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Li H, Xu W, Xiang S, Tao L, Fu W, Liu J, Liu W, Xiao Y, Peng L. Defining the Pluripotent Marker Genes for Identification of Teleost Fish Cell Pluripotency During Reprogramming. Front Genet 2022; 13:819682. [PMID: 35222539 PMCID: PMC8874021 DOI: 10.3389/fgene.2022.819682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
Pluripotency is a transient state in early embryos, which is regulated by an interconnected network of pluripotency-related genes. The pluripotent state itself seems to be highly dynamic, which leads to significant differences in the description of induced pluripotent stem cells from different species at the molecular level. With the application of cell reprogramming technology in fish, the establishment of a set of molecular standards for defining pluripotency will be important for the research and potential application of induced pluripotent stem cells in fish. In this study, by BLAST search and expression pattern analysis, we screen out four pluripotent genes (Oct4, Nanog, Tdgf1, and Gdf3) in zebrafish (Danio rerio) and crucian carp (Carassius). These genes were highly expressed in the short period of early embryonic development, but significantly down-regulated after differentiation. Moreover, three genes (Oct4, Nanog and Tdgf1) have been verified that are suitable for identifying the pluripotency of induced pluripotent stem cells in zebrafish and crucian carp. Our study expands the understanding of the pluripotent markers of induced pluripotent stem cells in fish.
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Affiliation(s)
- Huajin Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenting Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Sijia Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Leiting Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wen Fu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Jinhui Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenbin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
| | - Liangyue Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, China
- School of Life Sciences, Hunan Normal University, Changsha, China
- *Correspondence: Liangyue Peng,
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Uno Y, Nozu R, Kiyatake I, Higashiguchi N, Sodeyama S, Murakumo K, Sato K, Kuraku S. Cell culture-based karyotyping of orectolobiform sharks for chromosome-scale genome analysis. Commun Biol 2020; 3:652. [PMID: 33159152 PMCID: PMC7648076 DOI: 10.1038/s42003-020-01373-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/12/2020] [Indexed: 11/09/2022] Open
Abstract
Karyotyping, traditionally performed using cytogenetic techniques, is indispensable for validating genome assemblies whose sequence lengths can be scaled up to chromosome sizes using modern methods. Karyotype reports of chondrichthyans are scarce because of the difficulty in cell culture. Here, we focused on carpet shark species and the culture conditions for fibroblasts and lymphocytes. The utility of the cultured cells enabled the high-fidelity characterization of their karyotypes, namely 2n = 102 for the whale shark (Rhincodon typus) and zebra shark (Stegostoma fasciatum), and 2n = 106 for the brownbanded bamboo shark (Chiloscyllium punctatum) and whitespotted bamboo shark (C. plagiosum). We identified heteromorphic XX/XY sex chromosomes for the two latter species and demonstrated the first-ever fluorescence in situ hybridization of shark chromosomes prepared from cultured cells. Our protocols are applicable to diverse chondrichthyan species and will deepen the understanding of early vertebrate evolution at the molecular level.
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Affiliation(s)
- Yoshinobu Uno
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan. .,Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan.
| | - Ryo Nozu
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, Okinawa, Japan.,Okinawa Churaumi Aquarium, Okinawa, Japan
| | | | | | | | | | - Keiichi Sato
- Okinawa Churashima Research Center, Okinawa Churashima Foundation, Okinawa, Japan.,Okinawa Churaumi Aquarium, Okinawa, Japan
| | - Shigehiro Kuraku
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan
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Martínez-Páramo S, Horváth Á, Labbé C, Zhang T, Robles V, Herráez P, Suquet M, Adams S, Viveiros A, Tiersch TR, Cabrita E. Cryobanking of aquatic species. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2017; 472:156-177. [PMID: 29276317 PMCID: PMC5737826 DOI: 10.1016/j.aquaculture.2016.05.042] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
This review is focused on the applications of genome cryobanking of aquatic species including freshwater and marine fish, as well as invertebrates. It also reviews the latest advances in cryobanking of model species, widely used by the scientific community worldwide, because of their applications in several fields. The state of the art of cryopreservation of different cellular types (sperm, oocytes, embryos, somatic cells and primordial germ cells or early spermatogonia) is discussed focusing on the advantages and disadvantages of each procedure according to different applications. A special review on the need of standardization of protocols has also been carried out. In summary, this comprehensive review provides information on the practical details of applications of genome cryobanking in a range of aquatic species worldwide, including the cryobanks established in Europe, USA, Brazil, Australia and New Zealand, the species and type of cells that constitute these banks and the utilization of the samples preserved. STATEMENT OF RELEVANCE This review compiles the last advances on germplasm cryobanking of freshwater and marine fish species and invertebrates, with high value for commercial aquaculture or conservation. It is reviewed the most promising cryopreservation protocols for different cell types, embryos and larvae that could be applied in programs for genetic improvement, broodstock management or conservation of stocks to guarantee culture production.
