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Tamaoki J, Maeda H, Kobayashi I, Takeuchi M, Ohashi K, Gore A, Bonkhofer F, Patient R, Weinstein BM, Kobayashi M. LSD1 promotes the egress of hematopoietic stem and progenitor cells into the bloodstream during the endothelial-to-hematopoietic transition. Dev Biol 2023:S0012-1606(23)00111-2. [PMID: 37353106 PMCID: PMC10393020 DOI: 10.1016/j.ydbio.2023.06.012] [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: 02/02/2023] [Revised: 05/27/2023] [Accepted: 06/19/2023] [Indexed: 06/25/2023]
Abstract
During embryonic development, primitive and definitive waves of hematopoiesis take place to provide proper blood cells for each developmental stage, with the possible involvement of epigenetic factors. We previously found that lysine-specific demethylase 1 (LSD1/KDM1A) promotes primitive hematopoietic differentiation by shutting down the gene expression program of hemangioblasts in an Etv2/Etsrp-dependent manner. In the present study, we demonstrated that zebrafish LSD1 also plays important roles in definitive hematopoiesis in the development of hematopoietic stem and progenitor cells. A combination of genetic approaches and imaging analyses allowed us to show that LSD1 promotes the egress of hematopoietic stem and progenitor cells into the bloodstream during the endothelial-to-hematopoietic transition. Analysis of compound mutant lines with Etv2/Etsrp mutant zebrafish revealed that, unlike in primitive hematopoiesis, this function of LSD1 was independent of Etv2/Etsrp. The phenotype of LSD1 mutant zebrafish during the endothelial-to-hematopoietic transition was similar to that of previously reported compound knockout mice of Gfi1/Gfi1b, which forms a complex with LSD1 and represses endothelial genes. Moreover, co-knockdown of zebrafish Gfi1/Gfi1b genes inhibited the development of HSPCs. We therefore hypothesize that the shutdown of the Gfi1/Gfi1b-target genes during the endothelial-to-hematopoietic transition is one of the key evolutionarily conserved functions of LSD1 in definitive hematopoiesis.
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Affiliation(s)
- Junya Tamaoki
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan; Research Fellow of Japan Society for the Promotion of Science (JSPS), Japan
| | - Hiroki Maeda
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Isao Kobayashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Kanazawa, 920-1192, Japan
| | - Miki Takeuchi
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Ken Ohashi
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan
| | - Aniket Gore
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Florian Bonkhofer
- Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Roger Patient
- Molecular Hematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Brant M Weinstein
- Division of Developmental Biology, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, 305-8575, Japan.
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2
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Rubin SA, Baron CS, Pessoa Rodrigues C, Duran M, Corbin AF, Yang SP, Trapnell C, Zon LI. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish. J Exp Med 2022; 219:e20220038. [PMID: 35938989 PMCID: PMC9365674 DOI: 10.1084/jem.20220038] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023] Open
Abstract
The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ∼70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B- and T-cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.
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Affiliation(s)
- Sara A. Rubin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Chloé S. Baron
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Cecilia Pessoa Rodrigues
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexandra F. Corbin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Song P. Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA
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3
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Faisal M, Hassan M, Kumar A, Zubair M, Jamal M, Menghwar H, Saad M, Kloczkowski A. Hematopoietic Stem and Progenitor Cells (HSPCs) and Hematopoietic Microenvironment: Molecular and Bioinformatic Studies of the Zebrafish Models. Int J Mol Sci 2022; 23:ijms23137285. [PMID: 35806290 PMCID: PMC9266955 DOI: 10.3390/ijms23137285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/25/2022] [Accepted: 06/25/2022] [Indexed: 02/01/2023] Open
Abstract
Hematopoietic stem cells (HSCs) reside in a specialized microenvironment in a peculiar anatomic location which regulates the maintenance of stem cells and controls its functions. Recent scientific progress in experimental technologies have enabled the specific detection of epigenetic factors responsible for the maintenance and quiescence of the hematopoietic niche, which has improved our knowledge of regulatory mechanisms. The aberrant role of RNA-binding proteins and their impact on the disruption of stem cell biology have been reported by a number of recent studies. Despite recent modernization in hematopoietic microenvironment research avenues, our comprehension of the signaling mechanisms and interactive pathways responsible for integration of the hematopoietic niche is still limited. In the past few decades, zebrafish usage with regards to exploratory studies of the hematopoietic niche has expanded our knowledge for deeper understanding of novel cellular interactions. This review provides an update on the functional roles of different genetic and epigenetic factors and molecular signaling events at different sections of the hematopoietic microenvironment. The explorations of different molecular approaches and interventions of latest web-based tools being used are also outlined. This will help us to get more mechanistic insights and develop therapeutic options for the malignancies.
