis causes compensatory proliferation by setting off cellular division, thus contributing to the reconstitution of tissues. Inhibiting either ROS production, apoptosis or cellular proliferation impairs regeneration in a variety of model species.
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Affiliation(s)
- Aurore Vullien
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France - Université Côte d'Azur, CNRS, Inserm, IRCAN (Institute for Research on Cancer and Aging), 28 avenue de Valombrose, Nice, France
| | - Éric Röttinger
- Université Côte d'Azur, CNRS, Inserm, IRCAN (Institute for Research on Cancer and Aging), 28 avenue de Valombrose, Nice, France - Université Côte d'Azur, Institut fédératif de recherche - Ressources marines, Nice, France
| | - Michel Vervoort
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
| | - Eve Gazave
- Université de Paris, CNRS, Institut Jacques Monod, F-75006 Paris, France
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16
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Das RN, Yaniv K. Discovering New Progenitor Cell Populations through Lineage Tracing and In Vivo Imaging. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035618. [PMID: 32041709 DOI: 10.1101/cshperspect.a035618] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Identification of progenitor cells that generate differentiated cell types during development, regeneration, and disease states is central to understanding the mechanisms governing such transitions. For more than a century, different lineage-tracing strategies have been developed, which helped disentangle the complex relationship between progenitor cells and their progenies. In this review, we discuss how lineage-tracing analyses have evolved alongside technological advances, and how this approach has contributed to the identification of progenitor cells in different contexts of cell differentiation. We also highlight a few examples in which lineage-tracing experiments have been instrumental for resolving long-standing debates and for identifying unexpected cellular origins. This discussion emphasizes how this century-old quest to delineate cellular lineage relationships is still active, and new discoveries are being made with the development of newer methodologies.
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Affiliation(s)
- Rudra Nayan Das
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Karina Yaniv
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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17
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Alibardi L. Appendage regeneration in anamniotes utilizes genes active during larval-metamorphic stages that have been lost or altered in amniotes: The case for studying lizard tail regeneration. J Morphol 2020; 281:1358-1381. [PMID: 32865265 DOI: 10.1002/jmor.21251] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/20/2020] [Accepted: 07/25/2020] [Indexed: 12/17/2022]
Abstract
This review elaborates the idea that organ regeneration derives from specific evolutionary histories of vertebrates. Regenerative ability depends on genomic regulation of genes specific to the life-cycles that have differentially evolved in anamniotes and amniotes. In aquatic environments, where fish and amphibians live, one or multiple metamorphic transitions occur before the adult stage is reached. Each transition involves the destruction and remodeling of larval organs that are replaced with adult organs. After organ injury or loss in adult anamniotes, regeneration uses similar genes and developmental process than those operating during larval growth and metamorphosis. Therefore, the broad presence of regenerative capability across anamniotes is possible because generating new organs is included in their life history at metamorphic stages. Soft hyaluronate-rich regenerative blastemas grow in submersed or in hydrated environments, that is, essential conditions for regeneration, like during development. In adult anamniotes, the ability to regenerate different organs decreases in comparison to larval stages and becomes limited during aging. Comparisons of genes activated during metamorphosis and regeneration in anamniotes identify key genes unique to these processes, and include thyroid, wnt and non-coding RNAs developmental pathways. In the terrestrial environment, some genes or developmental pathways for metamorphic transitions were lost during amniote evolution, determining loss of regeneration. Among amniotes, the formation of soft and hydrated blastemas only occurs in lizards, a morphogenetic process that evolved favoring their survival through tail autotomy, leading to a massive although imperfect regeneration of the tail. Deciphering genes activity during lizard tail regeneration would address future attempts to recreate in other amniotes regenerative blastemas that grow into variably completed organs.