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Affiliation(s)
- Sonia Martínez-Páramo
- CCMAR-Centre of Marine Sciences, University of Algarve, Campus Gambelas, 8005-139 Faro, Portugal
| | - Ákos Horváth
- Department of Aquaculture, Szent István University, H-2100 Gödöllő, Hungary
| | - Catherine Labbé
- INRA, Fish Physiology and Genomics, Campus de Beaulieu, F-35000 Rennes, France
| | - Tiantian Zhang
- Faculty of Science and Technology, Bournemouth University, Talbot Campus, Fern Barrow, Poole, Dorset BH12 5BB, United Kingdom
| | - Vanesa Robles
- IEO, Spanish Oceanographic Institute, Santander Oceanographic Centre, El Bocal, Barrio Corbanera s/n Bocal, 39012 Monte, Santander, Spain
| | - Paz Herráez
- Department of Molecular Biology and INDEGSAL, University of León, 24071 León, Spain
| | - Marc Suquet
- IFREMER, PFOM Dept, Stn Expt Argenton, UMR, 6539 Argenton, France
| | - Serean Adams
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
- AgResearch, Private Bag 3123, Ruakura, Hamilton 3240, New Zealand
| | - Ana Viveiros
- Department of Animal Sciences, Federal University of Lavras, UFLA, MG 37200-000, Brazil
| | - Terrence R. Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Elsa Cabrita
- CCMAR-Centre of Marine Sciences, University of Algarve, Campus Gambelas, 8005-139 Faro, Portugal
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Barnes DW. Cell and molecular biology of the spiny dogfish Squalus acanthias and little skate Leucoraja erinacea: insights from in vitro cultured cells. JOURNAL OF FISH BIOLOGY 2012; 80:2089-2111. [PMID: 22497417 DOI: 10.1111/j.1095-8649.2011.03205.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Two of the most commonly used elasmobranch experimental model species are the spiny dogfish Squalus acanthias and the little skate Leucoraja erinacea. Comparative biology and genomics with these species have provided useful information in physiology, pharmacology, toxicology, immunology, evolutionary developmental biology and genetics. A wealth of information has been obtained using in vitro approaches to study isolated cells and tissues from these organisms under circumstances in which the extracellular environment can be controlled. In addition to classical work with primary cell cultures, continuously proliferating cell lines have been derived recently, representing the first cell lines from cartilaginous fishes. These lines have proved to be valuable tools with which to explore functional genomic and biological questions and to test hypotheses at the molecular level. In genomic experiments, complementary (c)DNA libraries have been constructed, and c. 8000 unique transcripts identified, with over 3000 representing previously unknown gene sequences. A sub-set of messenger (m)RNAs has been detected for which the 3' untranslated regions show elements that are remarkably well conserved evolutionarily, representing novel, potentially regulatory gene sequences. The cell culture systems provide physiologically valid tools to study functional roles of these sequences and other aspects of elasmobranch molecular cell biology and physiology. Information derived from the use of in vitro cell cultures is valuable in revealing gene diversity and information for genomic sequence assembly, as well as for identification of new genes and molecular markers, construction of gene-array probes and acquisition of full-length cDNA sequences.
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Affiliation(s)
- D W Barnes
- School of Science and Technology, Georgia Gwinnett College, 1000 University Center Lane, Lawrenceville, GA 30043, USA.