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Affiliation(s)
- Muhammad Faisal
- Division of Hematology, College of Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA;
| | - Mubashir Hassan
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
| | - Aman Kumar
- Department of Ophthalmology and Vision Sciences, The Ohio State University, Columbus, OH 43210, USA;
| | - Muhammad Zubair
- Department of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
| | - Muhammad Jamal
- Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan 430072, China;
| | - Harish Menghwar
- Axe Molecular Endocrinology and Nephrology, CHU de Quebec-Research Center (CHUL), Laval University, Quebec City, QC G1V 4G2, Canada;
| | - Muhammad Saad
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43205, USA;
| | - Andrzej Kloczkowski
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA;
- Department of Pediatrics, The Ohio State University, Columbus, OH 43205, USA
- Correspondence: ; Tel.: +1-614-355-6671
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4
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Stosik M, Tokarz-Deptuła B, Deptuła W. Haematopoiesis in Zebrafish (Danio Rerio). Front Immunol 2022; 13:902941. [PMID: 35720291 PMCID: PMC9201100 DOI: 10.3389/fimmu.2022.902941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
Haematopoiesis in fish and mammals is a complex process, and many aspects regarding its model and the differentiation of haematopoietic stem cells (HSCs) still remain enigmatic despite advanced studies. The effects of microenvironmental factors or HSCs niche and signalling pathways on haematopoiesis are also unclear. This review presents Danio rerio as a model organism for studies on haematopoiesis in vertebrates and discusses the development of this process during the embryonic period and in adult fish. It describes the role of the microenvironment of the haematopoietic process in regulating the formation and function of HSCs/HSPCs (hematopoietic stem/progenitor cells) and highlights facts and research areas important for haematopoiesis in fish and mammals.
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Affiliation(s)
- Michał Stosik
- Institute of Biological Science, Faculty of Biological Sciences, University of Zielona Góra, Zielona Góra, Poland
| | | | - Wiesław Deptuła
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Toruń, Poland
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Liu Y, Kassack ME, McFaul ME, Christensen LN, Siebert S, Wyatt SR, Kamei CN, Horst S, Arroyo N, Drummond IA, Juliano CE, Draper BW. Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary. eLife 2022; 11:76014. [PMID: 35588359 PMCID: PMC9191896 DOI: 10.7554/elife.76014] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function and the transcriptome profiles will provide a valuable resource for future studies.
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Affiliation(s)
- Yulong Liu
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Michelle E Kassack
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Matthew E McFaul
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Lana N Christensen
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Sydney R Wyatt
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Caramai N Kamei
- Mount Desert Island Biological Laboratory, Bar Harbor, United States
| | - Samuel Horst
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Nayeli Arroyo
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Iain A Drummond
- Mount Desert Island Biological Laboratory, Bar Harbor, United States
| | - Celina E Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
| | - Bruce W Draper
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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6
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Li Y, Tang C, Liu F, Zhu C, Liu F, Zhu P, Wang L. DNA methylation safeguards the generation of hematopoietic stem and progenitor cells by repression of Notch signaling. Development 2022; 149:275510. [PMID: 35502759 PMCID: PMC9188753 DOI: 10.1242/dev.200390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/21/2022] [Indexed: 11/20/2022]
Abstract
The earliest hematopoietic stem and progenitor cells (HSPCs) are generated from the ventral wall of the dorsal aorta, through endothelial-to-hematopoietic transition during vertebrate embryogenesis. Notch signaling is crucial for HSPC generation across vertebrates; however, the precise control of Notch during this process remains unclear. In the present study, we used multi-omics approaches together with functional assays to assess global DNA methylome dynamics during the endothelial cells to HSPCs transition in zebrafish, and determined that DNA methyltransferase 1 (Dnmt1) is essential for HSPC generation via repression of Notch signaling. Depletion of dnmt1 resulted in decreased DNA methylation levels and impaired HSPC production. Mechanistically, we found that loss of dnmt1 induced hypomethylation of Notch genes and consequently elevated Notch activity in hemogenic endothelial cells, thereby repressing the generation of HSPCs. This finding deepens our understanding of HSPC specification in vivo, which will provide helpful insights for designing new strategies for HSPC generation in vitro. Summary: Multi-omics approaches and functional assays reveal global DNA methylome dynamics and an indispensable role of DNA methyltransferase 1 in hematopoietic stem/progenitor cell generation through repression of Notch signaling.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences 1 , Beijing, 100101 , China
