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Kashima M, Komura R, Sato Y, Hashimoto C, Hirata H. A resource of single-cell gene expression profiles in a planarian Dugesia japonica. Dev Growth Differ 2024; 66:43-55. [PMID: 37779230 DOI: 10.1111/dgd.12893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The freshwater planarian Dugesia japonica maintains an abundant heterogeneous cell population called neoblasts, which include adult pluripotent stem cells. Thus, it is an excellent model organism for stem cell and regeneration research. Recently, many single-cell RNA sequencing (scRNA-seq) databases of several model organisms, including other planarian species, have become publicly available; these are powerful and useful resources to search for gene expression in various tissues and cells. However, the only scRNA-seq dataset for D. japonica has been limited by the number of genes detected. Herein, we collected D. japonica cells, and conducted an scRNA-seq analysis. A novel, automatic, iterative cell clustering strategy produced a dataset of 3,404 cells, which could be classified into 63 cell types based on gene expression profiles. We introduced two examples for utilizing the scRNA-seq dataset in this study using D. japonica. First, the dataset provided results consistent with previous studies as well as novel functionally relevant insights, that is, the expression of DjMTA and DjP2X-A genes in neoblasts that give rise to differentiated cells. Second, we conducted an integrative analysis of the scRNA-seq dataset and time-course bulk RNA-seq of irradiated animals, demonstrating that the dataset can help interpret differentially expressed genes captured via bulk RNA-seq. Using the R package "Seurat" and GSE223927, researchers can easily access and utilize this dataset.
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Affiliation(s)
- Makoto Kashima
- College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
- Department of Molecular Biology, Faculty of Science, Toho University, Funabashi, Japan
| | - Rei Komura
- College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
| | - Yuki Sato
- JT Biohistory Research Hall, Takatsuki, Japan
| | - Chikara Hashimoto
- JT Biohistory Research Hall, Takatsuki, Japan
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan
| | - Hiromi Hirata
- College of Science and Engineering, Aoyama Gakuin University, Sagamihara, Japan
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2
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Feng M, Xu Z, Yin D, Zhao Z, Zhou X, Song L. Toxic effects of sodium dodecyl sulfate on planarian Dugesia japonica. PeerJ 2023; 11:e15660. [PMID: 37456884 PMCID: PMC10340106 DOI: 10.7717/peerj.15660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/07/2023] [Indexed: 07/18/2023] Open
Abstract
Sodium dodecyl sulfate (SDS) is an anionic surfactant, which is widely used in various fields in human life. However, SDS discharged into the water environment has a certain impact on aquatic organisms. In this study, planarian Dugesia japonica (D. japonica) was used to identify the toxic effects of SDS. A series of SDS solutions with different concentrations were used to treat planarians for the acute toxicity test , and the results showed that the semi-lethal concentration (LC50) of SDS to D. japonica at 24 h, 48 h, 72 h, and 96 h were 4.29 mg/L, 3.76 mg/L, 3.45 mg/L, and 3.20 mg/L respectively. After the planarians were exposed to 0.5 mg/L and 1.0 mg/L SDS solutions for 1, 3, and 5 days, the activities of superoxide dismutase (SOD), catalase (CAT), and malondialdehyde (MDA) content were measured to detect the oxidative stress and lipid peroxidation in planarians. Random amplified polymorphic DNA (RAPD) analysis was performed to detect the genotoxicity caused by SDS to planarians. The results showed that the activities of SOD, CAT, and MDA content increased after the treatment, indicating that SDS induced oxidative stress in planarians. RAPD analysis showed that the genomic template stability (GTS) values of planarians treated by 0.5 mg/L and 1.0 mg/L SDS for 1, 3, and 5 days were 67.86%, 64.29%, 58.93%, and 64.29%, 60.71%, 48.21%, respectively. GTS values decreased with the increasing of SDS concentration and exposure time, indicating that SDS had genotoxicity to planarians in a time and dose-related manner. Fluorescent quantitative PCR (qPCR) was used to investigate the effects of SDS on gene expression of planarians. After the planarians were exposed to 1.0 mg/L SDS solution for 1, 3, and 5 days, the expression of caspase3 was upregulated, and that of piwiA, piwiB, PCNA, cyclinB, and RAD51 were downregulated. These results suggested that SDS might induce apoptosis, affect cell proliferation, differentiation, and DNA repair ability of planarian cells and cause toxic effects on planarian D. japonica.
