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Cui G, Dong K, Zhou JY, Li S, Wu Y, Han Q, Yao B, Shen Q, Zhao YL, Yang Y, Cai J, Zhang S, Yang YG. Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration. Nat Commun 2023; 14:3205. [PMID: 37268637 DOI: 10.1038/s41467-023-39016-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 05/25/2023] [Indexed: 06/04/2023] Open
Abstract
Whole-body regeneration of planarians is a natural wonder but how it occurs remains elusive. It requires coordinated responses from each cell in the remaining tissue with spatial awareness to regenerate new cells and missing body parts. While previous studies identified new genes essential to regeneration, a more efficient screening approach that can identify regeneration-associated genes in the spatial context is needed. Here, we present a comprehensive three-dimensional spatiotemporal transcriptomic landscape of planarian regeneration. We describe a pluripotent neoblast subtype, and show that depletion of its marker gene makes planarians more susceptible to sub-lethal radiation. Furthermore, we identified spatial gene expression modules essential for tissue development. Functional analysis of hub genes in spatial modules, such as plk1, shows their important roles in regeneration. Our three-dimensional transcriptomic atlas provides a powerful tool for deciphering regeneration and identifying homeostasis-related genes, and provides a publicly available online spatiotemporal analysis resource for planarian regeneration research.
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Affiliation(s)
- Guanshen Cui
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Kangning Dong
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jia-Yi Zhou
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
| | - Shang Li
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Wu
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Qinghua Han
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bofei Yao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
| | - Qunlun Shen
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Liang Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- China National Center for Bioinformation, Beijing, 100101, China
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun Cai
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Shihua Zhang
- NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
| | - Yun-Gui Yang
- CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, College of Future Technology, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- China National Center for Bioinformation, Beijing, 100101, China.
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, China.
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2
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Hjeij R, Aprea I, Poeta M, Nöthe-Menchen T, Bracht D, Raidt J, Honecker BI, Dougherty GW, Olbrich H, Schwartz O, Keller U, Nüsse H, Diderich KEM, Vogelberg C, Santamaria F, Omran H. Pathogenic variants in CLXN encoding the outer dynein arm docking-associated calcium-binding protein calaxin cause primary ciliary dyskinesia. Genet Med 2023; 25:100798. [PMID: 36727596 DOI: 10.1016/j.gim.2023.100798] [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: 10/20/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Primary ciliary dyskinesia (PCD) is a heterogeneous disorder that includes respiratory symptoms, laterality defects, and infertility caused by dysfunction of motile cilia. Most PCD-causing variants result in abnormal outer dynein arms (ODAs), which provide the generative force for respiratory ciliary beating and proper mucociliary clearance. METHODS In addition to studies in mouse and planaria, clinical exome sequencing and functional analyses in human were performed. RESULTS In this study, we identified homozygous pathogenic variants in CLXN (EFCAB1/ODAD5) in 3 individuals with laterality defects and respiratory symptoms. Consistently, we found that Clxn is expressed in mice left-right organizer. Transmission electron microscopy depicted ODA defects in distal ciliary axonemes. Immunofluorescence microscopy revealed absence of CLXN from the ciliary axonemes, absence of the ODA components DNAH5, DNAI1, and DNAI2 from the distal axonemes, and mislocalization or absence of DNAH9. In addition, CLXN was undetectable in ciliary axonemes of individuals with defects in the ODA-docking machinery: ODAD1, ODAD2, ODAD3, and ODAD4. Furthermore, SMED-EFCAB1-deficient planaria displayed ciliary dysmotility. CONCLUSION Our results revealed that pathogenic variants in CLXN cause PCD with defects in the assembly of distal ODAs in the respiratory cilia. CLXN should be referred to as ODA-docking complex-associated protein ODAD5.
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Affiliation(s)
- Rim Hjeij
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Isabella Aprea
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Marco Poeta
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Tabea Nöthe-Menchen
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Diana Bracht
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Johanna Raidt
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Barbara I Honecker
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Gerard W Dougherty
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Heike Olbrich
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Oliver Schwartz
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany
| | - Ulrike Keller
- Institute of Medical Physics and Biophysics, University of Muenster, Muenster, Germany
| | - Harald Nüsse
- Institute of Medical Physics and Biophysics, University of Muenster, Muenster, Germany
| | | | - Christian Vogelberg
- Pediatric Department, University Hospital Carl Gustav Carus Dresden, Technical University Dresden, Dresden, Germany
| | - Francesca Santamaria
- Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Heymut Omran
- Department of General Pediatrics, University Hospital Muenster, Muenster, Germany.
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Guo Y, Sun Y, Ma M, Huang Y, Zhang S, Tian Q. Djsnon, a downstream gene of Djfoxk1, is required for the regeneration of the planarian central nervous system. Biochem Biophys Res Commun 2023; 643:8-15. [PMID: 36584589 DOI: 10.1016/j.bbrc.2022.12.074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
Regulators of adult neurogenesis are crucial targets for neuronal repair. Freshwater planarians are ideal model systems for studying neuronal regeneration as they can regenerate their entire central nervous system (CNS) using pluripotent adult stem cells. Here, we identified Djfoxk1 in planarian Dugesia japonica to be required for planarian CNS regeneration. Knockdown of Djfoxk1 inhibits the regeneration of the cephalic ganglia, resulting in the failure of eye regeneration. By RNAi screening of Djfoxk1 downstream genes, we identified Djsnon as another regulator of planarian neuronal regeneration. Inhibition of Djsnon with RNA interference (RNAi) results in similar phenotypes caused by Djfoxk1 RNAi without affecting cell proliferation and wound healing. Our findings show that Djsnon as a downstream gene of Djfoxk1 regulates the regeneration of the planarian CNS.
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Affiliation(s)
- Yajun Guo
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yujia Sun
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Mengwen Ma
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yongding Huang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shoutao Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China; Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China.
| | - Qingnan Tian
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China.
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4
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Wnt/β-catenin signalling is required for pole-specific chromatin remodeling during planarian regeneration. Nat Commun 2023; 14:298. [PMID: 36653403 PMCID: PMC9849279 DOI: 10.1038/s41467-023-35937-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
For successful regeneration, the identity of the missing tissue must be specified according to the pre-existing tissue. Planarians are ideal for the study of the mechanisms underlying this process; the same field of cells can regrow a head or a tail according to the missing body part. After amputation, the differential activation of the Wnt/β-catenin signal specifies anterior versus posterior identity. Initially, both wnt1 and notum (Wnt inhibitor) are expressed in all wounds, but 48 hours later they are restricted to posterior or anterior facing wounds, respectively, by an unknown mechanism. Here we show that 12 hours after amputation, the chromatin accessibility of cells in the wound region changes according to the polarity of the pre-existing tissue in a Wnt/β-catenin-dependent manner. Genomic analyses suggest that homeobox transcription factors and chromatin-remodeling proteins are direct Wnt/β-catenin targets, which trigger the expression of posterior effectors. Finally, we identify FoxG as a wnt1 up-stream regulator, probably via binding to its first intron enhancer region.
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5
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Davidian D, LeGro M, Barghouth PG, Rojas S, Ziman B, Maciel EI, Ardell D, Escobar AL, Oviedo NJ. Restoration of DNA integrity and cell cycle by electric stimulation in planarian tissues damaged by ionizing radiation. J Cell Sci 2022; 135:274829. [PMID: 35322853 PMCID: PMC9264365 DOI: 10.1242/jcs.259304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 03/05/2022] [Indexed: 10/18/2022] Open
Abstract
Exposure to high levels of ionizing γ-radiation leads to irreversible DNA damage and cell death. Here, we establish that exogenous application of electric stimulation enables cellular plasticity to reestablish stem cell activity in tissues damaged by ionizing radiation. We show that sub-threshold direct current stimulation (DCS) rapidly restores pluripotent stem cell populations previously eliminated by lethally γ-irradiated tissues of the planarian flatworm Schmidtea mediterranea. Our findings reveal that DCS enhances DNA repair, transcriptional activity, and cell cycle entry in post-mitotic cells. These responses involve rapid increases in cytosolic [Ca2+] through the activation of L-type Cav channels and intracellular Ca2+ stores leading to the activation of immediate early genes and ectopic expression of stem cell markers in postmitotic cells. Overall, we show the potential of electric current stimulation to reverse the damaging effects of high dose γ-radiation in adult tissues. Furthermore, our results provide mechanistic insights describing how electric stimulation effectively translates into molecular responses capable of regulating fundamental cellular functions without the need for genetic or pharmacological intervention.
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Affiliation(s)
- Devon Davidian
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Melanie LeGro
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Paul G Barghouth
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Salvador Rojas
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Benjamin Ziman
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - Eli Isael Maciel
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Quantitative and Systems Biology Graduate Program, University of California, Merced, USA
| | - David Ardell
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Health Sciences Research Institute, University of California, Merced, USA
| | - Ariel L Escobar
- Department of Bioengineering, University of California, Merced, USA.,Health Sciences Research Institute, University of California, Merced, USA
| | - Néstor J Oviedo
- Department of Molecular & Cell Biology, University of California, Merced, USA.,Health Sciences Research Institute, University of California, Merced, USA
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6
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Coronel-Córdoba P, Molina MD, Cardona G, Fraguas S, Pascual-Carreras E, Saló E, Cebrià F, Adell T. FoxK1 is Required for Ectodermal Cell Differentiation During Planarian Regeneration. Front Cell Dev Biol 2022; 10:808045. [PMID: 35273960 PMCID: PMC8901602 DOI: 10.3389/fcell.2022.808045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Forkhead box (Fox) genes belong to the “winged helix” transcription factor superfamily. The function of some Fox genes is well known, such as the role of foxO in controlling metabolism and longevity and foxA in controlling differentiation of endodermal tissues. However, the role of some Fox factors is not yet well characterized. Such is the case of FoxK genes, which are mainly studied in mammals and have been implicated in diverse processes including cell proliferation, tissue differentiation and carcinogenesis. Planarians are free-living flatworms, whose importance in biomedical research lies in their regeneration capacity. Planarians possess a wide population of pluripotent adult stem cells, called neoblasts, which allow them to regenerate any body part after injury. In a recent study, we identified three foxK paralogs in the genome of Schmidtea mediterranea. In this study, we demonstrate that foxK1 inhibition prevents regeneration of the ectodermal tissues, including the nervous system and the epidermis. These results correlate with foxK1 expression in neoblasts and in neural progenitors. Although the triggering of wound genes expression, polarity reestablishment and proliferation was not affected after foxK1 silencing, the apoptotic response was decreased. Altogether, these results suggest that foxK1 would be required for differentiation and maintenance of ectodermal tissues.