| | - Chao Tang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College 2 , Tianjin, 300020 , China
| | - Fan Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College 2 , Tianjin, 300020 , China
| | - Caiying Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College 2 , Tianjin, 300020 , China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, University of Chinese Academy of Sciences 1 , Beijing, 100101 , China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College 2 , Tianjin, 300020 , China
| | - Lu Wang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College 2 , Tianjin, 300020 , China
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7
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Ma L, Tang Q, Gao X, Lee J, Lei R, Suzuki M, Zheng D, Ito K, Frenette PS, Dawlaty MM. Tet-mediated DNA demethylation regulates specification of hematopoietic stem and progenitor cells during mammalian embryogenesis. SCIENCE ADVANCES 2022; 8:eabm3470. [PMID: 35235365 PMCID: PMC8890710 DOI: 10.1126/sciadv.abm3470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/06/2022] [Indexed: 05/10/2023]
Abstract
Ten-eleven translocation (Tet) enzymes promote DNA demethylation by oxidizing 5-methylcytosine. They are expressed during development and are essential for mouse gastrulation. However, their postgastrulation functions are not well established. We find that global or endothelial-specific loss of all three Tet enzymes immediately after gastrulation leads to reduced number of hematopoietic stem and progenitor cells (HSPCs) and lethality in mid-gestation mouse embryos. This is due to defects in specification of HSPCs from endothelial cells (ECs) that compromise primitive and definitive hematopoiesis. Mechanistically, loss of Tet enzymes in ECs led to hypermethylation and down-regulation of NFκB1 and master hematopoietic transcription factors (Gata1/2, Runx1, and Gfi1b). Restoring Tet catalytic activity or overexpression of these factors in Tet-deficient ECs rescued hematopoiesis defects. This establishes Tet enzymes as activators of hematopoiesis programs in ECs for specification of HSPCs during embryogenesis, which is distinct from their roles in adult hematopoiesis, with implications in deriving HSPCs from pluripotent cells.
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Affiliation(s)
- Liyang Ma
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Qin Tang
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Xin Gao
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Joun Lee
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Run Lei
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Paul S. Frenette
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
| | - Meelad M. Dawlaty
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, 1301 Morris Park Ave., Bronx, NY 10461, USA
- Department of Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
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8
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Darden DB, Mira JC, Lopez MC, Stortz JA, Fenner BP, Kelly LS, Nacionales DC, Budharaju A, Loftus TJ, Baker HV, Moore FA, Brakenridge SC, Moldawer LL, Mohr AM, Efron PA. Identification of unique microRNA expression patterns in bone marrow hematopoietic stem and progenitor cells after hemorrhagic shock and multiple injuries in young and old adult mice. J Trauma Acute Care Surg 2021; 91:692-699. [PMID: 34252063 PMCID: PMC8463436 DOI: 10.1097/ta.0000000000003350] [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] [Indexed: 11/26/2022]
Abstract
BACKGROUND After severe trauma, the older host experiences more dysfunctional hematopoiesis of bone marrow (BM) hematopoietic stem and progenitor cells (HSPCs), and dysfunctional differentiation of circulating myeloid cells into effective innate immune cells. Our main objective was to compare BM HSPC microRNA (miR) responses of old and young mice in a clinically relevant model of severe trauma and shock. METHODS C57BL/6 adult male mice aged 8 to 12 weeks (young) and 18 to 24 months (old) underwent multiple injuries and hemorrhagic shock (polytrauma [PT]) that engenders the equivalent of major trauma (Injury Severity Score, >15). Pseudomonas pneumonia (PNA) was induced in some young and old adult mice 24 hours after PT. MicroRNA expression patterns were determined from lineage-negative enriched BM HSPCs isolated from PT and PT-PNA mice at 24 and 48 hours postinjury, respectively. Genome-wide expression and pathway analyses were also performed on bronchoalveolar lavage (BAL) leukocytes from both mouse cohorts. RESULTS MicroRNA expression significantly differed among all experimental conditions (p < 0.05), except for old-naive versus old-injured (PT or PT-PNA) mice, suggesting an inability of old mice to mount a robust early miR response to severe shock and injury. In addition, young adult mice had significantly more leukocytes obtained from their BAL, and there were greater numbers of polymorphonuclear cells compared with old mice (59.8% vs. 2.2%, p = 0.0069). Despite increased gene expression changes, BAL leukocytes from old mice demonstrated a more dysfunctional transcriptomic response to PT-PNA than young adult murine BAL leukocytes, as reflected in predicted upstream functional pathway analysis. CONCLUSION The miR expression pattern in BM HSPCs after PT (+/-PNA) is dissimilar in old versus young adult mice. In the acute postinjury phase, old adult mice are unable to mount a robust miR HSPC response. Hematopoietic stem and progenitor cell miR expression in old PT mice reflects a diminished functional status and a blunted capacity for terminal differentiation of myeloid cells.
