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Medina-Feliciano JG, Valentín-Tirado G, Luna-Martínez K, Miranda-Negrón Y, García-Arrarás JE. Single-cell RNA sequencing of the holothurian regenerating intestine reveals the pluripotency of the coelomic epithelium. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601561. [PMID: 39005414 PMCID: PMC11244903 DOI: 10.1101/2024.07.01.601561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
In holothurians, the regenerative process following evisceration involves the development of a "rudiment" or "anlage" at the injured end of the mesentery. This regenerating anlage plays a pivotal role in the formation of a new intestine. Despite its significance, our understanding of the molecular characteristics inherent to the constituent cells of this structure has remained limited. To address this gap, we employed state-of-the-art scRNA-seq and HCR-FISH analyses to discern the distinct cellular populations associated with the regeneration anlage. Through this approach, we successfully identified thirteen distinct cell clusters. Among these, two clusters exhibit characteristics consistent with putative mesenchymal cells, while another four show features akin to coelomocyte cell populations. The remaining seven cell clusters collectively form a large group encompassing the coelomic epithelium of the regenerating anlage and mesentery. Within this large group of clusters, we recognized previously documented cell populations such as muscle precursors, neuroepithelial cells and actively proliferating cells. Strikingly, our analysis provides data for identifying at least four other cellular populations that we define as the precursor cells of the growing anlage. Consequently, our findings strengthen the hypothesis that the coelomic epithelium of the anlage is a pluripotent tissue that gives rise to diverse cell types of the regenerating intestinal organ. Moreover, our results provide the initial view into the transcriptomic analysis of cell populations responsible for the amazing regenerative capabilities of echinoderms.
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Telmer CA, Karimi K, Chess MM, Agalakov S, Arshinoff BI, Lotay V, Wang DZ, Chu S, Pells TJ, Vize PD, Hinman VF, Ettensohn CA. Echinobase: a resource to support the echinoderm research community. Genetics 2024; 227:iyae002. [PMID: 38262680 PMCID: PMC11075573 DOI: 10.1093/genetics/iyae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 12/27/2023] [Indexed: 01/25/2024] Open
Abstract
Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein-protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community.
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Affiliation(s)
- Cheryl A Telmer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Kamran Karimi
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Macie M Chess
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Sergei Agalakov
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Bradley I Arshinoff
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Vaneet Lotay
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Dong Zhuo Wang
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Stanley Chu
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Troy J Pells
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada T2N 1N4
| | - Veronica F Hinman
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Charles A Ettensohn
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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Bump P, Lubeck L. Marine Invertebrates One Cell at A Time: Insights from Single-Cell Analysis. Integr Comp Biol 2023; 63:999-1009. [PMID: 37188638 PMCID: PMC10714908 DOI: 10.1093/icb/icad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/25/2023] [Accepted: 05/05/2023] [Indexed: 05/17/2023] Open
Abstract
Over the past decade, single-cell RNA-sequencing (scRNA-seq) has made it possible to study the cellular diversity of a broad range of organisms. Technological advances in single-cell isolation and sequencing have expanded rapidly, allowing the transcriptomic profile of individual cells to be captured. As a result, there has been an explosion of cell type atlases created for many different marine invertebrate species from across the tree of life. Our focus in this review is to synthesize current literature on marine invertebrate scRNA-seq. Specifically, we provide perspectives on key insights from scRNA-seq studies, including descriptive studies of cell type composition, how cells respond in dynamic processes such as development and regeneration, and the evolution of new cell types. Despite these tremendous advances, there also lie several challenges ahead. We discuss the important considerations that are essential when making comparisons between experiments, or between datasets from different species. Finally, we address the future of single-cell analyses in marine invertebrates, including combining scRNA-seq data with other 'omics methods to get a fuller understanding of cellular complexities. The full diversity of cell types across marine invertebrates remains unknown and understanding this diversity and evolution will provide rich areas for future study.
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Affiliation(s)
- Paul Bump
- Department of Organismic and Evolutionary Biology, Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Lauren Lubeck
- Department of Biology, Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA
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Arimoto A, Nishitsuji K, Hisata K, Satoh N, Tagawa K. Transcriptomic evidence for Brachyury expression in the caudal tip region of adult Ptychodera flava (Hemichordata). Dev Growth Differ 2023; 65:470-480. [PMID: 37483093 DOI: 10.1111/dgd.12882] [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: 02/02/2023] [Revised: 06/27/2023] [Accepted: 07/19/2023] [Indexed: 07/25/2023]
Abstract
Most metazoans have a single copy of the T-box transcription factor gene Brachyury. This gene is expressed in cells of the blastopore of late blastulae and the archenteron invagination region of gastrulae. It appears to be crucial for gastrulation and mesoderm differentiation of embryos. Although this expression pattern is shared by most deuterostomes, Brachyury expression has not been reported in adult stages. Here we show that Brachyury of an indirect developer, the hemichordate acorn worm Ptychodera flava, is expressed not only in embryonic cells, but also in cells of the caudal tip (anus) region of adults. This spatially restricted expression, shown by whole-mount in situ hybridization, was confirmed by Iso-Seq RNA sequencing and single-cell RNA-seq (scRNA-seq) analysis. Iso-Seq analysis showed that gene expression occurs only in the caudal region of adults, but not in anterior regions, including the stomochord. scRNA-seq analysis showed a cluster that contained Brachyury-expressing cells comprising epidermis- and mesoderm-related cells, but which is unlikely to be associated with the nervous system or muscle. Although further investigation is required to examine the roles of Brachyury in adults, this study provides important clues for extending studies on Brachyury expression involved in development of the most posterior region of deuterostomes.