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18
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Pende M, Vadiwala K, Schmidbaur H, Stockinger AW, Murawala P, Saghafi S, Dekens MPS, Becker K, Revilla-i-Domingo R, Papadopoulos SC, Zurl M, Pasierbek P, Simakov O, Tanaka EM, Raible F, Dodt HU. A versatile depigmentation, clearing, and labeling method for exploring nervous system diversity. SCIENCE ADVANCES 2020; 6:eaba0365. [PMID: 32523996 PMCID: PMC7259959 DOI: 10.1126/sciadv.aba0365] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Tissue clearing combined with deep imaging has emerged as a powerful alternative to classical histological techniques. Whereas current techniques have been optimized for imaging selected nonpigmented organs such as the mammalian brain, natural pigmentation remains challenging for most other biological specimens of larger volume. We have developed a fast DEpigmEntation-Plus-Clearing method (DEEP-Clear) that is easily incorporated in existing workflows and combines whole system labeling with a spectrum of detection techniques, ranging from immunohistochemistry to RNA in situ hybridization, labeling of proliferative cells (EdU labeling) and visualization of transgenic markers. With light-sheet imaging of whole animals and detailed confocal studies on pigmented organs, we provide unprecedented insight into eyes, whole nervous systems, and subcellular structures in animal models ranging from worms and squids to axolotls and zebrafish. DEEP-Clear thus paves the way for the exploration of species-rich clades and developmental stages that are largely inaccessible by regular imaging approaches.
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Affiliation(s)
- Marko Pende
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Karim Vadiwala
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hannah Schmidbaur
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Alexander W. Stockinger
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Prayag Murawala
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Marcus P. S. Dekens
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
| | - Roger Revilla-i-Domingo
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Sofia-Christina Papadopoulos
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
| | - Martin Zurl
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Pawel Pasierbek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Oleg Simakov
- Department of Neuroscience and Development, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Elly M. Tanaka
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Florian Raible
- Max Perutz Labs and Research Platform “Rhythms of Life”, University of Vienna, Vienna BioCenter, Dr. Bohr-Gasse 9/4, 1030 Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, building CH, 1040 Vienna, Austria
- Section for Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria
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19
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Shrestha R, Lieberth J, Tillman S, Natalizio J, Bloomekatz J. Using Zebrafish to Analyze the Genetic and Environmental Etiologies of Congenital Heart Defects. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1236:189-223. [PMID: 32304074 DOI: 10.1007/978-981-15-2389-2_8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Congenital heart defects (CHDs) are among the most common human birth defects. However, the etiology of a large proportion of CHDs remains undefined. Studies identifying the molecular and cellular mechanisms that underlie cardiac development have been critical to elucidating the origin of CHDs. Building upon this knowledge to understand the pathogenesis of CHDs requires examining how genetic or environmental stress changes normal cardiac development. Due to strong molecular conservation to humans and unique technical advantages, studies using zebrafish have elucidated both fundamental principles of cardiac development and have been used to create cardiac disease models. In this chapter we examine the unique toolset available to zebrafish researchers and how those tools are used to interrogate the genetic and environmental contributions to CHDs.
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Affiliation(s)
- Rabina Shrestha
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Jaret Lieberth
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Savanna Tillman
- Department of Biology, University of Mississippi, Oxford, MS, USA
| | - Joseph Natalizio
- Department of Biology, University of Mississippi, Oxford, MS, USA
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20
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Pei W, Xu L, Chen Z, Slevin CC, Pettie KP, Wincovitch S, Burgess SM. A subset of SMN complex members have a specific role in tissue regeneration via ERBB pathway-mediated proliferation. NPJ Regen Med 2020; 5:6. [PMID: 32218991 PMCID: PMC7096462 DOI: 10.1038/s41536-020-0089-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022] Open
Abstract
Spinal muscular atrophy (SMA) is the most common genetic disease in children. SMA is generally caused by mutations in the gene SMN1. The survival of motor neurons (SMN) complex consists of SMN1, Gemins (2-8), and Strap/Unrip. We previously demonstrated smn1 and gemin5 inhibited tissue regeneration in zebrafish. Here we investigated each individual SMN complex member and identified gemin3 as another regeneration-essential gene. These three genes are likely pan-regenerative, since they affect the regeneration of hair cells, liver, and caudal fin. RNA-Seq analysis reveals that smn1, gemin3, and gemin5 are linked to a common set of genetic pathways, including the tp53 and ErbB pathways. Additional studies indicated all three genes facilitate regeneration by inhibiting the ErbB pathway, thereby allowing cell proliferation in the injured neuromasts. This study provides a new understanding of the SMN complex and a potential etiology for SMA and potentially other rare unidentified genetic diseases with similar symptoms.