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Abstract
Stem cells have the potential for self-renewal and differentiation. First stem cell cultures were derived 30 years ago from early developing mouse embryos. These are pluripotent embryonic stem (ES) cells. Efforts towards ES cell derivation have been attempted in other mammalian and non-mammalian species. Work with stem cell culture in fish started 20 years ago. Laboratory fish species, in particular zebrafish and medaka, have been the focus of research towards stem cell cultures. Medaka is the second organism that generated ES cells and the first that gave rise to a spermatogonial stem cell line capable of test-tube sperm production. Most recently, the first haploid stem cells capable of producing whole animals have also been generated from medaka. ES-like cells have been reported also in zebrafish and several marine species. Attempts for germline transmission of ES cell cultures and gene targeting have been reported in zebrafish. Recent years have witnessed the progress in markers and procedures for ES cell characterization. These include the identification of fish homologs/paralogs of mammalian pluripotency genes and parameters for optimal chimera formation. In addition, fish germ cell cultures and transplantation have attracted considerable interest for germline transmission and surrogate production. Haploid ES cell nuclear transfer has proven in medaka the feasibility of semi-cloning as a novel assisted reproductive technology. In this special issue on "Fish Stem Cells and Nuclear Transfer", we will focus our review on medaka to illustrate the current status and perspective of fish stem cells in research and application. We will also mention semi-cloning as a new development to conventional nuclear transfer.
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Affiliation(s)
- Ni Hong
- Department of Biological Science, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore
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Parton A, Bayne CJ, Barnes DW. Analysis and functional annotation of expressed sequence tags from in vitro cell lines of elasmobranchs: Spiny dogfish shark (Squalus acanthias) and little skate (Leucoraja erinacea). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:199-206. [PMID: 20471924 DOI: 10.1016/j.cbd.2010.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/16/2010] [Accepted: 04/16/2010] [Indexed: 02/02/2023]
Abstract
Elasmobranchs are the most commonly used experimental models among the jawed, cartilaginous fish (Chondrichthyes). Previously we developed cell lines from embryos of two elasmobranchs, Squalus acanthias the spiny dogfish shark (SAE line), and Leucoraja erinacea the little skate (LEE-1 line). From these lines cDNA libraries were derived and expressed sequence tags (ESTs) generated. From the SAE cell line 4303 unique transcripts were identified, with 1848 of these representing unknown sequences (showing no BLASTX identification). From the LEE-1 cell line, 3660 unique transcripts were identified, and unknown, unique sequences totaled 1333. Gene Ontology (GO) annotation showed that GO assignments for the two cell lines were in general similar. These results suggest that the procedures used to derive the cell lines led to isolation of cell types of the same general embryonic origin from both species. The LEE-1 transcripts included GO categories "envelope" and "oxidoreductase activity" but the SAE transcripts did not. GO analysis of SAE transcripts identified the category "anatomical structure formation" that was not present in LEE-1 cells. Increased organelle compartments may exist within LEE-1 cells compared to SAE cells, and the higher oxidoreductase activity in LEE-1 cells may indicate a role for these cells in responses associated with innate immunity or in steroidogenesis. These EST libraries from elasmobranch cell lines provide information for assembly of genomic sequences and are useful in revealing gene diversity, new genes and molecular markers, as well as in providing means for elucidation of full-length cDNAs and probes for gene array analyses. This is the first study of this type with members of the Chondrichthyes.