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Affiliation(s)
- Asuka Arimoto
- Marine Biological Laboratory, Blue Innovation Division, Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Kuni Tagawa
- Marine Biological Laboratory, Blue Innovation Division, Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
- Faculty of Science and Technology, Maulana Malik Ibrahim State Islamic University of Malang, Kota Malang, Indonesia
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Pieplow C, Wessel G. Functional annotation of a hugely expanded nanos repertoire in Lytechinus variegatus, the green sea urchin. Mol Reprod Dev 2023; 90:310-322. [PMID: 37039283 PMCID: PMC10225336 DOI: 10.1002/mrd.23684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/18/2023] [Indexed: 04/12/2023]
Abstract
Nanos genes encode essential RNA-binding proteins involved in germline determination and germline stem cell maintenance. When examining diverse classes of echinoderms, typically three, sometimes four, nanos genes are present. In this analysis, we identify and annotate nine nanos orthologs in the green sea urchin, Lytechinus variegatus (Lv). All nine genes are transcribed and grouped into three distinct classes. Class one includes the germline Nanos, with one member: Nanos2. Class two includes Nanos3-like genes, with significant sequence similarity to Nanos3 in the purple sea urchin, Strongylocentrotus purpuratus (Sp), but with wildly variable expression patterns. The third class includes several previously undescribed nanos zinc-finger genes that may be the result of duplications of Nanos2. All nine nanos transcripts occupy unique genomic loci and are expressed with unique temporal profiles during development. Importantly, here we describe and characterize the unique genomic location, conservation, and phylogeny of the Lv ortholog of the well-studied Sp Nanos2. However, in addition to the conserved germline functioning Nanos2, the green sea urchin appears to be an outlier in the echinoderm phyla with eight additional nanos genes. We hypothesize that this expansion of nanos gene members may be the result of a previously uncharacterized L1-class transposon encoded on the opposite strand of a nanos2 pseudogene present on chromosome 12 in this species. The expansion of nanos genes described here represents intriguing insights into germline specification and nanos evolution in this species of sea urchin.
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Affiliation(s)
- Cosmo Pieplow
- MCB Department, Division of Biomedicine, Brown University, Providence RI 02912
| | - Gary Wessel
- MCB Department, Division of Biomedicine, Brown University, Providence RI 02912
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Tominaga H, Nishitsuji K, Satoh N. A single-cell RNA-seq analysis of early larval cell-types of the starfish, Patiria pectinifera: Insights into evolution of the chordate body plan. Dev Biol 2023; 496:52-62. [PMID: 36717049 DOI: 10.1016/j.ydbio.2023.01.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 01/29/2023]
Abstract
Ambulacrarians (echinoderms and hemichordates) are a sister group to chordates; thus, their larval cell-types may provide clues about evolution of chordate body plans. Although most genic information accumulated to date pertains to sea urchin embryogenesis, starfish embryogenesis represents a more ancestral mode than that of sea urchins. We performed single-cell RNA-seq analysis of cell-types from gastrulae and bipinnarial larvae of the starfish, Patiria pectinifera, and categorized them into 22 clusters, each of which is composed of cells with specific, shared profiles of development-relevant gene expression. Oral and aboral ectoderm, apical plate, hindgut or archenteron, midgut or intestine, pharynx, endomesoderm, stomodeum, and mesenchyme of the gastrulae, and neurons, ciliary bands, enterocoel and muscle of larvae were characterized by expression profiles of at least two relevant transcription factor genes and signaling molecular genes. Expression of Hox2, Hox7, Hox9/10, and Hox11/13b was detected in cells of clusters that form the larval enterocoel. By comparing homologous gene expression profiles in chordate embryos, we discuss and propose how the chordate body plan evolved from a deuterostome ancestor, from which the echinoderm body plan also evolved.