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Affiliation(s)
- Pablo Coronel-Córdoba
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - M Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Gemma Cardona
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Susanna Fraguas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Eudald Pascual-Carreras
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Emili Saló
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Francesc Cebrià
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Teresa Adell
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
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7
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Rosa MT, Loreto ELS. Revisiting the regeneration of Stenostomum leucops (Catenulida, Platyhelminthes). INVERTEBR REPROD DEV 2022. [DOI: 10.1080/07924259.2021.1994475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Marcos T. Rosa
- Programa de Pós-Graduação em Biodiversidade Animal, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Elgion L. S. Loreto
- Department of Biochemistry and Molecular Biology, Universidade Federal de Santa Maria, Santa Maria, Brazil
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8
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Transcription Factors Active in the Anterior Blastema of Schmidtea mediterranea. Biomolecules 2021; 11:biom11121782. [PMID: 34944426 PMCID: PMC8698962 DOI: 10.3390/biom11121782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/28/2022] Open
Abstract
Regeneration, the restoration of body parts after injury, is quite widespread in the animal kingdom. Species from virtually all Phyla possess regenerative abilities. Human beings, however, are poor regenerators. Yet, the progress of knowledge and technology in the fields of bioengineering, stem cells, and regenerative biology have fostered major advancements in regenerative medical treatments, which aim to regenerate tissues and organs and restore function. Human induced pluripotent stem cells can differentiate into any cell type of the body; however, the structural and cellular complexity of the human tissues, together with the inability of our adult body to control pluripotency, require a better mechanistic understanding. Planarians, with their capacity to regenerate lost body parts thanks to the presence of adult pluripotent stem cells could help providing such an understanding. In this paper, we used a top-down approach to shortlist blastema transcription factors (TFs) active during anterior regeneration. We found 44 TFs—31 of which are novel in planarian—that are expressed in the regenerating blastema. We analyzed the function of half of them and found that they play a role in the regeneration of anterior structures, like the anterior organizer, the positional instruction muscle cells, the brain, the photoreceptor, the intestine. Our findings revealed a glimpse of the complexity of the transcriptional network governing anterior regeneration in planarians, confirming that this animal model is the perfect playground to study in vivo how pluripotency copes with adulthood.
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9
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Morris J, Bealer EJ, Souza IDS, Repmann L, Bonelli H, Stanzione JF, Staehle MM. Chemical Exposure-Induced Developmental Neurotoxicity in Head-Regenerating Schmidtea Mediterranea. Toxicol Sci 2021; 185:220-231. [PMID: 34791476 DOI: 10.1093/toxsci/kfab132] [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] [Indexed: 11/13/2022] Open
Abstract
The growing number of commercially-used chemicals that are under-evaluated for developmental neurotoxicity (DNT) combined with the difficulty in describing the etiology of exposure-related neurodevelopmental toxicity has created a reticent threat to human health. Current means of screening chemicals for DNT are limited to expensive, time-consuming, and labor-intensive traditional laboratory animal models. In this study, we hypothesize that exposed head regenerating planarian flatworms can effectively and efficiently categorize DNT in known developmental neurotoxins (ethanol and bisphenol A (BPA)). Planarian flatworms are an established alternative animal model for neurodevelopmental studies and have remarkable regenerative abilities allowing neurodevelopment to be induced via head resection. Here, we observed changes in photophobic behavior and central nervous system (CNS) morphology to evaluate the impact of exposure to low concentrations of ethanol, BPA, and BPA industry alternatives bisphenol F (BPF), and bisguaiacol (BG) on neurodevelopment. Our studies show that exposure to 1% v/v ethanol during regeneration induces a recoverable 48-hour delay in the development of proper CNS integrity, which aligns with behavioral assessments of cognitive ability. Exposure to BPA and its alternatives induced deviations to neurodevelopment in a range of severities, distinguished by suppressions, delays, or a combination of the two. These results suggest that quick and inexpensive behavioral assessments are a viable surrogate for tedious and costly immunostaining studies, equipping more utility and resolution to the planarian model for neurodevelopmental toxicity in the future of mass chemical screening. These studies demonstrate that behavioral phenotypes observed following chemical exposure are classifiable and also temporally correlated to the anatomical development of the central nervous system in planaria. This will facilitate and accelerate toxicological screening assays with this alternative animal model.
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Affiliation(s)
- J Morris
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ
| | - E J Bealer
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ
| | - I D S Souza
- Department of Chemical Engineering, Rowan University, Glassboro, NJ
| | - L Repmann
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ
| | - H Bonelli
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ
| | - J F Stanzione
- Department of Chemical Engineering, Rowan University, Glassboro, NJ
| | - M M Staehle
- Department of Biomedical Engineering, Rowan University, Glassboro, NJ
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10
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Tian Q, Sun Y, Gao T, Li J, Fang H, Zhang S. Djnedd4L Is Required for Head Regeneration by Regulating Stem Cell Maintenance in Planarians. Int J Mol Sci 2021; 22:ijms222111707. [PMID: 34769140 PMCID: PMC8583885 DOI: 10.3390/ijms222111707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/22/2021] [Accepted: 10/24/2021] [Indexed: 12/02/2022] Open
Abstract
SUMOylation and ubiquitylation are homologous processes catalyzed by homologous enzymes, and they are involved in nearly all aspects of eukaryotic biology. Planarians, which have the remarkable ability to regenerate their central nervous system (CNS), provide an excellent opportunity to investigate the molecular processes of CNS regeneration in vivo. In this study, we analyzed gene expression profiles during head regeneration with an RNA-seq-based screening approach and found that Djnedd4L and Djubc9 were required for head regeneration in planarians. RNA interference targeting of Djubc9 caused the phospho-H3 mitotic cells to decrease in quantity, or even become absent as a part of the Djubc9 RNAi phenotype, which also showed the collapse of the stem cell lineage along with the reduced expression of epidermal differentiation markers. Furthermore, we found that Djnedd4L RNAi induced increased cell division and promoted the premature differentiation during regeneration. Taken together, our findings show that Djubc9 and Djnedd4L are required for stem cell maintenance in the planarian Dugesia japonica, which helps to elucidate the role of SUMOylation and ubiquitylation in regulating the regeneration process.
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Affiliation(s)
- Qingnan Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Q.T.); (Y.S.); (T.G.); (J.L.)
| | - Yujia Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Q.T.); (Y.S.); (T.G.); (J.L.)
| | - Tingting Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Q.T.); (Y.S.); (T.G.); (J.L.)
| | - Jiaxin Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Q.T.); (Y.S.); (T.G.); (J.L.)
| | - Huimin Fang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Q.T.); (Y.S.); (T.G.); (J.L.)
- Correspondence: (H.F.); (S.Z.)
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China; (Q.T.); (Y.S.); (T.G.); (J.L.)
- Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou 450001, China
- Correspondence: (H.F.); (S.Z.)
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11
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Nowotarski SH, Davies EL, Robb SMC, Ross EJ, Matentzoglu N, Doddihal V, Mir M, McClain M, Sánchez Alvarado A. Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. Development 2021; 148:271068. [PMID: 34318308 PMCID: PMC8353266 DOI: 10.1242/dev.196097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 06/28/2021] [Indexed: 12/23/2022]
Abstract
As the planarian research community expands, the need for an interoperable data organization framework for tool building has become increasingly apparent. Such software would streamline data annotation and enhance cross-platform and cross-species searchability. We created the Planarian Anatomy Ontology (PLANA), an extendable relational framework of defined Schmidtea mediterranea (Smed) anatomical terms used in the field. At publication, PLANA contains over 850 terms describing Smed anatomy from subcellular to system levels across all life cycle stages, in intact animals and regenerating body fragments. Terms from other anatomy ontologies were imported into PLANA to promote interoperability and comparative anatomy studies. To demonstrate the utility of PLANA as a tool for data curation, we created resources for planarian embryogenesis, including a staging series and molecular fate-mapping atlas, and the Planarian Anatomy Gene Expression database, which allows retrieval of a variety of published transcript/gene expression data associated with PLANA terms. As an open-source tool built using FAIR (findable, accessible, interoperable, reproducible) principles, our strategy for continued curation and versioning of PLANA also provides a platform for community-led growth and evolution of this resource. Summary: Description of the construction of an anatomy ontology tool for planaria with examples of its potential use to curate and mine data across multiple experimental platforms.
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Affiliation(s)
- Stephanie H Nowotarski
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Erin L Davies
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Sofia M C Robb
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Eric J Ross
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicolas Matentzoglu
- European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Viraj Doddihal
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Mol Mir
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melainia McClain
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Alejandro Sánchez Alvarado
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
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12
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Bohr TE, Shiroor DA, Adler CE. Planarian stem cells sense the identity of the missing pharynx to launch its targeted regeneration. eLife 2021; 10:e68830. [PMID: 34156924 PMCID: PMC8219383 DOI: 10.7554/elife.68830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/22/2021] [Indexed: 12/25/2022] Open
Abstract
In order to regenerate tissues successfully, stem cells must detect injuries and restore missing cell types through largely unknown mechanisms. Planarian flatworms have an extensive stem cell population responsible for regenerating any organ after amputation. Here, we compare planarian stem cell responses to different injuries by either amputation of a single organ, the pharynx, or removal of tissues from other organs by decapitation. We find that planarian stem cells adopt distinct behaviors depending on what tissue is missing to target progenitor and tissue production towards missing tissues. Loss of non-pharyngeal tissues only increases non-pharyngeal progenitors, while pharynx removal selectively triggers division and expansion of pharynx progenitors. By pharmacologically inhibiting either mitosis or activation of the MAP kinase ERK, we identify a narrow window of time during which stem cell division and ERK signaling produces pharynx progenitors necessary for regeneration. These results indicate that planarian stem cells can tailor their output to match the regenerative needs of the animal.