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Affiliation(s)
- Dijoia B. Darden
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Juan C. Mira
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Maria-Cecilia Lopez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Julie A. Stortz
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Brittany P. Fenner
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Lauren S. Kelly
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Dina C. Nacionales
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Ashrita Budharaju
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Tyler J. Loftus
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Henry V. Baker
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Frederick A. Moore
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Scott C. Brakenridge
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Lyle L. Moldawer
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Alicia M. Mohr
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Philip A. Efron
- Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
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9
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Sugden WW, North TE. Making Blood from the Vessel: Extrinsic and Environmental Cues Guiding the Endothelial-to-Hematopoietic Transition. Life (Basel) 2021; 11:life11101027. [PMID: 34685398 PMCID: PMC8539454 DOI: 10.3390/life11101027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/25/2021] [Accepted: 09/27/2021] [Indexed: 01/10/2023] Open
Abstract
It is increasingly recognized that specialized subsets of endothelial cells carry out unique functions in specific organs and regions of the vascular tree. Perhaps the most striking example of this specialization is the ability to contribute to the generation of the blood system, in which a distinct population of “hemogenic” endothelial cells in the embryo transforms irreversibly into hematopoietic stem and progenitor cells that produce circulating erythroid, myeloid and lymphoid cells for the lifetime of an animal. This review will focus on recent advances made in the zebrafish model organism uncovering the extrinsic and environmental factors that facilitate hemogenic commitment and the process of endothelial-to-hematopoietic transition that produces blood stem cells. We highlight in particular biomechanical influences of hemodynamic forces and the extracellular matrix, metabolic and sterile inflammatory cues present during this developmental stage, and outline new avenues opened by transcriptomic-based approaches to decipher cell–cell communication mechanisms as examples of key signals in the embryonic niche that regulate hematopoiesis.
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Affiliation(s)
- Wade W. Sugden
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
| | - Trista E. North
- Stem Cell Program, Department of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA;
- Developmental and Regenerative Biology Program, Harvard Medical School, Boston, MA 02115, USA
- Correspondence:
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10
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Greenspan LJ, Weinstein BM. To be or not to be: endothelial cell plasticity in development, repair, and disease. Angiogenesis 2021; 24:251-269. [PMID: 33449300 PMCID: PMC8205957 DOI: 10.1007/s10456-020-09761-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023]
Abstract
Endothelial cells display an extraordinary plasticity both during development and throughout adult life. During early development, endothelial cells assume arterial, venous, or lymphatic identity, while selected endothelial cells undergo additional fate changes to become hematopoietic progenitor, cardiac valve, and other cell types. Adult endothelial cells are some of the longest-lived cells in the body and their participation as stable components of the vascular wall is critical for the proper function of both the circulatory and lymphatic systems, yet these cells also display a remarkable capacity to undergo changes in their differentiated identity during injury, disease, and even normal physiological changes in the vasculature. Here, we discuss how endothelial cells become specified during development as arterial, venous, or lymphatic endothelial cells or convert into hematopoietic stem and progenitor cells or cardiac valve cells. We compare findings from in vitro and in vivo studies with a focus on the zebrafish as a valuable model for exploring the signaling pathways and environmental cues that drive these transitions. We also discuss how endothelial plasticity can aid in revascularization and repair of tissue after damage- but may have detrimental consequences under disease conditions. By better understanding endothelial plasticity and the mechanisms underlying endothelial fate transitions, we can begin to explore new therapeutic avenues.
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Affiliation(s)
- Leah J Greenspan
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20892, USA.