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Affiliation(s)
- Hitoshi Tominaga
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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Schwaiger M, Andrikou C, Dnyansagar R, Murguia PF, Paganos P, Voronov D, Zimmermann B, Lebedeva T, Schmidt HA, Genikhovich G, Benvenuto G, Arnone MI, Technau U. An ancestral Wnt-Brachyury feedback loop in axial patterning and recruitment of mesoderm-determining target genes. Nat Ecol Evol 2022; 6:1921-1939. [PMID: 36396969 DOI: 10.1038/s41559-022-01905-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/12/2022] [Indexed: 11/18/2022]
Abstract
Transcription factors are crucial drivers of cellular differentiation during animal development and often share ancient evolutionary origins. The T-box transcription factor Brachyury plays a pivotal role as an early mesoderm determinant and neural repressor in vertebrates; yet, the ancestral function and key evolutionary transitions of the role of this transcription factor remain obscure. Here, we present a genome-wide target-gene screen using chromatin immunoprecipitation sequencing in the sea anemone Nematostella vectensis, an early branching non-bilaterian, and the sea urchin Strongylocentrotus purpuratus, a representative of the sister lineage of chordates. Our analysis reveals an ancestral gene regulatory feedback loop connecting Brachyury, FoxA and canonical Wnt signalling involved in axial patterning that predates the cnidarian-bilaterian split about 700 million years ago. Surprisingly, we also found that part of the gene regulatory network controlling the fate of neuromesodermal progenitors in vertebrates was already present in the common ancestor of cnidarians and bilaterians. However, while several endodermal and neuronal Brachyury target genes are ancestrally shared, hardly any of the key mesodermal downstream targets in vertebrates are found in the sea anemone or the sea urchin. Our study suggests that a limited number of target genes involved in mesoderm formation were newly acquired in the vertebrate lineage, leading to a dramatic shift in the function of this ancestral developmental regulator.
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Affiliation(s)
- Michaela Schwaiger
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
- Friedrich Miescher Institute for Biomedical Research, Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Carmen Andrikou
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Rohit Dnyansagar
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Patricio Ferrer Murguia
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | | | - Danila Voronov
- Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Bob Zimmermann
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Tatiana Lebedeva
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | - Heiko A Schmidt
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria
| | | | | | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences,University of Vienna, Vienna, Austria.
- Max Perutz Labs, University of Vienna, Vienna, Austria.
- Research Platform 'Single Cell Regulation of Stem Cells', University of Vienna, Vienna, Austria.
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Chen PH, Tjong WY, Yang HC, Liu HY, Stern A, Chiu DTY. Glucose-6-Phosphate Dehydrogenase, Redox Homeostasis and Embryogenesis. Int J Mol Sci 2022; 23:ijms23042017. [PMID: 35216131 PMCID: PMC8878822 DOI: 10.3390/ijms23042017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 12/04/2022] Open
Abstract
Normal embryogenesis requires complex regulation and precision, which depends on multiple mechanistic details. Defective embryogenesis can occur by various mechanisms. Maintaining redox homeostasis is of importance during embryogenesis. NADPH, as produced from the action of glucose-6-phosphate dehydrogenase (G6PD), has an important role in redox homeostasis, serving as a cofactor for glutathione reductase in the recycling of glutathione from oxidized glutathione and for NADPH oxidases and nitric oxide synthases in the generation of reactive oxygen (ROS) and nitrogen species (RNS). Oxidative stress differentially influences cell fate and embryogenesis. While low levels of stress (eustress) by ROS and RNS promote cell growth and differentiation, supra-physiological concentrations of ROS and RNS can lead to cell demise and embryonic lethality. G6PD-deficient cells and organisms have been used as models in embryogenesis for determining the role of redox signaling in regulating cell proliferation, differentiation and migration. Embryogenesis is also modulated by anti-oxidant enzymes, transcription factors, microRNAs, growth factors and signaling pathways, which are dependent on redox regulation. Crosstalk among transcription factors, microRNAs and redox signaling is essential for embryogenesis.
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Affiliation(s)
- Po-Hsiang Chen
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan; (P.-H.C.); (W.-Y.T.); (D.T.-Y.C.)
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan
| | - Wen-Ye Tjong
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan; (P.-H.C.); (W.-Y.T.); (D.T.-Y.C.)
- Research Center for Chinese Herbal Medicine, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan
| | - Hung-Chi Yang
- Department of Medical Laboratory Science and Biotechnology, Yuanpei University of Medical Technology, Hsinchu 30015, Taiwan
- Correspondence: ; Tel.: +886-3-6108175; Fax: +886-3-6102327
| | - Hui-Ya Liu
- Department of Medical Biotechnology and Laboratory Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
| | - Arnold Stern
- Grossman School of Medicine, New York University, New York, NY 10016, USA;
| | - Daniel Tsun-Yee Chiu
- Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan 33303, Taiwan; (P.-H.C.); (W.-Y.T.); (D.T.-Y.C.)
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