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Affiliation(s)
- Tisha E Bohr
- Department of Molecular Medicine, Cornell University College of Veterinary MedicineIthacaUnited States
| | - Divya A Shiroor
- Department of Molecular Medicine, Cornell University College of Veterinary MedicineIthacaUnited States
| | - Carolyn E Adler
- Department of Molecular Medicine, Cornell University College of Veterinary MedicineIthacaUnited States
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13
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Fontenla S, Rinaldi G, Tort JF. Lost and Found: Piwi and Argonaute Pathways in Flatworms. Front Cell Infect Microbiol 2021; 11:653695. [PMID: 34123869 PMCID: PMC8191739 DOI: 10.3389/fcimb.2021.653695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
Platyhelminthes comprise one of the major phyla of invertebrate animals, inhabiting a wide range of ecosystems, and one of the most successful in adapting to parasitic life. Small non-coding RNAs have been implicated in regulating complex developmental transitions in model parasitic species. Notably, parasitic flatworms have lost Piwi RNA pathways but gained a novel Argonaute gene. Herein, we analyzed, contrasted and compared the conservation of small RNA pathways among several free-living species (a paraphyletic group traditionally known as ‘turbellarians’) and parasitic species (organized in the monophyletic clade Neodermata) to disentangle possible adaptations during the transition to parasitism. Our findings showed that complete miRNA and RNAi pathways are present in all analyzed free-living flatworms. Remarkably, whilst all ‘turbellarians’ have Piwi proteins, these were lost in parasitic Neodermantans. Moreover, two clusters of Piwi class Argonaute genes are present in all ‘turbellarians’. Interestingly, we identified a divergent Piwi class Argonaute in free living flatworms exclusively, which we named ‘Fliwi’. In addition, other key proteins of the Piwi pathways were conserved in ‘turbellarians’, while none of them were detected in Neodermatans. Besides Piwi and the canonical Argonaute proteins, a flatworm-specific class of Argonautes (FL-Ago) was identified in the analyzed species confirming its ancestrallity to all Platyhelminthes. Remarkably, this clade was expanded in parasitic Neodermatans, but not in free-living species. These phyla-specific Argonautes showed lower sequence conservation compared to other Argonaute proteins, suggesting that they might have been subjected to high evolutionary rates. However, key residues involved in the interaction with the small RNA and mRNA cleavage in the canonical Argonautes were more conserved in the FL-Agos than in the Piwi Argonautes. Whether this is related to specialized functions and adaptations to parasitism in Neodermatans remains unclear. In conclusion, differences detected in gene conservation, sequence and structure of the Argonaute family suggest tentative biological and evolutionary diversifications that are unique to Platyhelminthes. The remarkable divergencies in the small RNA pathways between free-living and parasitic flatworms indicate that they may have been involved in the adaptation to parasitism of Neodermatans.
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Affiliation(s)
- Santiago Fontenla
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
| | | | - Jose F Tort
- Departamento de Genética, Facultad de Medicina, Universidad de la República (UDELAR), Montevideo, Uruguay
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14
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Fraguas S, Cárcel S, Vivancos C, Molina MD, Ginés J, Mazariegos J, Sekaran T, Bartscherer K, Romero R, Cebrià F. CREB-binding protein (CBP) gene family regulates planarian survival and stem cell differentiation. Dev Biol 2021; 476:53-67. [PMID: 33774010 DOI: 10.1016/j.ydbio.2021.02.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 12/21/2022]
Abstract
In developmental biology, the regulation of stem cell plasticity and differentiation remains an open question. CBP(CREB-binding protein)/p300 is a conserved gene family that functions as a transcriptional co-activator and plays important roles in a wide range of cellular processes, including cell death, the DNA damage response, and tumorigenesis. The acetyl transferase activity of CBPs is particularly important, as histone and non-histone acetylation results in changes in chromatin architecture and protein activity that affect gene expression. Many studies have described the conserved functions of CBP/p300 in stem cell proliferation and differentiation. The planarian Schmidtea mediterranea is an excellent model for the in vivo study of the molecular mechanisms underlying stem cell differentiation during regeneration. However, how this process is regulated genetically and epigenetically is not well-understood yet. We identified 5 distinct Smed-cbp genes in S. mediterranea that show different expression patterns. Functional analyses revealed that Smed-cbp-2 appears to be essential for stem cell maintenance. On the other hand, the silencing of Smed-cbp-3 resulted in the growth of blastemas that were apparently normal, but remained largely unpigmented and undifferentiated. Smed-cbp-3 silencing also affected the differentiation of several cell lineages including neural, epidermal, digestive, and excretory cell types. Finally, we analysed the predicted interactomes of CBP-2 and CBP-3 as an initial step to better understand their functions in planarian stem cell biology. Our results indicate that planarian cbp genes play key roles in stem cell maintenance and differentiation.
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Affiliation(s)
- Susanna Fraguas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Spain
| | - Sheila Cárcel
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Coral Vivancos
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Ma Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Spain
| | - Jordi Ginés
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Judith Mazariegos
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | | | | | - Rafael Romero
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain
| | - Francesc Cebrià
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Spain; Institute of Biomedicine of the University of Barcelona (IBUB), Spain.
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15
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Tian Q, Sun Y, Gao T, Li J, Hao Z, Fang H, Zhang S. TBX2/3 is required for regeneration of dorsal-ventral and medial-lateral polarity in planarians. J Cell Biochem 2021; 122:731-738. [PMID: 33586232 DOI: 10.1002/jcb.29905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 11/24/2020] [Accepted: 01/21/2021] [Indexed: 12/24/2022]
Abstract
The molecular mechanisms responsible for axis establishment during non-embryonic processes remain elusive. The planarian flatworm is an ideal model organism to study body axis polarization and patterning in vivo. Here, we identified a homolog of the TBX2/3 in the planarian Dugesia japonica. RNA interference (RNAi) knockdown of TBX2/3 results in the ectopic formation of protrusions in the midline of the dorsal surface which shows an abnormal expression of midline and ventral cell markers. Additionally, the TBX2/3 RNAi animals also show the duplication of expression of the boundary marker at the lateral edge. Furthermore, TBX2/3 is expressed in muscle cells and co-expressed with bmp4. Inhibition of bone morphogenetic protein (BMP) signaling reduces the expression of TBX2/3 at the midline. These results suggest that TBX2/3 RNAi results in phenotypic characters caused by inhibition of the BMP signal, indicating that TBX2/3 is required for DV and ML patterning, and might be a downstream gene of BMP signaling.
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Affiliation(s)
- Qingnan Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yujia Sun
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Tingting Gao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaxin Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhitai Hao
- Department of Biochemistry and Molecular Pharmacology, School of Medicine, New York University, New York, USA
| | - Huimin Fang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shoutao Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China.,Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou, Henan, China
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16
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Maciel EI, Valle Arevalo A, Ziman B, Nobile CJ, Oviedo NJ. Epithelial Infection With Candida albicans Elicits a Multi-System Response in Planarians. Front Microbiol 2021; 11:629526. [PMID: 33519792 PMCID: PMC7840899 DOI: 10.3389/fmicb.2020.629526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Candida albicans is one of the most common fungal pathogens of humans. Prior work introduced the planarian Schmidtea mediterranea as a new model system to study the host response to fungal infection at the organismal level. In the current study, we analyzed host-pathogen changes that occurred in situ during early infection with C. albicans. We found that the transcription factor Bcr1 and its downstream adhesin Als3 are required for C. albicans to adhere to and colonize the planarian epithelial surface, and that adherence of C. albicans triggers a multi-system host response that is mediated by the Dectin signaling pathway. This infection response is characterized by two peaks of stem cell divisions and transcriptional changes in differentiated tissues including the nervous and the excretory systems. This response bears some resemblance to a wound-like response to physical injury; however, it takes place without visible tissue damage and it engages a distinct set of progenitor cells. Overall, we identified two C. albicans proteins that mediate epithelial infection of planarians and a comprehensive host response facilitated by diverse tissues to effectively clear the infection.
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Affiliation(s)
- Eli Isael Maciel
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, United States
| | - Ashley Valle Arevalo
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, United States
| | - Benjamin Ziman
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Quantitative and Systems Biology Graduate Program, University of California, Merced, Merced, CA, United States
| | - Clarissa J Nobile
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Health Sciences Research Institute, University of California, Merced, Merced, CA, United States
| | - Néstor J Oviedo
- Department of Molecular & Cell Biology, University of California, Merced, Merced, CA, United States.,Health Sciences Research Institute, University of California, Merced, Merced, CA, United States
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17
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Sal F, Prados J, Urcelay GP. Nicotine chronic tolerance development and withdrawal in the planaria (Schmidtea mediterranea). Pharmacol Biochem Behav 2020; 200:173075. [PMID: 33245983 DOI: 10.1016/j.pbb.2020.173075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/18/2020] [Accepted: 11/16/2020] [Indexed: 11/18/2022]
Abstract
Chronic nicotine exposure reduces sensitivity to the effects of nicotine, which then results in behavioural changes and tolerance development. In the planaria, a valuable first-stage preclinical model for addictive behaviour, acute nicotine administration has been shown to steadily alter the motility of the animals, a result that has been interpreted as evidence of tolerance and withdrawal effects; however, chronic exposure - typically regarded as a condition for the development of tolerance - and the role of the contextual cues have not been systematically assessed. The present study assessed the acute and chronic effects of nicotine on the motility of planarians (Schmidtea mediterranea). The animals in the experimental groups received long chronic exposure to nicotine (ten daily 30 min exposures); a control group was exposed to water in the same context but in the absence of the drug. The motility of the animals was closely monitored on every exposure. Following this phase, all the animals were subject to three different tests: in the presence of the exposure context (without the drug, Test 1); in the presence of nicotine in the exposure context (Test 2); and in the presence of the drug in a novel context (Test 3). Exposure to nicotine consistently reduced motility; the motility in the presence of nicotine increased with repeated exposures to the drug, an instance of tolerance development. Tolerance development was dependent on nicotinic receptor activation, because it was blocked by the co-administration of mecamylamine. However, this tolerance was found to be independent of the contextual cues where the effects of the drug had been experienced. The results are discussed by reference to the existent theories of tolerance development to drugs.
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Affiliation(s)
- Fatih Sal
- Department of Neuroscience, Psychology & Behaviour, University of Leicester, UK
| | - Jose Prados
- Department of Neuroscience, Psychology & Behaviour, University of Leicester, UK
| | - Gonzalo P Urcelay
- Department of Neuroscience, Psychology & Behaviour, University of Leicester, UK.
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18
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Ziman B, Barghouth PG, Maciel EI, Oviedo NJ. TRAF-like Proteins Regulate Cellular Survival in the Planarian Schmidtea mediterranea. iScience 2020; 23:101665. [PMID: 33134895 PMCID: PMC7586133 DOI: 10.1016/j.isci.2020.101665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022] Open
Abstract
Tissue homeostasis relies on the timely renewal of cells that have been damaged or have surpassed their biological age. Nonetheless, the underlying molecular mechanism coordinating tissue renewal is unknown. The planarian Schmidtea mediterranea harbors a large population of stem cells that continuously divide to support the restoration of tissues throughout the body. Here, we identify that TNF Receptor Associated Factors (TRAFs) play critical roles in cellular survival during tissue repair in S. mediterranea. Disruption with RNA-interference of TRAF signaling results in rapid morphological defects and lethality within 2 weeks. The TRAF phenotype is accompanied by an increased number of mitoses and cell death. Our results also reveal TRAF signaling is required for proper regeneration of the nervous system. Taken together, we find functional conservation of TRAF-like proteins in S. mediterranea as they act as crucial regulators of cellular survival during tissue homeostasis and regeneration.
