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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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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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Kashima M, Agata K, Shibata N. What is the role of PIWI family proteins in adult pluripotent stem cells? Insights from asexually reproducing animals, planarians. Dev Growth Differ 2020; 62:407-422. [PMID: 32621324 DOI: 10.1111/dgd.12688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/26/2020] [Accepted: 06/09/2020] [Indexed: 02/06/2023]
Abstract
Planarians have a remarkable regenerative ability owing to their adult pluripotent stem cells (aPSCs), which are called "neoblasts." Planarians maintain a considerable number of neoblasts throughout their adulthood to supply differentiated cells for the maintenance of tissue homeostasis and asexual reproduction (fission followed by regeneration). Thus, planarians serve as a good model to study the regulatory mechanisms of in vivo aPSCs. In asexually reproducing invertebrates, such as sponge, Hydra, and planaria, piwi family genes are the markers most commonly expressed in aPSCs. While piwi family genes are known as guardians against transposable elements in the germline cells of animals that only sexually propagate, their functions in the aPSC system have remained elusive. In this review, we introduce recent knowledge on the PIWI family proteins in the aPSC system in planarians and other organisms and discuss how PIWI family proteins contribute to the regulation of the aPSC system.
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Affiliation(s)
- Makoto Kashima
- College of Science and Engineering, Aoyama Gakuin University, Sagamihara Chuo Ku, Japan
| | - Kiyokazu Agata
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
| | - Norito Shibata
- Department of Integrated Science and Technology, National Institute of Technology, Tsuyama College, Tsuyama-City, Japan
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Mori M, Narahashi M, Hayashi T, Ishida M, Kumagai N, Sato Y, Bagherzadeh R, Agata K, Inoue T. Calcium ions in the aquatic environment drive planarians to food. ZOOLOGICAL LETTERS 2019; 5:31. [PMID: 31720007 PMCID: PMC6836377 DOI: 10.1186/s40851-019-0147-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 10/21/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Even subtle changes in environmental factors can exert behavioral effects on creatures, which may alter interspecific interactions and eventually affect the ecosystem. However, how changes in environmental factors impact complex behaviors regulated by neural processes is largely unknown. The freshwater planarian Dugesia japonica, a free-living flatworm, displays distinct behavioral traits mediated by sensitive perception of environmental cues. Planarians are thus useful organisms for examining interactions between environmental changes and specific behaviors of animals. RESULTS Here we found that feeding behavior was suppressed when the concentration of ions in the breeding water was low, while other behaviors were unaffected, resulting in differences in population size. Notably, the decline in feeding behavior was reversed in an ion-concentration-dependent manner soon after the planarians were moved to ion-containing water, which suggests that ions in environmental water rapidly promote feeding behavior in planarians. Moreover, the concentration of ions in the environmental water affected the feeding behavior by modulating the sensitivity of the response to foods. Finally, we found that calcium ions in the aquatic environment were required for the feeding behavior, and exposure to higher levels of calcium ions enhanced the feeding behavior, showing that there was a good correlation between the concentration of calcium ions and the responsiveness of planarians to foods. CONCLUSIONS Environmental calcium ions are indispensable for and potentiate the activity level of the feeding behavior of planarians. Our findings suggest that the ions in the aquatic environment profoundly impact the growth and survival of aquatic animals via modulating their neural activities and behaviors.
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Affiliation(s)
- Masato Mori
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
| | - Maria Narahashi
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Japan
| | - Miyuki Ishida
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
| | - Nobuyoshi Kumagai
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
| | - Yuki Sato
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
| | - Reza Bagherzadeh
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, Banihashem, Tehran, Iran
- Department of Developmental Biology, University of Science and Culture, Banihashem, Tehran, Iran
| | - Kiyokazu Agata
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, Japan
- National Institute for Basic Biology, National Institutes of Natural Science, 38 Nishigonaka, Myodaiji, Okazaki, Japan
| | - Takeshi Inoue
- Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, Japan
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