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Affiliation(s)
- Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Lisha Xu
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Claire C. Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Kade P. Pettie
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Stephen Wincovitch
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, Bethesda, MD 20892 USA
| | - Shawn M. Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD 20892 USA
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21
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Chromatin dynamics in regeneration epithelia: Lessons from Drosophila imaginal discs. Semin Cell Dev Biol 2020; 97:55-62. [DOI: 10.1016/j.semcdb.2019.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 12/21/2022]
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22
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Rodriguez AM, Kang J. Regeneration enhancers: Starting a journey to unravel regulatory events in tissue regeneration. Semin Cell Dev Biol 2020; 97:47-54. [PMID: 30953740 PMCID: PMC6783330 DOI: 10.1016/j.semcdb.2019.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/19/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022]
Abstract
Regeneration, an ability to replace lost body parts, is widespread across animal species. While mammals poorly regenerate most tissues, teleost fish and urodele amphibians possess remarkable regenerative capacity. Earlier work demonstrated that genes driving regeneration are evolutionarily conserved, indicating that a key factor in diverse tissue regeneration is not the presence or absence of regeneration-driving genes but the mechanisms controlling activation of these genes after injury. Thus, understanding the regulatory events of tissue regeneration could provide the means for unlocking latent capacities for tissue regeneration. After injury, cells undergo extensive epigenetic changes to establish new transcriptional programs for tissue regeneration. Gene transcription in eukaryotes is a complicated process that requires specific interactions between trans-acting regulators and cis-regulatory DNA elements. Among cis-regulatory elements, enhancers are essential to control precise gene expression. Recently, multiple regeneration/injury-associated enhancers have been identified in several model organisms. In this review, we highlight recently discovered regeneration/injury enhancers and their specific characteristics. We also discuss how abnormal regulation of regeneration enhancers influences animal development and physiology. Investigation of regeneration enhancers potentially allows us to begin understanding the fundamental biology of tissue regeneration and inspires new solutions for manipulating regenerative ability.
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Affiliation(s)
- Anjelica M Rodriguez
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA
| | - Junsu Kang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin - Madison, Madison, WI, 53705, USA.
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23
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Abstract
Regeneration is a remarkable phenomenon that has been the subject of awe and bafflement for hundreds of years. Although regeneration competence is found in highly divergent organisms throughout the animal kingdom, recent advances in tools used for molecular and genomic characterization have uncovered common genes, molecular mechanisms, and genomic features in regenerating animals. In this review we focus on what is known about how genome regulation modulates cellular potency during regeneration. We discuss this regulation in the context of complex tissue regeneration in animals, from Hydra to humans, with reference to ex vivo-cultured cell models of pluripotency when appropriate. We emphasize the importance of a detailed molecular understanding of both the mechanisms that regulate genomic output and the functional assays that assess the biological relevance of such molecular characterizations.
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Affiliation(s)
- Elizabeth M Duncan
- Department of Biology, University of Kentucky, Lexington, Kentucky 40506, USA
| | - Alejandro Sánchez Alvarado
- Howard Hughes Medical Institute, Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;
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24
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Cigliola V, Ghila L, Chera S, Herrera PL. Tissue repair brakes: A common paradigm in the biology of regeneration. Stem Cells 2019; 38:330-339. [PMID: 31722129 DOI: 10.1002/stem.3118] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 10/09/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022]
Abstract
To date, most attention on tissue regeneration has focused on the exploration of positive cues promoting or allowing the engagement of natural cellular restoration upon injury. In contrast, the signals fostering cell identity maintenance in the vertebrate body have been poorly investigated; yet they are crucial, for their counteraction could become a powerful method to induce and modulate regeneration. Here we review the mechanisms inhibiting pro-regenerative spontaneous adaptive cell responses in different model organisms and organs. The pharmacological or genetic/epigenetic modulation of such regenerative brakes could release a dormant but innate adaptive competence of certain cell types and therefore boost tissue regeneration in different situations.