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Affiliation(s)
- Benjamin Ziman
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Paul G. Barghouth
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Eli Isael Maciel
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Néstor J. Oviedo
- Department of Molecular and Cell Biology, University of California, Merced, CA 95343, USA
- Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
- Health Sciences Research Institute, University of California, Merced, CA 95343, USA
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19
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CFAP45 deficiency causes situs abnormalities and asthenospermia by disrupting an axonemal adenine nucleotide homeostasis module. Nat Commun 2020; 11:5520. [PMID: 33139725 PMCID: PMC7606486 DOI: 10.1038/s41467-020-19113-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 09/25/2020] [Indexed: 11/08/2022] Open
Abstract
Axonemal dynein ATPases direct ciliary and flagellar beating via adenosine triphosphate (ATP) hydrolysis. The modulatory effect of adenosine monophosphate (AMP) and adenosine diphosphate (ADP) on flagellar beating is not fully understood. Here, we describe a deficiency of cilia and flagella associated protein 45 (CFAP45) in humans and mice that presents a motile ciliopathy featuring situs inversus totalis and asthenospermia. CFAP45-deficient cilia and flagella show normal morphology and axonemal ultrastructure. Proteomic profiling links CFAP45 to an axonemal module including dynein ATPases and adenylate kinase as well as CFAP52, whose mutations cause a similar ciliopathy. CFAP45 binds AMP in vitro, consistent with structural modelling that identifies an AMP-binding interface between CFAP45 and AK8. Microtubule sliding of dyskinetic sperm from Cfap45−/− mice is rescued with the addition of either AMP or ADP with ATP, compared to ATP alone. We propose that CFAP45 supports mammalian ciliary and flagellar beating via an adenine nucleotide homeostasis module. The mechanism by which adenosine monophosphate modulates dynein ATPase-mediated ciliary and flagellar beating remains obscure. Here the authors identify an axonemal module including cilia and flagella associated protein 45 that supports adenine nucleotide homeostasis and underlies a human ciliopathy
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20
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Castillo-Lara S, Pascual-Carreras E, Abril JF. PlanExp: intuitive integration of complex RNA-seq datasets with planarian omics resources. Bioinformatics 2020; 36:1889-1895. [PMID: 31647529 DOI: 10.1093/bioinformatics/btz802] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 01/16/2023] Open
Abstract
MOTIVATION There is an increasing amount of transcriptomic and genomic data available for planarians with the advent of both traditional and single-cell RNA sequencing technologies. Therefore, exploring, visualizing and making sense of all these data in order to understand planarian regeneration and development can be challenging. RESULTS In this work, we present PlanExp, a web-application to explore and visualize gene expression data from different RNA-seq experiments (both traditional and single-cell RNA-seq) for the planaria Schmidtea mediterranea. PlanExp provides tools for creating different interactive plots, such as heatmaps, scatterplots, etc. and links them with the current sequence annotations both at the genome and the transcript level thanks to its integration with the PlanNET web application. PlanExp also provides a full gene/protein network editor, a prediction of genetic interactions from single-cell RNA-seq data, and a network expression mapper that will help researchers to close the gap between systems biology and planarian regeneration. AVAILABILITY AND IMPLEMENTATION PlanExp is freely available at https://compgen.bio.ub.edu/PlanNET/planexp. The source code is available at https://compgen.bio.ub.edu/PlanNET/downloads. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- S Castillo-Lara
- Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB); Universitat de Barcelona, Catalonia, Spain
| | - E Pascual-Carreras
- Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB); Universitat de Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Universitat de Barcelona, Catalonia, Spain
- Institut de Biomedicina de la Universitat de Barcelona (IBUB); Universitat de Barcelona, Catalonia, Spain
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21
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Molecular impact of launch related dynamic vibrations and static hypergravity in planarians. NPJ Microgravity 2020; 6:25. [PMID: 32964111 PMCID: PMC7478964 DOI: 10.1038/s41526-020-00115-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023] Open
Abstract
Although many examples of simulated and real microgravity demonstrating their profound effect on biological systems are described in literature, few reports deal with hypergravity and vibration effects, the levels of which are severely increased during the launch preceding the desired microgravity period. Here, we used planarians, flatworms that can regenerate any body part in a few days. Planarians are an ideal model to study the impact of launch-related hypergravity and vibration during a regenerative process in a "whole animal" context. Therefore, planarians were subjected to 8.5 minutes of 4 g hypergravity (i.e. a human-rated launch level) in the Large Diameter Centrifuge (LDC) and/or to vibrations (20-2000 Hz, 11.3 G rms) simulating the conditions of a standard rocket launch. The transcriptional levels of genes (erg-1, runt-1, fos, jnk, and yki) related with the early stress response were quantified through qPCR. The results show that early response genes are severely deregulated after static and dynamic loads but more so after a combined exposure of dynamic (vibration) and static (hypergravity) loads, more closely simulating real launch exposure profiles. Importantly, at least four days after the exposure, the transcriptional levels of those genes are still deregulated. Our results highlight the deep impact that short exposures to hypergravity and vibration have in organisms, and thus the implications that space flight launch could have. These phenomena should be taken into account when planning for well-controlled microgravity studies.
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22
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Arenas Gómez CM, Sabin KZ, Echeverri K. Wound healing across the animal kingdom: Crosstalk between the immune system and the extracellular matrix. Dev Dyn 2020; 249:834-846. [PMID: 32314465 PMCID: PMC7383677 DOI: 10.1002/dvdy.178] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 04/10/2020] [Accepted: 04/11/2020] [Indexed: 12/11/2022] Open
Abstract
Tissue regeneration is widespread in the animal kingdom. To date, key roles for different molecular and cellular programs in regeneration have been described, but the ultimate blueprint for this talent remains elusive. In animals capable of tissue regeneration, one of the most crucial stages is wound healing, whose main goal is to close the wound and prevent infection. In this stage, it is necessary to avoid scar formation to facilitate the activation of the immune system and remodeling of the extracellular matrix, key factors in promoting tissue regeneration. In this review, we will discuss the current state of knowledge regarding the role of the immune system and the interplay with the extracellular matrix to trigger a regenerative response.
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Affiliation(s)
- Claudia M. Arenas Gómez
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Keith Z. Sabin
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Karen Echeverri
- Eugene Bell Center for Regenerative Biology and Tissue Engineering, Marine Biological LaboratoryWoods HoleMassachusettsUSA
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23
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Shiroor DA, Bohr TE, Adler CE. Injury Delays Stem Cell Apoptosis after Radiation in Planarians. Curr Biol 2020; 30:2166-2174.e3. [PMID: 32386527 DOI: 10.1016/j.cub.2020.03.054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 02/17/2020] [Accepted: 03/20/2020] [Indexed: 12/31/2022]
Abstract
Stem cells are continuously exposed to multiple stresses, including radiation and tissue injury. As central drivers of tissue repair and regeneration, it is necessary to understand how their behavior is influenced by these stressors. Planarians have an abundant population of stem cells that are rapidly eliminated after radiation exposure via apoptosis. Low doses of radiation eliminate the majority of these stem cells, allowing a few to remain [1]. Here, we combine radiation with injury to define how stem cells respond to tissue damage. We find that a variety of injuries induced within a defined window of time surrounding radiation cause stem cells to outlast those in uninjured animals. Injury stimulates localized cell death adjacent to wounds [2], in the same regions where stem cells persist. This persistence occurs in the absence of proliferation. Instead, stem cells are retained near the wound due to delayed apoptosis, which we quantify by combining fluorescence-activated cell sorting (FACS) with annexin V staining. Pharmacological inhibition of the mitogen-activated protein (MAP) kinase extracellular signal-regulated kinase (ERK) prevents stem cell persistence after injury, implicating wound-induced ERK activity in this response. By combining radiation with injury, our work reveals a novel connection between dying cells and stem cells that remain. Furthermore, the ability to induce stem cell persistence after radiation provides a paradigm to study mechanisms that may contribute to unanticipated consequences of injury, such as tumorigenesis.
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Affiliation(s)
- Divya A Shiroor
- Department of Molecular Medicine, Cornell University of Veterinary Medicine, 930 Campus Road, Ithaca, NY 14853, USA
| | - Tisha E Bohr
- Department of Molecular Medicine, Cornell University of Veterinary Medicine, 930 Campus Road, Ithaca, NY 14853, USA
| | - Carolyn E Adler
- Department of Molecular Medicine, Cornell University of Veterinary Medicine, 930 Campus Road, Ithaca, NY 14853, USA.
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24
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Roy J, Cheung E, Bhatti J, Muneem A, Lobo D. Curation and annotation of planarian gene expression patterns with segmented reference morphologies. Bioinformatics 2020; 36:2881-2887. [DOI: 10.1093/bioinformatics/btaa023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/07/2019] [Accepted: 01/14/2020] [Indexed: 12/30/2022] Open
Abstract
Abstract
Motivation
Morphological and genetic spatial data from functional experiments based on genetic, surgical and pharmacological perturbations are being produced at an extraordinary pace in developmental and regenerative biology. However, our ability to extract knowledge from these large datasets are hindered due to the lack of formalization methods and tools able to unambiguously describe, centralize and interpret them. Formalizing spatial phenotypes and gene expression patterns is especially challenging in organisms with highly variable morphologies such as planarian worms, which due to their extraordinary regenerative capability can experimentally result in phenotypes with almost any combination of body regions or parts.
Results
Here, we present a computational methodology and mathematical formalism to encode and curate the morphological outcomes and gene expression patterns in planaria. Worm morphologies are encoded with mathematical graphs based on anatomical ontology terms to automatically generate reference morphologies. Gene expression patterns are registered to these standard reference morphologies, which can then be annotated automatically with anatomical ontology terms by analyzing the spatial expression patterns and their textual descriptions. This methodology enables the curation and annotation of complex experimental morphologies together with their gene expression patterns in a centralized standardized dataset, paving the way for the extraction of knowledge and reverse-engineering of the much sought-after mechanistic models in planaria and other regenerative organisms.