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11
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Bergo V, Trompouki E. New tools for 'ZEBRA-FISHING'. Brief Funct Genomics 2021:elab001. [PMID: 33605988 DOI: 10.1093/bfgp/elab001] [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: 10/23/2020] [Revised: 12/14/2020] [Accepted: 01/04/2021] [Indexed: 11/14/2022] Open
Abstract
Zebrafish has been established as a classical model for developmental studies, yet in the past years, with the explosion of novel technological methods, the use of zebrafish as a model has expanded. One of the prominent fields that took advantage of zebrafish as a model organism early on is hematopoiesis, the process of blood cell generation from hematopoietic stem and progenitor cells (HSPCs). In zebrafish, HSPCs are born early during development in the aorta-gonad-mesonephros region and then translocate to the caudal hematopoietic tissue, where they expand and finally take residence in the kidney marrow. This journey is tightly regulated at multiple levels from extracellular signals to chromatin. In order to delineate the mechanistic underpinnings of this process, next-generation sequencing techniques could be an important ally. Here, we describe genome-wide approaches that have been undertaken to delineate zebrafish hematopoiesis.
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12
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Akdogan-Ozdilek B, Duval KL, Goll MG. Chromatin dynamics at the maternal to zygotic transition: recent advances from the zebrafish model. F1000Res 2020; 9. [PMID: 32528656 PMCID: PMC7262572 DOI: 10.12688/f1000research.21809.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/17/2020] [Indexed: 01/02/2023] Open
Abstract
Early animal development is characterized by intense reorganization of the embryonic genome, including large-scale changes in chromatin structure and in the DNA and histone modifications that help shape this structure. Particularly profound shifts in the chromatin landscape are associated with the maternal-to-zygotic transition, when the zygotic genome is first transcribed and maternally loaded transcripts are degraded. The accessibility of the early zebrafish embryo facilitates the interrogation of chromatin during this critical window of development, making it an important model for early chromatin regulation. Here, we review our current understanding of chromatin dynamics during early zebrafish development, highlighting new advances as well as similarities and differences between early chromatin regulation in zebrafish and other species.
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Affiliation(s)
| | | | - Mary G Goll
- Department of Genetics, University of Georgia, Athens, GA, USA
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13
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Meyer DN, Crofts EJ, Akemann C, Gurdziel K, Farr R, Baker BB, Weber D, Baker TR. Developmental exposure to Pb 2+ induces transgenerational changes to zebrafish brain transcriptome. CHEMOSPHERE 2020; 244:125527. [PMID: 31816550 PMCID: PMC7015790 DOI: 10.1016/j.chemosphere.2019.125527] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/27/2019] [Accepted: 11/30/2019] [Indexed: 05/24/2023]
Abstract
Lead (Pb2+) is a major public health hazard for urban children, with profound and well-characterized developmental and behavioral implications across the lifespan. The ability of early Pb2+ exposure to induce epigenetic changes is well-established, suggesting that Pb2+-induced neurobehavioral deficits may be heritable across generations. Understanding the long-term and multigenerational repercussions of lead exposure is crucial for clarifying both the genotypic alterations behind these behavioral outcomes and the potential mechanism of heritability. To study this, zebrafish (Danio rerio) embryos (<2 h post fertilization; EK strain) were exposed for 24 h to waterborne Pb2+ at a concentration of 10 μM. This exposed F0 generation was raised to adulthood and spawned to produce the F1 generation, which was subsequently spawned to produce the F2 generation. Previous avoidance conditioning studies determined that a 10 μM Pb2+ dose resulted in learning impairments persisting through the F2 generation. RNA was extracted from control- and 10 μM Pb2+-lineage F2 brains, (n = 10 for each group), sequenced, and transcript expression was quantified utilizing Quant-Seq. 648 genes were differentially expressed in the brains of F2 lead-lineage fish versus F2 control-lineage fish. Pathway analysis revealed altered genes in processes including synaptic function and plasticity, neurogenesis, endocrine homeostasis, and epigenetic modification, all of which are implicated in lead-induced neurobehavioral deficits and/or their inheritance. These data will inform future investigations to elucidate the mechanism of adult-onset and transgenerational health effects of developmental lead exposure.
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Affiliation(s)
- Danielle N Meyer
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI, USA; Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Emily J Crofts
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Camille Akemann
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI, USA; Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Katherine Gurdziel
- Applied Genome Technology Center, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Rebecca Farr
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Bridget B Baker
- Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI, USA; Division of Laboratory Animal Resources, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Daniel Weber
- Children's Environmental Health Sciences Core Center, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Tracie R Baker
- Department of Pharmacology, School of Medicine, Wayne State University, Detroit, MI, USA; Institute of Environmental Health Sciences, School of Medicine, Wayne State University, Detroit, MI, USA.