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Affiliation(s)
- Valentina Cigliola
- Department of Cell Biology, Regeneration Next, Duke University Medical Center, Durham, North Carolina
| | - Luiza Ghila
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Simona Chera
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Pedro L Herrera
- Department of Genetic Medicine & Development, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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25
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Genetic Reprogramming of Positional Memory in a Regenerating Appendage. Curr Biol 2019; 29:4193-4207.e4. [PMID: 31786062 DOI: 10.1016/j.cub.2019.10.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/01/2019] [Accepted: 10/21/2019] [Indexed: 12/31/2022]
Abstract
Certain vertebrates such as salamanders and zebrafish are able to regenerate complex tissues (e.g., limbs and fins) with remarkable fidelity. However, how positional information of the missing structure is recalled by appendage stump cells has puzzled researchers for centuries. Here, we report that sizing information for adult zebrafish tailfins is encoded within proliferating blastema cells during a critical period of regeneration. Using a chemical mutagenesis screen, we identified a temperature-sensitive allele of the gene encoding DNA polymerase alpha subunit 2 (pola2) that disrupts fin regeneration in zebrafish. Temperature shift assays revealed a 48-h window of regeneration, during which positional identities could be disrupted in pola2 mutants, leading to regeneration of miniaturized appendages. These fins retained memory of the new size in subsequent rounds of amputation and regeneration. Similar effects were observed upon transient genetic or pharmacological disruption of progenitor cell proliferation after plucking of zebrafish scales or head or tail amputation in amphioxus and annelids. Our results provide evidence that positional information in regenerating tissues is not hardwired but malleable, based on regulatory mechanisms that appear to be evolutionarily conserved across distantly related phyla.
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26
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Akhtar RW, Liu Z, Wang D, Ba H, Shah SAH, Li C. Identification of proteins that mediate the role of androgens in antler regeneration using label free proteomics in sika deer (Cervus nippon). Gen Comp Endocrinol 2019; 283:113235. [PMID: 31369730 DOI: 10.1016/j.ygcen.2019.113235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 07/21/2019] [Accepted: 07/28/2019] [Indexed: 01/04/2023]
Abstract
Deer antlers offer a unique model to study organ regeneration in mammals. Antler regeneration relies on the pedicle periosteum (PP) cells and is triggered by a decrease in circulating testosterone (T). The molecular mechanism for antler regeneration is however, unclear. Label-free liquid chromatography-mass spectrometry (LC-MS/MS) was used to identify differentially-expressed proteins (DEPs) in the regeneration-potentiated PP (under low T environment) over the non-regeneration-potentiated PP (under high T environment). Out of total 273 DEPs, 189 were significantly up-regulated and 84 were down-regulated from these comparisons: after castration vs before castration, natural T vs before castration, and exogenous T vs before castration. We focused on the analysis only of those DEPs that were present in fully permissive environment to antler regeneration (low T). Nine transduction pathways were identified through the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, including the estrogen signaling pathway. A total of 639 gene ontology terms were found to be significantly enriched in regeneration-potentiated PP (low T) from the DEPs. Reliability of the label free LC-MS/MS was determined by qRT-PCR to estimate the expression level of selected genes. The results suggest that up-regulated heat shock proteins (HSP90AB1, HSP90B1), peptidyl-prolyl cis-trans isomerase 4 (FKBP4), mitogen-activated protein kinase 3 (MAPK3) and calreticulin (CALR) and down-regulated SHC-transforming protein 1 (SHC1), heat shock protein family A member 1A (HSPA1A) and proto-oncogene tyrosine-protein kinase (SRC) may be associated directly or indirectly with antler regeneration. Further studies are required to investigate the roles of these proteins in regeneration using appropriate in vivo models.
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Affiliation(s)
- Rana Waseem Akhtar
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Zhen Liu
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Datao Wang
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China.
| | - Hengxing Ba
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun 130112, China.
| | - Syed Aftab Hussain Shah
- Pakistan Scientific & Technological Information Centre (PASTIC), Quaid-i-Azam University Campus, Islamabad, Pakistan
| | - Chunyi Li
- Institute of Special Wild Economic Animals and Plants, Chinese Academy of Agricultural Sciences, Changchun 130112, China; State Key Laboratory for Molecular Biology of Special Economic Animals, Changchun 130112, China; Changchun Sci-Tech University, Changchun, China.