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Affiliation(s)
- Minmin Feng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Zhenbiao Xu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Dandan Yin
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Zelong Zhao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Xiuyuan Zhou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Linxia Song
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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Kim IV, Demtröder T, Kuhn CD. Isolation and Library Preparation of Planarian piRNAs. Methods Mol Biol 2023; 2680:29-54. [PMID: 37428369 DOI: 10.1007/978-1-0716-3275-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
In planarian flatworms, piRNAs and SMEDWI (Schmidtea mediterranea PIWI) proteins are both essential for the animals' impressive regenerative ability and for their survival. A knockdown of SMEDWI proteins disrupts the specification of the planarian germline and impairs stem cell differentiation, resulting in lethal phenotypes. As the molecular targets of PIWI proteins and thus their biological function are determined by PIWI-bound small RNAs, termed piRNAs (for PIWI-interacting RNAs), it is imperative to study the wealth of PIWI-bound piRNAs using next-generation sequencing-based techniques. Prior to sequencing, piRNAs bound to individual SMEDWI proteins must be isolated. To that end, we established an immunoprecipitation protocol that can be applied to all planarian SMEDWI proteins. Co-immunoprecipitated piRNAs are visualized by using qualitative radioactive 5'-end labeling, which detects even trace amounts of small RNAs. Next, isolated piRNAs are subjected to a library preparation protocol that has been optimized for the efficient capture of piRNAs, whose 3'-ends carry a 2'-O-methyl modification. Successfully prepared piRNA libraries are subjected to Illumina-based next-generation sequencing. Obtained data are analyzed as presented in the accompanying manuscript.
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Affiliation(s)
- Iana V Kim
- RNA Biochemistry, University of Bayreuth, Bayreuth, Germany
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Tim Demtröder
- RNA Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Claus-D Kuhn
- RNA Biochemistry, University of Bayreuth, Bayreuth, Germany.
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Gambino G, Iacopetti P, Guidi P, Ippolito C, Linsalata S, Salvetti A, Rossi L. Cell quiescence in planarian stem cells, interplay between p53 and nutritional stimuli. Open Biol 2022; 12:220216. [PMID: 36541101 PMCID: PMC9768645 DOI: 10.1098/rsob.220216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cell quiescence appeared early in evolution as an adaptive response to adverse conditions (i.e. nutrient depletion). In metazoans, quiescence has been involved in additional processes like tissue homeostasis, which is made possible by the presence of adult stem cells (ASCs). Cell cycle control machinery is a common hub for quiescence entrance, and evidence indicates a role for p53 in establishing the quiescent state of undamaged cells. Mechanisms responsible for waking up quiescent cells remain elusive, and nutritional stimulus, as a legacy of its original role, still appears to be a player in quiescence exit. Planarians, rich in ASCs, represent a suitable system in which we characterized a quiescent population of ASCs, the dorsal midline cord (DMC) cells, exhibiting unique transcriptional features and maintained quiescent by p53 and awakened upon feeding. The function of DMC cells is puzzling and we speculate that DMC cells, despite retaining ancient properties, might represent a functional drift in which quiescence has been recruited to provide evolutionary advantages.
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Affiliation(s)
- Gaetana Gambino
- Department of Clinical and Experimental Medicine, University of Pisa, Via Volta 4, 56126 Pisa, Italy
| | - Paola Iacopetti
- Department of Clinical and Experimental Medicine, University of Pisa, Via Volta 4, 56126 Pisa, Italy
| | - Patrizia Guidi
- Department of Clinical and Experimental Medicine, University of Pisa, Via Volta 4, 56126 Pisa, Italy
| | - Chiara Ippolito
- Department of Clinical and Experimental Medicine, University of Pisa, Via Roma 55, 56126 Pisa, Italy
| | - Stefania Linsalata
- Medical Physics Unit, Azienda Ospedaliera Universitaria Pisana, Via Roma 67, 56126 Pisa, Italy
| | - Alessandra Salvetti
- Department of Clinical and Experimental Medicine, University of Pisa, Via Volta 4, 56126 Pisa, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, Via Volta 4, 56126 Pisa, Italy
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Wu W, Liu S, Wu H, Chen M, Gao L, Zhao B, Liu B, Pang Q. DjPtpn11 is an essential modulator of planarian (Dugesia japonica) regeneration. Int J Biol Macromol 2022; 209:1054-1064. [PMID: 35452697 DOI: 10.1016/j.ijbiomac.2022.04.095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 11/19/2022]
Abstract
Freshwater planarian Dugesia japonica is an excellent model organism for investigating stem cell behavior during regeneration. Despite studies showing that numerous genetic factors are involved in regeneration, much more research is required to fully understand the molecular mechanisms that orchestrate regeneration. In this study, we identified an evolutionarily conserved gene DjPtpn11(DjShp2). DjPtpn11 transcripts are expressed in neoblasts and some differentiated cells, with a high expression at the newly formed blastema. Its silencing by RNA interference (RNAi) affected anterior regeneration and inhibited the regeneration of posterior regions, including cholinergic and serotonergic neuron regeneration. In adult planarians, DjPtpn11 knockdown did not affect neoblast survival and proliferation but might prevent the stem cell migration and differentiation through ERK signaling. DjPtpn11 was demonstrated to be necessary for the anterior blastema cell differentiation partially via regulating ERK-DjMkpA activity. DjPtpn11 also influenced posterior specification via DjIslet, suggesting that DjPtpn11 may be involved in regulating the Wnt signaling pathway during the development of posterior blastema. Together, these data identified that DjPtpn11 is an essential modulator for the regeneration of planarians, and it may influence the appropriate differentiation of blastema cells.