Availability and implementation
We implemented this methodology in a user-friendly graphical software tool, PlanGexQ, freely available together with the data in the manuscript at https://lobolab.umbc.edu/plangexq.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joy Roy
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Eric Cheung
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Junaid Bhatti
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Abraar Muneem
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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25
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Meddeb E, Charni M, Ben Abdallah R, Raboudi F, Fattouch S. A molecular study of Tunisian populations of Dugesia sicula (Plathelminthes, Tricladida) through an identification of a set of genes. C R Biol 2019; 342:291-298. [PMID: 31786144 DOI: 10.1016/j.crvi.2019.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 10/30/2019] [Indexed: 10/25/2022]
Abstract
Cell regeneration is a natural repair of different types of tissue after an injury or a lesion, and is associated with asexual reproduction in some animals such as planarians. Its understanding and improvement could have repercussions for tissue repair and regeneration as far as humans are concerned. In this context, we have proceeded to an essential step, which is the identification of the genes involved in planarian regeneration in the model species. Dugesia sicula Lepori (D. sicula) is distributed around the Mediterranean Sea, and this population is found in most of Tunisian dams. The collection of identified genes is already known in other species. DjFoxG, DjPC2, DjotxA, and Cathepsin-D were identified by the PCR technique and their expression was confirmed by RT-PCR and in situ hybridization. DjFoxG gene, the FoxG1 homolog, is expressed throughout the planarian body, abundantly on stem cells. Consecutively, we choose a central nervous system (CNS) marker; the prohormone convertase 2 (DjPC2) gene. DjotxA was observed in the brain and especially in the region surrounding the eyes (visual cells). The regenerative cells of the gut of D. sicula were scored by the Cathepsin-D gene expression, which belongs to the aspartyl protease family. We found significant results through RT-PCR and In Situ Hybridization (ISH) techniques, confirming the expression of DjFoxG, DjPC2, DjotxA and Cathepsin-D genes in our specimens.
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Affiliation(s)
- Emna Meddeb
- Laboratory of Food and Molecular Biochemistry, National Institute of Applied Sciences and Technology (INSAT), University of Carthage, Zone Urbaine Nord, 1080 Tunis, Tunisia; Faculty of Sciences of Bizerte, University of Carthage, Tunis, Tunisia.
| | - Mohamed Charni
- Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia; College of Sciences and Humanities of Dawadmi, Shaqra University, Shaqra, Kingdom of Saudi Arabia
| | - Rim Ben Abdallah
- Laboratory of Food and Molecular Biochemistry, National Institute of Applied Sciences and Technology (INSAT), University of Carthage, Zone Urbaine Nord, 1080 Tunis, Tunisia; Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Faten Raboudi
- ISAJC, Bir El Bey, University of Tunis, Tunis, Tunisia
| | - Sami Fattouch
- Laboratory of Food and Molecular Biochemistry, National Institute of Applied Sciences and Technology (INSAT), University of Carthage, Zone Urbaine Nord, 1080 Tunis, Tunisia
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26
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Mehta AS, Singh A. Insights into regeneration tool box: An animal model approach. Dev Biol 2019; 453:111-129. [PMID: 30986388 PMCID: PMC6684456 DOI: 10.1016/j.ydbio.2019.04.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
For ages, regeneration has intrigued countless biologists, clinicians, and biomedical engineers. In recent years, significant progress made in identification and characterization of a regeneration tool kit has helped the scientific community to understand the mechanism(s) involved in regeneration across animal kingdom. These mechanistic insights revealed that evolutionarily conserved pathways like Wnt, Notch, Hedgehog, BMP, and JAK/STAT are involved in regeneration. Furthermore, advancement in high throughput screening approaches like transcriptomic analysis followed by proteomic validations have discovered many novel genes, and regeneration specific enhancers that are specific to highly regenerative species like Hydra, Planaria, Newts, and Zebrafish. Since genetic machinery is highly conserved across the animal kingdom, it is possible to engineer these genes and regeneration specific enhancers in species with limited regeneration properties like Drosophila, and mammals. Since these models are highly versatile and genetically tractable, cross-species comparative studies can generate mechanistic insights in regeneration for animals with long gestation periods e.g. Newts. In addition, it will allow extrapolation of regenerative capabilities from highly regenerative species to animals with low regeneration potential, e.g. mammals. In future, these studies, along with advancement in tissue engineering applications, can have strong implications in the field of regenerative medicine and stem cell biology.
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Affiliation(s)
- Abijeet S Mehta
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA; Premedical Program, University of Dayton, Dayton, OH, 45469, USA; Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA; The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA; Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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27
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Ivankovic M, Haneckova R, Thommen A, Grohme MA, Vila-Farré M, Werner S, Rink JC. Model systems for regeneration: planarians. Development 2019; 146:146/17/dev167684. [PMID: 31511248 DOI: 10.1242/dev.167684] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Planarians are a group of flatworms. Some planarian species have remarkable regenerative abilities, which involve abundant pluripotent adult stem cells. This makes these worms a powerful model system for understanding the molecular and evolutionary underpinnings of regeneration. By providing a succinct overview of planarian taxonomy, anatomy, available tools and the molecular orchestration of regeneration, this Primer aims to showcase both the unique assets and the questions that can be addressed with this model system.
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Affiliation(s)
- Mario Ivankovic
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Radmila Haneckova
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Albert Thommen
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Markus A Grohme
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Miquel Vila-Farré
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany.,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
| | - Steffen Werner
- FOM Institute AMOLF, Department of Systems Biology, Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Jochen C Rink
- Max Planck Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany .,Department of Tissue Dynamics and Regeneration, Max Planck Institute for Biophysical Chemistry, am Fassberg 11, 37077 Göttingen, Germany
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28
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Tian Q, Zhao G, Sun Y, Yuan D, Guo Q, Zhang Y, Liu J, Zhang S. Exportin-1 is required for the maintenance of the planarian epidermal lineage. Int J Biol Macromol 2019; 126:1050-1055. [PMID: 30615964 DOI: 10.1016/j.ijbiomac.2019.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 01/27/2023]
Abstract
Nucleocytoplasmic transport is essential for normal cellular function that mediates cargo transport from the cytoplasm to the nucleus. However, the mechanisms of nucleocytoplasmic transport that integrate stem cell development remain largely unknown. Since it has a large population of stem cells, the planarian flatworm is an ideal system for the study of adult stem cell lineage development in vivo. Here, we focus on exportin-1, which is the most conserved nuclear export receptor. Homologs of exportin-1 have no currently known role in stem cell biology. RNA interference targeting exportin-1 caused a failure in anterior and posterior regeneration, and resulted in curly and lysis phenotypes in both intact and regenerating flatworms. During the course of exportin-1 RNAi phenotype, cell division was significantly decreased, and the expression of the epidermal cell markers (vimentin and laminB) were lost from the intact body. Additionally, the expression levels of the neoblast marker piwiA decreased. By contrast, the expression levels of the epidermal progenitor markers NB21.11e and AGAT1 increased. These results suggest that exportin-1 is required for the maintenance of the epidermal lineage in planarians. Inhibition of exportin-1 could promote the premature differentiation of neoblasts to the epidermal lineages, disrupting the proper epidermal maturation.
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Affiliation(s)
- Qingnan Tian
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Guixia Zhao
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yujia Sun
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Dandan Yuan
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qi Guo
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yizhe Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaqian Liu
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China.
| | - Shoutao Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou, Henan, China.
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29
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Schmidt D, Reuter H, Hüttner K, Ruhe L, Rabert F, Seebeck F, Irimia M, Solana J, Bartscherer K. The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea. PLoS Genet 2018; 14:e1007828. [PMID: 30557303 PMCID: PMC6312358 DOI: 10.1371/journal.pgen.1007828] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/31/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023] Open
Abstract
In multicellular organisms, cell type diversity and fate depend on specific sets of transcript isoforms generated by post-transcriptional RNA processing. Here, we used Schmidtea mediterranea, a flatworm with extraordinary regenerative abilities and a large pool of adult stem cells, as an in vivo model to study the role of Uridyl-rich small nuclear RNAs (UsnRNAs), which participate in multiple RNA processing reactions including splicing, in stem cell regulation. We characterized the planarian UsnRNA repertoire, identified stem cell-enriched variants and obtained strong evidence for an increased rate of UsnRNA 3'-processing in stem cells compared to their differentiated counterparts. Consistently, components of the Integrator complex showed stem cell-enriched expression and their depletion by RNAi disrupted UsnRNA processing resulting in global changes of splicing patterns and reduced processing of histone mRNAs. Interestingly, loss of Integrator complex function disrupted both stem cell maintenance and regeneration of tissues. Our data show that the function of the Integrator complex in UsnRNA 3'-processing is conserved in planarians and essential for maintaining their stem cell pool. We propose that cell type-specific modulation of UsnRNA composition and maturation contributes to in vivo cell fate choices, such as stem cell self-renewal in planarians.
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Affiliation(s)
- David Schmidt
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
- * E-mail: (DS); (KB)
| | - Hanna Reuter
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Katja Hüttner
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Larissa Ruhe
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Franziska Rabert
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Florian Seebeck
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Solana
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kerstin Bartscherer
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
- Hubrecht Institute for Developmental Biology and Stem Cell Research, CT Utrecht, The Netherlands
- * E-mail: (DS); (KB)
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30
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Bhambri A, Dhaunta N, Patel SS, Hardikar M, Bhatt A, Srikakulam N, Shridhar S, Vellarikkal S, Pandey R, Jayarajan R, Verma A, Kumar V, Gautam P, Khanna Y, Khan JA, Fromm B, Peterson KJ, Scaria V, Sivasubbu S, Pillai B. Large scale changes in the transcriptome of Eisenia fetida during regeneration. PLoS One 2018; 13:e0204234. [PMID: 30260966 PMCID: PMC6160089 DOI: 10.1371/journal.pone.0204234] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 09/05/2018] [Indexed: 12/16/2022] Open
Abstract
Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum Annelida, in which the genomes of the marine oligochaete Capitella telata and the freshwater leech Helobdella robusta have been sequenced and studied. Herein, we report the transcriptomic changes in Eisenia fetida (Indian isolate) during regeneration. Following injury, E. fetida regenerates the posterior segments in a time spanning several weeks. We analyzed gene expression changes both in the newly regenerating cells and in the adjacent tissue, at early (15days post amputation), intermediate (20days post amputation) and late (30 days post amputation) by RNAseq based de novo assembly and comparison of transcriptomes. We also generated a draft genome sequence of this terrestrial red worm using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm showed that many miRNA gene families have undergone extensive duplications. Sox4, a master regulator of TGF-beta mediated epithelial-mesenchymal transition was induced in the newly regenerated tissue. Genes for several proteins such as sialidases and neurotrophins were identified amongst the differentially expressed transcripts. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. We identified 315 novel differentially expressed transcripts in the transcriptome, that have no homolog in any other species. Surprisingly, 82% of these novel differentially expressed transcripts showed poor potential for coding proteins, suggesting that novel ncRNAs may play a critical role in regeneration of earthworm.