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14
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Fillatre J, Fauny JD, Fels JA, Li C, Goll M, Thisse C, Thisse B. TEADs, Yap, Taz, Vgll4s transcription factors control the establishment of Left-Right asymmetry in zebrafish. eLife 2019; 8:45241. [PMID: 31513014 PMCID: PMC6759317 DOI: 10.7554/elife.45241] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/11/2019] [Indexed: 12/15/2022] Open
Abstract
In many vertebrates, establishment of Left-Right (LR) asymmetry results from the activity of a ciliated organ functioning as the LR Organizer (LRO). While regulation of the formation of this structure by major signaling pathways has been described, the transcriptional control of LRO formation is poorly understood. Using the zebrafish model, we show that the transcription factors and cofactors mediating or regulating the transcriptional outcome of the Hippo signaling pathway play a pivotal role in controlling the expression of genes essential to the formation of the LRO including ligands and receptors of signaling pathways involved in this process and most genes required for motile ciliogenesis. Moreover, the transcription cofactor, Vgll4l regulates epigenetic programming in LRO progenitors by controlling the expression of writers and readers of DNA methylation marks. Altogether, our study uncovers a novel and essential role for the transcriptional effectors and regulators of the Hippo pathway in establishing LR asymmetry.
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Affiliation(s)
- Jonathan Fillatre
- Department of Cell Biology, University of Virginia, Charlottesville, United States
| | - Jean-Daniel Fauny
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, Illkirch-Graffenstaden, France.,Institut de Biologie Moléculaire et Cellulaire, Strasbourg, France
| | | | - Cheng Li
- Department of Genetics, University of Georgia, Athens, United States
| | - Mary Goll
- Department of Genetics, University of Georgia, Athens, United States
| | - Christine Thisse
- Department of Cell Biology, University of Virginia, Charlottesville, United States.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, Illkirch-Graffenstaden, France
| | - Bernard Thisse
- Department of Cell Biology, University of Virginia, Charlottesville, United States.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/Université de Strasbourg, Illkirch-Graffenstaden, France
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15
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Bonkhofer F, Rispoli R, Pinheiro P, Krecsmarik M, Schneider-Swales J, Tsang IHC, de Bruijn M, Monteiro R, Peterkin T, Patient R. Blood stem cell-forming haemogenic endothelium in zebrafish derives from arterial endothelium. Nat Commun 2019; 10:3577. [PMID: 31395869 PMCID: PMC6687740 DOI: 10.1038/s41467-019-11423-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 07/10/2019] [Indexed: 02/07/2023] Open
Abstract
Haematopoietic stem cells are generated from the haemogenic endothelium (HE) located in the floor of the dorsal aorta (DA). Despite being integral to arteries, it is controversial whether HE and arterial endothelium share a common lineage. Here, we present a transgenic zebrafish runx1 reporter line to isolate HE and aortic roof endothelium (ARE)s, excluding non-aortic endothelium. Transcriptomic analysis of these populations identifies Runx1-regulated genes and shows that HE initially expresses arterial markers at similar levels to ARE. Furthermore, runx1 expression depends on prior arterial programming by the Notch ligand dll4. Runx1−/− mutants fail to downregulate arterial genes in the HE, which remains integrated within the DA, suggesting that Runx1 represses the pre-existing arterial programme in HE to allow progression towards the haematopoietic fate. These findings strongly suggest that, in zebrafish, aortic endothelium is a precursor to HE, with potential implications for pluripotent stem cell differentiation protocols for the generation of transplantable HSCs. HSCs emerge from haemogenic endothelium (HE) in the dorsal aorta but whether these tissues share a common lineage is unclear. Here, the authors use a zebrafish runx1 reporter to show that HE maintains an arterial gene expression profile in the absence of Runx1, suggesting the aortic endothelium as a precursor of HE.
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Affiliation(s)
- Florian Bonkhofer
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Rossella Rispoli
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.,Division of Genetics and Molecular Medicine, NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London, UK
| | - Philip Pinheiro
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Monika Krecsmarik
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK.,BHF Centre of Research Excellence, Oxford, UK
| | - Janina Schneider-Swales
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Ingrid Ho Ching Tsang
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Marella de Bruijn
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Rui Monteiro
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK. .,BHF Centre of Research Excellence, Oxford, UK. .,Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Tessa Peterkin
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Roger Patient
- Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK. .,BHF Centre of Research Excellence, Oxford, UK.