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Affiliation(s)
- Weiwei Wu
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Shuo Liu
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Hao Wu
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Meishan Chen
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Lili Gao
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Bosheng Zhao
- Laboratory of Developmental and Evolutionary Biology, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Baohua Liu
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China.; Shenzhen University of Health Science Center, Shenzhen 518060, China
| | - Qiuxiang Pang
- Anti-aging & Regenerative Medicine Research Institution, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China.; Laboratory of Developmental and Evolutionary Biology, School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China.
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Kashima M, Miyata A, Shibata N. Planarian PIWI-piRNA Interaction Analysis Using Immunoprecipitation and piRNA Sequencing. Methods Mol Biol 2022; 2509:69-81. [PMID: 35796957 DOI: 10.1007/978-1-0716-2380-0_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The freshwater planarian Dugesia japonica is a good in vivo model for studying the function of piwi genes in adult pluripotent stem cell (aPSC) due to their abundant aPSCs. Generally, PIWI family proteins encoded by piwi genes bind to small noncoding RNAs called piRNAs (PIWI-interacting piRNAs). The analysis of PIWI-piRNA complexes in the planarian is useful for revealing the functions of piwi genes in the aPSC system. In this chapter, we present an immunoprecipitation protocol for PIWI-piRNA complexes from whole planarians.
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Affiliation(s)
- Makoto Kashima
- College of Science and Engineering, Aoyama Gakuin University, Sagamihara Chuo Ku, Kanagawa, Japan.
| | - Atsumi Miyata
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Norito Shibata
- Department of Integrated Science and Technology, National Institute of Technology, Tsuyama College, Tsuyama-City, Okayama, Japan
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Molina MD, Cebrià F. Decoding Stem Cells: An Overview on Planarian Stem Cell Heterogeneity and Lineage Progression. Biomolecules 2021; 11:1532. [PMID: 34680165 PMCID: PMC8533874 DOI: 10.3390/biom11101532] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 01/26/2023] Open
Abstract
Planarians are flatworms capable of whole-body regeneration, able to regrow any missing body part after injury or amputation. The extraordinary regenerative capacity of planarians is based upon the presence in the adult of a large population of somatic pluripotent stem cells. These cells, called neoblasts, offer a unique system to study the process of stem cell specification and differentiation in vivo. In recent years, FACS-based isolation of neoblasts, RNAi functional analyses as well as high-throughput approaches such as single-cell sequencing have allowed a rapid progress in our understanding of many different aspects of neoblast biology. Here, we summarize our current knowledge on the molecular signatures that define planarian neoblasts heterogeneity, which includes a percentage of truly pluripotent stem cells, and guide the commitment of pluripotent neoblasts into lineage-specific progenitor cells, as well as their differentiation into specific planarian cell types.
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Affiliation(s)
- M. Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), 08028 Barcelona, Spain
| | - Francesc Cebrià
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine of the University of Barcelona (IBUB), 08028 Barcelona, Spain
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Abstract
P-element-induced wimpy testis (PIWI)-interacting RNAs (piRNAs) are regulatory small non-coding RNAs that participate in transposon inactivation, chromatin regulation, and endogenous gene regulation. Numerous genetic and epigenetic factors regulate cell proliferation and tumor metastasis. PIWI proteins and piRNAs have been revealed to function in regulating upstream or downstream of oncogenes or tumor-suppressor genes in cancer tissues. In the present review, we summarize major recent findings in uncovering the regulation and role of PIWI proteins and piRNAs in tumorigenesis and highlight some of the promising applications of specific piRNAs in cancer therapeutics and as cancer biomarkers.
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