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Affiliation(s)
- Aksheev Bhambri
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Neeraj Dhaunta
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Surendra Singh Patel
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Mitali Hardikar
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Abhishek Bhatt
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Nagesh Srikakulam
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shruti Shridhar
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Shamsudheen Vellarikkal
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit - TRISUTRA, CSIR-IGIB, New Delhi, India
| | - Rijith Jayarajan
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ankit Verma
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Vikram Kumar
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Pradeep Gautam
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Yukti Khanna
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Kevin J. Peterson
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Vinod Scaria
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Sridhar Sivasubbu
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
| | - Beena Pillai
- CSIR – Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
- Academy of Scientific & Innovative Research (AcSIR), Mathura Road, Delhi, India
- * E-mail:
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31
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Swapna LS, Molinaro AM, Lindsay-Mosher N, Pearson BJ, Parkinson J. Comparative transcriptomic analyses and single-cell RNA sequencing of the freshwater planarian Schmidtea mediterranea identify major cell types and pathway conservation. Genome Biol 2018; 19:124. [PMID: 30143032 PMCID: PMC6109357 DOI: 10.1186/s13059-018-1498-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 08/01/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND In the Lophotrochozoa/Spiralia superphylum, few organisms have as high a capacity for rapid testing of gene function and single-cell transcriptomics as the freshwater planaria. The species Schmidtea mediterranea in particular has become a powerful model to use in studying adult stem cell biology and mechanisms of regeneration. Despite this, systematic attempts to define gene complements and their annotations are lacking, restricting comparative analyses that detail the conservation of biochemical pathways and identify lineage-specific innovations. RESULTS In this study we compare several transcriptomes and define a robust set of 35,232 transcripts. From this, we perform systematic functional annotations and undertake a genome-scale metabolic reconstruction for S. mediterranea. Cross-species comparisons of gene content identify conserved, lineage-specific, and expanded gene families, which may contribute to the regenerative properties of planarians. In particular, we find that the TRAF gene family has been greatly expanded in planarians. We further provide a single-cell RNA sequencing analysis of 2000 cells, revealing both known and novel cell types defined by unique signatures of gene expression. Among these are a novel mesenchymal cell population as well as a cell type involved in eye regeneration. Integration of our metabolic reconstruction further reveals the extent to which given cell types have adapted energy and nucleotide biosynthetic pathways to support their specialized roles. CONCLUSIONS In general, S. mediterranea displays a high level of gene and pathway conservation compared with other model systems, rendering it a viable model to study the roles of these pathways in stem cell biology and regeneration.
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Affiliation(s)
| | - Alyssa M Molinaro
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nicole Lindsay-Mosher
- Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Bret J Pearson
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Ontario Institute for Cancer Research, Toronto, ON, Canada.
| | - John Parkinson
- Hospital for Sick Children, Toronto, ON, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada. .,Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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32
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Tissue Extracts for Quantitative Mass Spectrometry of Planarian Proteins Using SILAC. Methods Mol Biol 2018. [PMID: 29916177 DOI: 10.1007/978-1-4939-7802-1_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
SILAC (stable isotope labeling by amino acids in cell culture) proteomics enables the relative quantification of proteins in one or more biological samples by mass spectrometry. This technology is based on the metabolic incorporation of heavy isotope-labeled essential amino acids into nascent proteins in vivo. Here, we describe the preparation of SILAC protein samples from planarians, flatworms with high regenerative potential and tissue plasticity. Applications for SILAC proteomics of planarians include the analysis of protein abundances, protein-protein interactions and turnover rates during stem cell-based regeneration and tissue homeostasis.
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33
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Castillo-Lara S, Abril JF. PlanNET: homology-based predicted interactome for multiple planarian transcriptomes. Bioinformatics 2018; 34:1016-1023. [PMID: 29186384 PMCID: PMC5860622 DOI: 10.1093/bioinformatics/btx738] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/24/2017] [Accepted: 11/23/2017] [Indexed: 01/30/2023] Open
Abstract
Motivation Planarians are emerging as a model organism to study regeneration in animals. However, the little available data of protein-protein interactions hinders the advances in understanding the mechanisms underlying its regenerating capabilities. Results We have developed a protocol to predict protein-protein interactions using sequence homology data and a reference Human interactome. This methodology was applied on 11 Schmidtea mediterranea transcriptomic sequence datasets. Then, using Neo4j as our database manager, we developed PlanNET, a web application to explore the multiplicity of networks and the associated sequence annotations. By mapping RNA-seq expression experiments onto the predicted networks, and allowing a transcript-centric exploration of the planarian interactome, we provide researchers with a useful tool to analyse possible pathways and to design new experiments, as well as a reproducible methodology to predict, store, and explore protein interaction networks for non-model organisms. Availability and implementation The web application PlanNET is available at https://compgen.bio.ub.edu/PlanNET. The source code used is available at https://compgen.bio.ub.edu/PlanNET/downloads. Contact jabril@ub.edu. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- S Castillo-Lara
- Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - J F Abril
- Computational Genomics Laboratory, Genetics, Microbiology and Statistics Department, Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Catalonia, Spain
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34
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Abstract
RNA in situ hybridization techniques are an important tool for the study of gene expression patterns in freshwater planarians. Here I describe a RNA in situ hybridization method on histological paraffin sections of planarian tissue. This protocol allows the visualization of gene expression at cellular or subcellular resolution. Following paraffin-embedding and sectioning of planarians, the resulting sections are hybridized with hapten-labeled RNA probes. Subsequent immunological probe detection is carried out with either chromogenic or fluorescent development. This protocol can be performed alone, or in combination with other immunodetection techniques, and represents a useful alternative to whole-mount protocols more commonly used in the community.
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Affiliation(s)
- Jordi Solana
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
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35
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Brown DDR, Molinaro AM, Pearson BJ. The planarian TCF/LEF factor Smed-tcf1 is required for the regeneration of dorsal-lateral neuronal subtypes. Dev Biol 2017; 433:374-383. [PMID: 29291981 DOI: 10.1016/j.ydbio.2017.08.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 10/18/2022]
Abstract
The adult brain of the planarian Schmidtea mediterranea (a freshwater flatworm) is a dynamic structure with constant cell turnover as well as the ability to completely regenerate de novo. Despite this, function and pattern is achieved in a reproducible manner from individual to individual in terms of the correct spatial and temporal production of specific neuronal subtypes. Although several signaling molecules have been found to be key to scaling and cell turnover, the mechanisms by which specific neural subtypes are specified remain largely unknown. Here we performed a 6 day RNAseq time course on planarians that were regenerating either 0, 1, or 2 heads in order to identify novel regulators of brain regeneration. Focusing on transcription factors, we identified a TCF/LEF factor, Smed-tcf1, which was required to correctly pattern the dorsal-lateral cell types of the regenerating brain. The most severely affected neurons in Smed-tcf1(RNAi) animals were the dorsal GABAergic neurons, which failed to regenerate, leading to an inability of the animals to phototaxis away from light. Together, Smed-tcf1 is a critical regulator, required to pattern the dorsal-lateral region of the regenerating planarian brain.
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Affiliation(s)
- David D R Brown
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada M5G0A4; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5G0A4
| | - Alyssa M Molinaro
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada M5G0A4; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5G0A4
| | - Bret J Pearson
- Hospital for Sick Children, Program in Developmental and Stem Cell Biology, Toronto, ON, Canada M5G0A4; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5G0A4; Ontario Institute for Cancer Research, Toronto, ON, Canada M5G0A4.
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Generic wound signals initiate regeneration in missing-tissue contexts. Nat Commun 2017; 8:2282. [PMID: 29273738 PMCID: PMC5741630 DOI: 10.1038/s41467-017-02338-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 11/22/2017] [Indexed: 11/08/2022] Open
Abstract
Despite the identification of numerous regulators of regeneration in different animal models, a fundamental question remains: why do some wounds trigger the full regeneration of lost body parts, whereas others resolve by mere healing? By selectively inhibiting regeneration initiation, but not the formation of a wound epidermis, here we create headless planarians and finless zebrafish. Strikingly, in both missing-tissue contexts, injuries that normally do not trigger regeneration activate complete restoration of heads and fin rays. Our results demonstrate that generic wound signals have regeneration-inducing power. However, they are interpreted as regeneration triggers only in a permissive tissue context: when body parts are missing, or when tissue-resident polarity signals, such as Wnt activity in planarians, are modified. Hence, the ability to decode generic wound-induced signals as regeneration-initiating cues may be the crucial difference that distinguishes animals that regenerate from those that cannot. Some wounds trigger regeneration, while others simply heal but how this is regulated is unclear. Here, by manipulating ERK and Wnt signalling pathways, the authors create headless planarians and finless zebrafish and show that wounds that normally only trigger wound healing can activate regeneration of heads and bones.
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Shettigar N, Joshi A, Dalmeida R, Gopalkrishna R, Chakravarthy A, Patnaik S, Mathew M, Palakodeti D, Gulyani A. Hierarchies in light sensing and dynamic interactions between ocular and extraocular sensory networks in a flatworm. SCIENCE ADVANCES 2017; 3:e1603025. [PMID: 28782018 PMCID: PMC5533540 DOI: 10.1126/sciadv.1603025] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 06/27/2017] [Indexed: 05/23/2023]
Abstract
Light sensing has independently evolved multiple times under diverse selective pressures but has been examined only in a handful among the millions of light-responsive organisms. Unsurprisingly, mechanistic insights into how differential light processing can cause distinct behavioral outputs are limited. We show how an organism can achieve complex light processing with a simple "eye" while also having independent but mutually interacting light sensing networks. Although planarian flatworms lack wavelength-specific eye photoreceptors, a 25 nm change in light wavelength is sufficient to completely switch their phototactic behavior. Quantitative photoassays, eye-brain confocal imaging, and RNA interference/knockdown studies reveal that flatworms are able to compare small differences in the amounts of light absorbed at the eyes through a single eye opsin and convert them into binary behavioral outputs. Because planarians can fully regenerate, eye-brain injury-regeneration studies showed that this acute light intensity sensing and processing are layered on simple light detection. Unlike intact worms, partially regenerated animals with eyes can sense light but cannot sense finer gradients. Planarians also show a "reflex-like," eye-independent (extraocular/whole-body) response to low ultraviolet A light, apart from the "processive" eye-brain-mediated (ocular) response. Competition experiments between ocular and extraocular sensory systems reveal dynamic interchanging hierarchies. In intact worms, cerebral ocular response can override the reflex-like extraocular response. However, injury-regeneration again offers a time window wherein both responses coexist, but the dominance of the ocular response is reversed. Overall, we demonstrate acute light intensity-based behavioral switching and two evolutionarily distinct but interacting light sensing networks in a regenerating organism.