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16
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Packaging development: how chromatin controls transcription in zebrafish embryogenesis. Biochem Soc Trans 2019; 47:713-724. [DOI: 10.1042/bst20180617] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/15/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022]
Abstract
Abstract
How developmental gene expression is activated, co-ordinated and maintained is one of the biggest questions in developmental biology. While transcription factors lead the way in directing developmental gene expression, their accessibility to the correct repertoire of genes can depend on other factors such as DNA methylation, the presence of particular histone variants and post-translational modifications of histones. Collectively, factors that modify DNA or affect its packaging and accessibility contribute to a chromatin landscape that helps to control the timely expression of developmental genes. Zebrafish, perhaps better known for their strength as a model of embryology and organogenesis during development, are coming to the fore as a powerful model for interpreting the role played by chromatin in gene expression. Several recent advances have shown that zebrafish exhibit both similarities and differences to other models (and humans) in the way that they employ chromatin mechanisms of gene regulation. Here, I review how chromatin influences developmental transcriptional programmes during early zebrafish development, patterning and organogenesis. Lastly, I briefly highlight the importance of zebrafish chromatin research towards the understanding of human disease and transgenerational inheritance.
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17
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Zhou W, Tian D, He J, Yan X, Zhao J, Yuan X, Peng S. Prolonged exposure to carbon nanoparticles induced methylome remodeling and gene expression in zebrafish heart. J Appl Toxicol 2018; 39:322-332. [PMID: 30289172 DOI: 10.1002/jat.3721] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 08/06/2018] [Accepted: 08/06/2018] [Indexed: 01/15/2023]
Abstract
Growing black carbon (BC) emission has become one of the major urgent environmental issues facing human beings. Usually, BC or BC-containing carbon nanoparticles (CNPs) were recognized as non-directly toxic components of atmospheric particulate matter. However, epidemiology studies have provided much evidence of the associations of exposure of particulate-containing carbon particles with cardiovascular diseases. There are still no related studies to support the epidemiological conclusions. Hence, in this article we exposed adult zebrafish to CNPs for 60 days, and then explored the heart location and potential adverse effects on cardiac tissues of these nanosized carbon particles. Our results first showed direct visualization of cardiac endothelial uptake and heart deposition of CNPs in zebrafish. In addition, CNPs caused significant ultrastructural alterations in myocardial tissue and induced the expression of inflammatory cytokines in a dose-dependent manner, resulting in sub-endocardial inflammation and cell apoptosis. Moreover, our data demonstrated the perturbations caused by CNPs on DNA methylation, suggesting that DNA methylome remodeling might play a critical role in CNP-induced cardiotoxicity in zebrafish heart. Therefore, this study not only proved a laboratory link between CNP exposure and cardiotoxicity in vivo, but also indicated a possible toxicity mechanism involved.
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Affiliation(s)
- Wei Zhou
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Academy of Military Medical Sciences, Beijing, 100850, China
| | - Dongdong Tian
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Department of Pharmacy, Hebei General Hospital, Shijiazhuang, 050000, China
| | - Jun He
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Academy of Military Medical Sciences, Beijing, 100850, China
| | - Xiabei Yan
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Academy of Military Medical Sciences, Beijing, 100850, China
| | - Jun Zhao
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Academy of Military Medical Sciences, Beijing, 100850, China
| | - Xiaoyan Yuan
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Academy of Military Medical Sciences, Beijing, 100850, China
| | - Shuangqing Peng
- Evaluation and Research Centre for Toxicology, Institute of Disease Control and Prevention, PLA, Beijing, 100071, China.,Academy of Military Medical Sciences, Beijing, 100850, China
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18
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Rissone A, Burgess SM. Rare Genetic Blood Disease Modeling in Zebrafish. Front Genet 2018; 9:348. [PMID: 30233640 PMCID: PMC6127601 DOI: 10.3389/fgene.2018.00348] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 01/06/2023] Open
Abstract
Hematopoiesis results in the correct formation of all the different blood cell types. In mammals, it starts from specific hematopoietic stem and precursor cells residing in the bone marrow. Mature blood cells are responsible for supplying oxygen to every cell of the organism and for the protection against pathogens. Therefore, inherited or de novo genetic mutations affecting blood cell formation or the regulation of their activity are responsible for numerous diseases including anemia, immunodeficiency, autoimmunity, hyper- or hypo-inflammation, and cancer. By definition, an animal disease model is an analogous version of a specific clinical condition developed by researchers to gain information about its pathophysiology. Among all the model species used in comparative medicine, mice continue to be the most common and accepted model for biomedical research. However, because of the complexity of human diseases and the intrinsic differences between humans and other species, the use of several models (possibly in distinct species) can often be more helpful and informative than the use of a single model. In recent decades, the zebrafish (Danio rerio) has become increasingly popular among researchers, because it represents an inexpensive alternative compared to mammalian models, such as mice. Numerous advantages make it an excellent animal model to be used in genetic studies and in particular in modeling human blood diseases. Comparing zebrafish hematopoiesis to mammals, it is highly conserved with few, significant differences. In addition, the zebrafish model has a high-quality, complete genomic sequence available that shows a high level of evolutionary conservation with the human genome, empowering genetic and genomic approaches. Moreover, the external fertilization, the high fecundity and the transparency of their embryos facilitate rapid, in vivo analysis of phenotypes. In addition, the ability to manipulate its genome using the last genome editing technologies, provides powerful tools for developing new disease models and understanding the pathophysiology of human disorders. This review provides an overview of the different approaches and techniques that can be used to model genetic diseases in zebrafish, discussing how this animal model has contributed to the understanding of genetic diseases, with a specific focus on the blood disorders.