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27
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Aztekin C, Hiscock TW, Marioni JC, Gurdon JB, Simons BD, Jullien J. Identification of a regeneration-organizing cell in the Xenopus tail. Science 2019; 364:653-658. [PMID: 31097661 PMCID: PMC6986927 DOI: 10.1126/science.aav9996] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/17/2019] [Indexed: 12/17/2022]
Abstract
Unlike mammals, Xenopus laevis tadpoles have a high regenerative potential. To characterize this regenerative response, we performed single-cell RNA sequencing after tail amputation. By comparing naturally occurring regeneration-competent and -incompetent tadpoles, we identified a previously unrecognized cell type, which we term the regeneration-organizing cell (ROC). ROCs are present in the epidermis during normal tail development and specifically relocalize to the amputation plane of regeneration-competent tadpoles, forming the wound epidermis. Genetic ablation or manual removal of ROCs blocks regeneration, whereas transplantation of ROC-containing grafts induces ectopic outgrowths in early embryos. Transcriptional profiling revealed that ROCs secrete ligands associated with key regenerative pathways, signaling to progenitors to reconstitute lost tissue. These findings reveal the cellular mechanism through which ROCs form the wound epidermis and ensure successful regeneration.
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Affiliation(s)
- C Aztekin
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - T W Hiscock
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - J C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J B Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - B D Simons
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Applied Mathematics and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
- Wellcome Trust Centre for Stem Cell Research, University of Cambridge, Cambridge, UK
| | - J Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK.
- Department of Zoology, University of Cambridge, Cambridge, UK
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28
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Abstract
In this review, Leach and Morrisey focus on lung regeneration to explore the importance of facultative regeneration controlled by functional and differentiated cell lineages as well as how they are positioned and regulated by distinct tissue niches. Tissue regeneration involves various types of cellular and molecular responses depending on the type of tissue and the injury or disease that is inflicted. While many tissues contain dedicated stem/progenitor cell lineages, many others contain cells that, during homeostasis, are considered physiologically functional and fully differentiated but, after injury or in disease states, exhibit stem/progenitor-like activity. Recent identification of subsets of defined cell types as facultative stem/progenitor cells has led to a re-examination of how certain tissues respond to injury to mount a regenerative response. In this review, we focus on lung regeneration to explore the importance of facultative regeneration controlled by functional and differentiated cell lineages as well as how they are positioned and regulated by distinct tissue niches. Additionally, we discuss the molecular signals to which cells respond in their differentiated state during homeostasis and those signals that promote effective regeneration of damaged or lost cells and structures after injury.
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Affiliation(s)
- John P Leach
- Department of Medicine, Department of Cell and Developmental Biology, Penn Center for Pulmonary Biology, Penn Cardiovascular Institute, Penn Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Edward E Morrisey
- Department of Medicine, Department of Cell and Developmental Biology, Penn Center for Pulmonary Biology, Penn Cardiovascular Institute, Penn Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
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29
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Vizcaya-Molina E, Klein CC, Serras F, Mishra RK, Guigó R, Corominas M. Damage-responsive elements in Drosophila regeneration. Genome Res 2018; 28:1852-1866. [PMID: 30459214 PMCID: PMC6280756 DOI: 10.1101/gr.233098.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/10/2018] [Indexed: 12/21/2022]
Abstract
One of the most important questions in regenerative biology is to unveil how and when genes change expression and trigger regeneration programs. The resetting of gene expression patterns during response to injury is governed by coordinated actions of genomic regions that control the activity of multiple sequence-specific DNA binding proteins. Using genome-wide approaches to interrogate chromatin function, we here identify the elements that regulate tissue recovery in Drosophila imaginal discs, which show a high regenerative capacity after genetically induced cell death. Our findings indicate there is global coregulation of gene expression as well as a regeneration program driven by different types of regulatory elements. Novel enhancers acting exclusively within damaged tissue cooperate with enhancers co-opted from other tissues and other developmental stages, as well as with endogenous enhancers that show increased activity after injury. Together, these enhancers host binding sites for regulatory proteins that include a core set of conserved transcription factors that control regeneration across metazoans.