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Affiliation(s)
- Nishan Shettigar
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
- Shanmugha Arts, Science, Technology and Research Academy (SASTRA) University, Tirumalaisamudram, Thanjavur 613401, India
| | - Asawari Joshi
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
| | - Rimple Dalmeida
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
- Shanmugha Arts, Science, Technology and Research Academy (SASTRA) University, Tirumalaisamudram, Thanjavur 613401, India
| | - Rohini Gopalkrishna
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
| | - Anirudh Chakravarthy
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
| | - Siddharth Patnaik
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
| | - Manoj Mathew
- National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
| | - Dasaradhi Palakodeti
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
| | - Akash Gulyani
- Institute for Stem Cell Biology and Regenerative Medicine (inStem), National Centre for Biological Sciences, GKVK Post, Bangalore 560065, India
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Morton JM, Saad MA, Beane WS. Surgical Ablation Assay for Studying Eye Regeneration in Planarians. J Vis Exp 2017. [PMID: 28448039 DOI: 10.3791/55594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
In the study of adult stem cells and regenerative mechanisms, planarian flatworms are a staple in vivo model system. This is due in large part to their abundant pluripotent stem cell population and ability to regenerate all cell and tissue types after injuries that would be catastrophic for most animals. Recently, planarians have gained popularity as a model for eye regeneration. Their ability to regenerate the entire eye (comprised of two tissue types: pigment cells and photoreceptors) allows for the dissection of the mechanisms regulating visual system regeneration. Eye ablation has several advantages over other techniques (such as decapitation or hole punch) for examining eye-specific pathways and mechanisms, the most important of which is that regeneration is largely restricted to eye tissues alone. The purpose of this video article is to demonstrate how to reliably remove the planarian optic cup without disturbing the brain or surrounding tissues. The handling of worms and maintenance of an established colony is also described. This technique uses a 31 G, 5/16-inch insulin needle to surgically scoop out the optic cup of planarians immobilized on a cold plate. This method encompasses both single and double eye ablation, with eyes regenerating within 1-2 weeks, allowing for a wide range of applications. In particular, this ablation technique can be easily combined with pharmacological and genetic (RNA interference) screens for a better understanding of regenerative mechanisms and their evolution, eye stem cells and their maintenance, and phototaxic behavioral responses and their neurological basis.
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Affiliation(s)
- Jacob M Morton
- Department of Biological Sciences, Western Michigan University
| | - Marwa A Saad
- Department of Biological Sciences, Western Michigan University
| | - Wendy S Beane
- Department of Biological Sciences, Western Michigan University;
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Ross KG, Currie KW, Pearson BJ, Zayas RM. Nervous system development and regeneration in freshwater planarians. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [DOI: 10.1002/wdev.266] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/10/2017] [Accepted: 01/20/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Kelly G. Ross
- Department of Biology San Diego State University San Diego CA USA
| | - Ko W. Currie
- Program in Developmental and Stem Cell Biology The Hospital for Sick Children Toronto Canada
- Department of Molecular Genetics University of Toronto Toronto Canada
- Ontario Institute for Cancer Research Toronto Canada
| | - Bret J. Pearson
- Program in Developmental and Stem Cell Biology The Hospital for Sick Children Toronto Canada
- Department of Molecular Genetics University of Toronto Toronto Canada
- Ontario Institute for Cancer Research Toronto Canada
| | - Ricardo M. Zayas
- Department of Biology San Diego State University San Diego CA USA
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Seebeck F, März M, Meyer AW, Reuter H, Vogg MC, Stehling M, Mildner K, Zeuschner D, Rabert F, Bartscherer K. Integrins are required for tissue organization and restriction of neurogenesis in regenerating planarians. Development 2017; 144:795-807. [PMID: 28137894 PMCID: PMC5374344 DOI: 10.1242/dev.139774] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 01/11/2017] [Indexed: 12/13/2022]
Abstract
Tissue regeneration depends on proliferative cells and on cues that regulate cell division, differentiation, patterning and the restriction of these processes once regeneration is complete. In planarians, flatworms with high regenerative potential, muscle cells express some of these instructive cues. Here, we show that members of the integrin family of adhesion molecules are required for the integrity of regenerating tissues, including the musculature. Remarkably, in regenerating β1-integrin RNAi planarians, we detected increased numbers of mitotic cells and progenitor cell types, as well as a reduced ability of stem cells and lineage-restricted progenitor cells to accumulate at wound sites. These animals also formed ectopic spheroid structures of neural identity in regenerating heads. Interestingly, those polarized assemblies comprised a variety of neural cells and underwent continuous growth. Our study indicates that integrin-mediated cell adhesion is required for the regenerative formation of organized tissues and for restricting neurogenesis during planarian regeneration. Highlighted article: Integrin signaling acts to recruit and localize progenitor cells following injury, thereby promoting the correct organization of regenerating planarian tissue.
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Affiliation(s)
- Florian Seebeck
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany.,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Martin März
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany.,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Anna-Wiebke Meyer
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany.,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Hanna Reuter
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany.,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Matthias C Vogg
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany.,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Karina Mildner
- Electron Microscopy Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Dagmar Zeuschner
- Electron Microscopy Unit, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Franziska Rabert
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany.,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Kerstin Bartscherer
- Max Planck Research Group Stem Cells & Regeneration, Max Planck Institute for Molecular Biomedicine, Von-Esmarch-Str. 54, Münster 48149, Germany .,Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
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Abstract
Runx genes have been identified in all metazoans and considerable conservation of function observed across a wide range of phyla. Thus, insight gained from studying simple model organisms is invaluable in understanding RUNX biology in higher animals. Consequently, this chapter will focus on the Runx genes in the diploblasts, which includes sea anemones and sponges, as well as the lower triploblasts, including the sea urchin, nematode, planaria and insect. Due to the high degree of functional redundancy amongst vertebrate Runx genes, simpler model organisms with a solo Runx gene, like C. elegans, are invaluable systems in which to probe the molecular basis of RUNX function within a whole organism. Additionally, comparative analyses of Runx sequence and function allows for the development of novel evolutionary insights. Strikingly, recent data has emerged that reveals the presence of a Runx gene in a protist, demonstrating even more widespread occurrence of Runx genes than was previously thought. This review will summarize recent progress in using invertebrate organisms to investigate RUNX function during development and regeneration, highlighting emerging unifying themes.
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Affiliation(s)
- S Hughes
- Faculteit Techniek, Hogeschool van Arnhem en Nijmegen, Laan van Scheut 2, 6503 GL, Nijmegen, The Netherlands
| | - A Woollard
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
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Proteomic Analysis Reveals the Contribution of TGFβ/Smad4 Signaling Pathway to Cell Differentiation During Planarian Tail Regeneration. Appl Biochem Biotechnol 2016; 182:529-545. [DOI: 10.1007/s12010-016-2342-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/24/2016] [Indexed: 02/06/2023]
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Chan JD, Zhang D, Liu X, Zarowiecki M, Berriman M, Marchant JS. Utilizing the planarian voltage-gated ion channel transcriptome to resolve a role for a Ca 2+ channel in neuromuscular function and regeneration. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:1036-1045. [PMID: 27771293 DOI: 10.1016/j.bbamcr.2016.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 10/13/2016] [Accepted: 10/17/2016] [Indexed: 12/22/2022]
Abstract
The robust regenerative capacity of planarian flatworms depends on the orchestration of signaling events from early wounding responses through the stem cell enacted differentiative outcomes that restore appropriate tissue types. Acute signaling events in excitable cells play an important role in determining regenerative polarity, rationalized by the discovery that sub-epidermal muscle cells express critical patterning genes known to control regenerative outcomes. These data imply a dual conductive (neuromuscular signaling) and instructive (anterior-posterior patterning) role for Ca2+ signaling in planarian regeneration. Here, to facilitate study of acute signaling events in the excitable cell niche, we provide a de novo transcriptome assembly from the planarian Dugesia japonica allowing characterization of the diverse ionotropic portfolio of this model organism. We demonstrate the utility of this resource by proceeding to characterize the individual role of each of the planarian voltage-operated Ca2+ channels during regeneration, and demonstrate that knockdown of a specific voltage operated Ca2+ channel (Cav1B) that impairs muscle function uniquely creates an environment permissive for anteriorization. Provision of the full transcriptomic dataset should facilitate further investigations of molecules within the planarian voltage-gated channel portfolio to explore the role of excitable cell physiology on regenerative outcomes. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
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Affiliation(s)
- John D Chan
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, United States
| | - Dan Zhang
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, United States
| | - Xiaolong Liu
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, United States
| | - Magdalena Zarowiecki
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Matthew Berriman
- Parasite Genomics Group, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Jonathan S Marchant
- Department of Pharmacology, University of Minnesota Medical School, MN 55455, United States; The Stem Cell Institute, University of Minnesota Medical School, MN 55455, United States.