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Affiliation(s)
- Angela Parton
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672, USA
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Hwang JH, Parton A, Czechanski A, Ballatori N, Barnes D. Arachidonic acid-induced expression of the organic solute and steroid transporter-beta (Ost-beta) in a cartilaginous fish cell line. Comp Biochem Physiol C Toxicol Pharmacol 2008; 148:39-47. [PMID: 18407792 PMCID: PMC2471870 DOI: 10.1016/j.cbpc.2008.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Revised: 03/06/2008] [Accepted: 03/06/2008] [Indexed: 12/11/2022]
Abstract
The organic solute and steroid transporter (OST/Ost) is a unique membrane transport protein heterodimer composed of subunits designated alpha and beta, that transports conjugated steroids and prostaglandin E(2) across the plasma membrane. Ost was first identified in the liver of the cartilaginous fish Leucoraja erinacea, the little skate, and subsequently was found in many other species, including humans and rodents. The present study describes the isolation of a new cell line, LEE-1, derived from an early embryo of L. erinacea, and characterizes the expression of Ost in these cells. The mRNA size and amino acid sequence of Ost-beta in LEE-1 were identical to that previously reported for Ost-beta from skate liver, and the primary structure was identical to that of the spiny dogfish shark (Squalus acanthias) with the exception of a single amino acid. Ost-beta was found both on the plasma membrane and intracellularly in LEE-1 cells, consistent with its localization in other cell types. Interestingly, arachidonic acid, the precursor to eicosanoids, strongly induced Ost-beta expression in LEE-1 cells and a lipid mixture containing arachidonic acid also induced Ost-alpha. Overall, the present study describes the isolation of a novel marine cell line, and shows that this cell line expresses relatively high levels of Ost when cultured in the presence of arachidonic acid. Although the function of this transport protein in embryo-derived cells is unknown, it may play a role in the disposition of eicosanoids or steroid-derived molecules.
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Affiliation(s)
- Jae-Ho Hwang
- Mount Desert Island Biological Laboratory, P.O. Box 60, Salisbury Cove, ME, 04672, USA
| | - Angela Parton
- Mount Desert Island Biological Laboratory, P.O. Box 60, Salisbury Cove, ME, 04672, USA
| | - Anne Czechanski
- Mount Desert Island Biological Laboratory, P.O. Box 60, Salisbury Cove, ME, 04672, USA
| | - Nazzareno Ballatori
- Mount Desert Island Biological Laboratory, P.O. Box 60, Salisbury Cove, ME, 04672, USA
- Department of Environmental Medicine, University of Rochester School of Medicine, Rochester, N.Y., 14642, USA
| | - David Barnes
- Mount Desert Island Biological Laboratory, P.O. Box 60, Salisbury Cove, ME, 04672, USA
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Kobayashi H, Parton A, Czechanski A, Durkin C, Kong CC, Barnes D. Multidrug resistance-associated protein 3 (Mrp3/Abcc3/Moat-D) is expressed in the SAE Squalus acanthias shark embryo-derived cell line. Zebrafish 2008; 4:261-75. [PMID: 18284333 DOI: 10.1089/zeb.2007.0520] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The multidrug resistance-associated protein 3 (MRP3/Mrp3) is a member of the ATP-binding cassette (ABC) protein family of membrane transporters and related proteins that act on a variety of xenobiotic and anionic molecules to transfer these substrates in an ATP-dependent manner. In recent years, useful comparative information regarding evolutionarily conserved structure and transport functions of these proteins has accrued through the use of primitive marine animals such as cartilaginous fish. Until recently, one missing tool in comparative studies with cartilaginous fish was cell culture. We have derived from the embryo of Squalus acanthias, the spiny dogfish shark, the S. acanthias embryo (SAE) mesenchymal stem cell line. This is the first continuously proliferating cell line from a cartilaginous fish. We identified expression of Mrp3 in this cell line, cloned the molecule, and examined molecular and cellular physiological aspects of the protein. Shark Mrp3 is characterized by three membrane-spanning domains and two nucleotide-binding domains. Multiple alignments with other species showed that the shark Mrp3 amino acid sequence was well conserved. The shark sequence was overall 64% identical to human MRP3, 72% identical to chicken Mrp3, and 71% identical to frog and stickleback Mrp3. Highest identity between shark and human amino acid sequence (82%) was seen in the carboxyl-terminal nucleotide-binding domain of the proteins. Cell culture experiments showed that mRNA for the protein was induced as much as 25-fold by peptide growth factors, fetal bovine serum, and lipid nutritional components, with the largest effect mediated by a combination of lipids including unsaturated and saturated fatty acids, cholesterol, and vitamin E.
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Affiliation(s)
- Hiroshi Kobayashi
- Mount Desert Island Biological Laboratory, Salisbury Cove, Maine 04672, USA
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