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Affiliation(s)
- Elena Vizcaya-Molina
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
| | - Cecilia C Klein
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain
| | - Florenci Serras
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
| | - Rakesh K Mishra
- The Centre for Cellular and Molecular Biology (CCMB), Hyderabad 500007, India
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Catalonia, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08003, Catalonia, Spain
| | - Montserrat Corominas
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia and Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona 08028, Catalonia, Spain
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30
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King BL, Rosenstein MC, Smith AM, Dykeman CA, Smith GA, Yin VP. RegenDbase: a comparative database of noncoding RNA regulation of tissue regeneration circuits across multiple taxa. NPJ Regen Med 2018; 3:10. [PMID: 29872545 PMCID: PMC5973935 DOI: 10.1038/s41536-018-0049-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 12/16/2022] Open
Abstract
Regeneration is an endogenous process of tissue repair that culminates in complete restoration of tissue and organ function. While regenerative capacity in mammals is limited to select tissues, lower vertebrates like zebrafish and salamanders are endowed with the capacity to regenerate entire limbs and most adult tissues, including heart muscle. Numerous profiling studies have been conducted using these research models in an effort to identify the genetic circuits that accompany tissue regeneration. Most of these studies, however, are confined to an individual injury model and/or research organism and focused primarily on protein encoding transcripts. Here we describe RegenDbase, a new database with the functionality to compare and contrast gene regulatory pathways within and across tissues and research models. RegenDbase combines pipelines that integrate analysis of noncoding RNAs in combination with protein encoding transcripts. We created RegenDbase with a newly generated comprehensive dataset for adult zebrafish heart regeneration combined with existing microarray and RNA-sequencing studies on multiple injured tissues. In this current release, we detail microRNA-mRNA regulatory circuits and the biological processes these interactions control during the early stages of heart regeneration. Moreover, we identify known and putative novel lncRNAs and identify their potential target genes based on proximity searches. We postulate that these candidate factors underscore robust regenerative capacity in lower vertebrates. RegenDbase provides a systems-level analysis of tissue regeneration genetic circuits across injury and animal models and addresses the growing need to understand how noncoding RNAs influence these changes in gene expression.
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Affiliation(s)
- Benjamin L. King
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
| | - Michael C. Rosenstein
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Present Address: RockStep Solutions, Portland, ME 04101 USA
| | - Ashley M. Smith
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Christina A. Dykeman
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
| | - Grace A. Smith
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469 USA
- University of Maine Honors College, University of Maine, Orono, ME 04469 USA
| | - Viravuth P. Yin
- Kathryn Davis Center for Regenerative Biology and Medicine, Mount Desert Island Biological Laboratory, Salisbury Cove, ME 04672 USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME 04469 USA
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31
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Affiliation(s)
- Karen Echeverri
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, USA.
| | - Ricardo M Zayas
- Department of Biology, San Diego State University, San Diego, CA, USA.
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32
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Gordon T, Shenkar N. Solitary Ascidians as Model Organisms in Regenerative Biology Studies. Results Probl Cell Differ 2018; 65:321-336. [PMID: 30083926 DOI: 10.1007/978-3-319-92486-1_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Regeneration, the process of replacing lost or damaged body parts, has long captured human imagination and is a key feature among all animal phyla. Due to their close phylogenetic relationship to vertebrates and their high regenerative abilities, ascidians (Chordata, Ascidiacea) are often used as models to shed light on the cellular and genetic process involved in tissue regeneration. Surprisingly, ascidian regeneration studies are based on only a few model species. In this chapter, we point out the important potential of solitary ascidians in regenerative and stem cell studies. We review recent studies of regeneration among solitary ascidians and discuss the cellular mechanism of tissue regeneration and the possible involvement of circulating cells in these processes. New data regarding the relationship between age and regeneration abilities of the solitary ascidian Polycarpa mytiligera (Stolidobranchia, Styelidae) are presented. The unique regeneration abilities found in P. mytiligera following evisceration of its digestive system and following amputation of its neural complex and siphon-associated structures and nerves imply on its potential to serve as a novel model system for understanding tissue regeneration.
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Affiliation(s)
- Tal Gordon
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
| | - Noa Shenkar
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,The Steinhardt Museum of Natural History, Israel National Center for Biodiversity Studies, Tel-Aviv University, Tel-Aviv, Israel
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