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Roberts-Galbraith RH, Brubacher JL, Newmark PA. A functional genomics screen in planarians reveals regulators of whole-brain regeneration. eLife 2016; 5. [PMID: 27612384 PMCID: PMC5055394 DOI: 10.7554/elife.17002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 09/02/2016] [Indexed: 12/17/2022] Open
Abstract
Planarians regenerate all body parts after injury, including the central nervous system (CNS). We capitalized on this distinctive trait and completed a gene expression-guided functional screen to identify factors that regulate diverse aspects of neural regeneration in Schmidtea mediterranea. Our screen revealed molecules that influence neural cell fates, support the formation of a major connective hub, and promote reestablishment of chemosensory behavior. We also identified genes that encode signaling molecules with roles in head regeneration, including some that are produced in a previously uncharacterized parenchymal population of cells. Finally, we explored genes downregulated during planarian regeneration and characterized, for the first time, glial cells in the planarian CNS that respond to injury by repressing several transcripts. Collectively, our studies revealed diverse molecules and cell types that underlie an animal’s ability to regenerate its brain. DOI:http://dx.doi.org/10.7554/eLife.17002.001 Animals differ in the extent to which they can regenerate missing body parts after injury. Humans regenerate poorly after many injuries, especially when the brain becomes damaged after stroke, disease or trauma. On the other hand, planarians – small worms that live in fresh water – regenerate exceptionally well. A whole planarian can regenerate from small pieces of tissue. The ability of planarians to regenerate their nervous system relies on stem cells called neoblasts, which can migrate through the body and divide to replace lost cells. However, the specific mechanisms responsible for regenerating nervous tissue are largely unknown. Roberts-Galbraith et al. carried out a screen to identify genes that tell planarians whether to regenerate a new brain, what cells to make and how to arrange them. The study revealed over thirty genes that allow planarians to regenerate their brains after their heads have been amputated. These genes play several different roles in the animal. Some of the genes help neoblasts to make decisions about what kinds of cells they should become. One gene is needed to make an important connection in the planarian brain after injury. Another helps to restore the ability of the planarian to sense its food. The experiments also show that some key genes are switched on in a new cell type that might produce signals to support regeneration. Lastly, Roberts-Galbraith et al. found that the planarian nervous system contains cells called glia. Previous studies have shown that many of the cells in the human brain are glia and that these cells help nerve cells to survive and work properly. The discovery of glia in planarians means that it will be possible to use these worms to study how glia support brain regeneration and how glia themselves are replaced after injury. In the long term, this work might lead to discoveries that shed light on how tissue regeneration could be improved in humans. DOI:http://dx.doi.org/10.7554/eLife.17002.002
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Affiliation(s)
- Rachel H Roberts-Galbraith
- Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States
| | - John L Brubacher
- Department of Biology, Canadian Mennonite University, Winnipeg, Canada
| | - Phillip A Newmark
- Department of Cell and Developmental Biology, Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, United States
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A transcriptional time-course analysis of oral vs. aboral whole-body regeneration in the Sea anemone Nematostella vectensis. BMC Genomics 2016; 17:718. [PMID: 27605362 PMCID: PMC5015328 DOI: 10.1186/s12864-016-3027-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/20/2016] [Indexed: 02/07/2023] Open
Abstract
Background The ability of regeneration is essential for the homeostasis of all animals as it allows the repair and renewal of tissues and body parts upon normal turnover or injury. The extent of this ability varies greatly in different animals with the sea anemone Nematostella vectensis, a basal cnidarian model animal, displaying remarkable whole-body regeneration competence. Results In order to study this process in Nematostella we performed an RNA-Seq screen wherein we analyzed and compared the transcriptional response to bisection in the wound-proximal body parts undergoing oral (head) or aboral (tail) regeneration at several time points up to the initial restoration of the basic body shape. The transcriptional profiles of regeneration responsive genes were analyzed so as to define the temporal pattern of differential gene expression associated with the tissue-specific oral and aboral regeneration. The identified genes were characterized according to their GO (gene ontology) assignations revealing groups that were enriched in the regeneration process with particular attention to their affiliation to the major developmental signaling pathways. While some of the genes and gene groups thus analyzed were previously known to be active in regeneration, we have also revealed novel and surprising candidate genes such as cilia-associated genes that likely participate in this important developmental program. Conclusions This work highlighted the main groups of genes which showed polarization upon regeneration, notably the proteinases, multiple transcription factors and the Wnt pathway genes that were highly represented, all displaying an intricate temporal balance between the two sides. In addition, the evolutionary comparison performed between regeneration in different animal model systems may reveal the basic mechanisms playing a role in this fascinating process. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3027-1) contains supplementary material, which is available to authorized users.
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(Neo)blast from the past: new insights into planarian stem cell lineages. Curr Opin Genet Dev 2016; 40:74-80. [PMID: 27379899 DOI: 10.1016/j.gde.2016.06.007] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/18/2016] [Accepted: 06/16/2016] [Indexed: 12/20/2022]
Abstract
Collectively, planarian stem cells (neoblasts) are totipotent and are required for tissue homeostasis and regeneration. Recent work has begun to test the long-standing question of whether all neoblasts have the same potential, or whether they actually represent molecularly distinct subpopulations with distinct tissue restriction. Here, we summarize the current state of the field in neoblast lineage organization. It is clear that at least some neoblasts are totipotent, whereas other neoblasts represent functionally distinct molecular subclasses with restricted potential. In addition to neoblast subclasses, tissue-specific progenitors have also been identified, though their ability to proliferate is largely unknown. Together, neoblast lineage development, subclasses, and cell hierarchies are becoming elucidated, showing the complex regulation required for proper tissue homeostasis and regeneration in planarians.
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Owlarn S, Bartscherer K. Go ahead, grow a head! A planarian's guide to anterior regeneration. ACTA ACUST UNITED AC 2016; 3:139-55. [PMID: 27606065 PMCID: PMC5011478 DOI: 10.1002/reg2.56] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 04/08/2016] [Accepted: 04/15/2016] [Indexed: 12/12/2022]
Abstract
The unique ability of some planarian species to regenerate a head de novo, including a functional brain, provides an experimentally accessible system in which to study the mechanisms underlying regeneration. Here, we summarize the current knowledge on the key steps of planarian head regeneration (head‐versus‐tail decision, anterior pole formation and head patterning) and their molecular and cellular basis. Moreover, instructive properties of the anterior pole as a putative organizer and in coordinating anterior midline formation are discussed. Finally, we highlight that regeneration initiation occurs in a two‐step manner and hypothesize that wound‐induced and existing positional cues interact to detect tissue loss and together determine the appropriate regenerative outcomes.
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Affiliation(s)
- Suthira Owlarn
- Max Planck Research Group Stem Cells and Regeneration Max Planck Institute for Molecular Biomedicine Von-Esmarch-Str. 5448149 Münster Germany; Medical Faculty University of Münster Albert-Schweitzer-Campus 148149 Münster Germany; CiM-IMPRS Graduate School Schlossplatz 548149 Münster Germany
| | - Kerstin Bartscherer
- Max Planck Research Group Stem Cells and Regeneration Max Planck Institute for Molecular Biomedicine Von-Esmarch-Str. 5448149 Münster Germany; Medical Faculty University of Münster Albert-Schweitzer-Campus 148149 Münster Germany
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48
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Wurtzel O, Cote LE, Poirier A, Satija R, Regev A, Reddien PW. A Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians. Dev Cell 2016; 35:632-645. [PMID: 26651295 DOI: 10.1016/j.devcel.2015.11.004] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 10/02/2015] [Accepted: 11/06/2015] [Indexed: 12/27/2022]
Abstract
Regeneration starts with injury. Yet how injuries affect gene expression in different cell types and how distinct injuries differ in gene expression remain unclear. We defined the transcriptomes of major cell types of planarians--flatworms that regenerate from nearly any injury--and identified 1,214 tissue-specific markers across 13 cell types. RNA sequencing on 619 single cells revealed that wound-induced genes were expressed either in nearly all cell types or specifically in one of three cell types (stem cells, muscle, or epidermis). Time course experiments following different injuries indicated that a generic wound response is activated with any injury regardless of the regenerative outcome. Only one gene, notum, was differentially expressed early between anterior- and posterior-facing wounds. Injury-specific transcriptional responses emerged 30 hr after injury, involving context-dependent patterning and stem-cell-specialization genes. The regenerative requirement of every injury is different; however, our work demonstrates that all injuries start with a common transcriptional response.
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Affiliation(s)
- Omri Wurtzel
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lauren E Cote
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amber Poirier
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rahul Satija
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; New York Genome Center, New York, NY 10013, USA; Department of Biology, New York University, New York, NY 10003, USA
| | - Aviv Regev
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Peter W Reddien
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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49
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Currie KW, Brown DDR, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ. HOX gene complement and expression in the planarian Schmidtea mediterranea. EvoDevo 2016; 7:7. [PMID: 27034770 PMCID: PMC4815179 DOI: 10.1186/s13227-016-0044-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/09/2016] [Indexed: 12/21/2022] Open
Abstract
Background Freshwater planarians are well known for their regenerative abilities. Less well known is how planarians maintain spatial patterning in long-lived adult animals or how they re-pattern tissues during regeneration. HOX genes are good candidates to regulate planarian spatial patterning, yet the full complement or genomic clustering of planarian HOX genes has not yet been described, primarily because only a few have been detectable by in situ hybridization, and none have given morphological phenotypes when knocked down by RNAi. Results Because the planarian Schmidteamediterranea (S. mediterranea) is unsegmented, appendage less, and morphologically simple, it has been proposed that it may have a simplified HOX gene complement. Here, we argue against this hypothesis and show that S. mediterranea has a total of 13 HOX genes, which represent homologs to all major axial categories, and can be detected by whole-mount in situ hybridization using a highly sensitive method. In addition, we show that planarian HOX genes do not cluster in the genome, yet 5/13 have retained aspects of axially restricted expression. Finally, we confirm HOX gene axial expression by RNA deep-sequencing 6 anterior–posterior “zones” of the animal, which we provide as a dataset to the community to discover other axially restricted transcripts. Conclusions Freshwater planarians have an unappreciated HOX gene complexity, with all major axial categories represented. However, we conclude based on adult expression patterns that planarians have a derived body plan and their asexual lifestyle may have allowed for large changes in HOX expression from the last common ancestor between arthropods, flatworms, and vertebrates. Using our in situ method and axial zone RNAseq data, it should be possible to further understand the pathways that pattern the anterior–posterior axis of adult planarians. Electronic supplementary material The online version of this article (doi:10.1186/s13227-016-0044-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ko W Currie
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada
| | - David D R Brown
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada
| | - Shujun Zhu
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada
| | - ChangJiang Xu
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5G10A4 Canada
| | - Veronique Voisin
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5G10A4 Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada ; Donnelly Centre for Cellular and Biomolecular Research, Toronto, ON M5G10A4 Canada
| | - Bret J Pearson
- Program in Developmental and Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G10A4 Canada ; Department of Molecular Genetics, University of Toronto, Toronto, ON M5G10A4 Canada ; Ontario Institute for Cancer Research, Toronto, ON M5G10A4 Canada
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Peiris TH, Ramirez D, Barghouth PG, Ofoha U, Davidian D, Weckerle F, Oviedo NJ. Regional signals in the planarian body guide stem cell fate in the presence of genomic instability. Development 2016; 143:1697-709. [PMID: 27013241 DOI: 10.1242/dev.131318] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 03/10/2016] [Indexed: 12/28/2022]
Abstract
Cellular fate decisions are influenced by their topographical location in the adult body. For instance, tissue repair and neoplastic growth are greater in anterior than in posterior regions of adult animals. However, the molecular underpinnings of these regional differences are unknown. We identified a regional switch in the adult planarian body upon systemic disruption of homologous recombination with RNA-interference of Rad51 Rad51 knockdown increases DNA double-strand breaks (DSBs) throughout the body, but stem cells react differently depending on their location along the anteroposterior axis. In the presence of extensive DSBs, cells in the anterior part of the body resist death, whereas cells in the posterior region undergo apoptosis. Furthermore, we found that proliferation of cells with DNA damage is induced in the presence of brain tissue and that the retinoblastoma pathway enables overproliferation of cells with DSBs while attending to the demands of tissue growth and repair. Our results implicate both autonomous and non-autonomous mechanisms as key mediators of regional cell behavior and cellular transformation in the adult body.
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Affiliation(s)
- T Harshani Peiris
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Daniel Ramirez
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Paul G Barghouth
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Udokanma Ofoha
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Devon Davidian
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA
| | - Frank Weckerle
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA
| | - Néstor J Oviedo
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, CA 95343, USA Quantitative and Systems Biology Graduate Program, University of California, Merced, CA 95343, USA Health Sciences Research Institute, University of California, Merced, CA 95343, USA
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