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Affiliation(s)
- Alberto Rissone
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, United States
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19
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Gore AV, Tomins KA, Iben J, Ma L, Castranova D, Davis AE, Parkhurst A, Jeffery WR, Weinstein BM. An epigenetic mechanism for cavefish eye degeneration. Nat Ecol Evol 2018; 2:1155-1160. [PMID: 29807993 PMCID: PMC6023768 DOI: 10.1038/s41559-018-0569-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 05/02/2018] [Indexed: 12/23/2022]
Abstract
Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss-of-eyes phenotype in the Pachón blind cave morph of the Mexican tetra Astyanax mexicanus, no inactivating mutations have been found in any of these genes. Here, we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave A. mexicanus. By performing parallel analyses in A. mexicanus cave and surface morphs, and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and downregulated genes in the cave morph are also linked to human eye disorders, suggesting that the function of these genes is conserved across vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.
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Affiliation(s)
- Aniket V Gore
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
| | - Kelly A Tomins
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - James Iben
- Molecular Genomics Laboratory, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Li Ma
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Daniel Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Andrew E Davis
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Amy Parkhurst
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - William R Jeffery
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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20
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Dobrzycki T, Krecsmarik M, Bonkhofer F, Patient R, Monteiro R. An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation. Biol Open 2018. [PMID: 29535102 PMCID: PMC5936060 DOI: 10.1242/bio.031096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Advances in genome engineering have resulted in the generation of numerous zebrafish mutant lines. A commonly used method to assess gene expression in the mutants is in situ hybridisation (ISH). Because the embryos can be distinguished by genotype after ISH, comparing gene expression between wild-type and mutant siblings can be done blinded and in parallel. Such experimental design reduces the technical variation between samples and minimises the risk of bias. This approach, however, requires an efficient method of genomic DNA extraction from post-ISH fixed zebrafish samples to ascribe phenotype to genotype. Here we describe a method to obtain PCR-quality DNA from 95-100% of zebrafish embryos, suitable for genotyping after ISH. In addition, we provide an image analysis protocol for quantifying gene expression of ISH-probed embryos, adaptable for the analysis of different expression patterns. Finally, we show that intensity-based image analysis enables accurate representation of the variability of gene expression detected by ISH and that it can complement quantitative methods like qRT-PCR. By combining genotyping after ISH and computer-based image analysis, we have established a high-confidence, unbiased methodology to assign gene expression levels to specific genotypes, and applied it to the analysis of molecular phenotypes of newly generated lmo4a mutants. Summary: Our optimised protocol to genotype zebrafish mutant embryos after in situ hybridisation and digitally quantify the in situ signal will help to standardise existing experimental designs and methods of analysis.
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Affiliation(s)
- Tomasz Dobrzycki
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Monika Krecsmarik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,BHF Centre of Research Excellence, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Florian Bonkhofer
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Roger Patient
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,BHF Centre of Research Excellence, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rui Monteiro
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK .,BHF Centre of Research Excellence, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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21
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Jessop P, Ruzov A, Gering M. Developmental Functions of the Dynamic DNA Methylome and Hydroxymethylome in the Mouse and Zebrafish: Similarities and Differences. Front Cell Dev Biol 2018; 6:27. [PMID: 29616219 PMCID: PMC5869911 DOI: 10.3389/fcell.2018.00027] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/05/2018] [Indexed: 12/25/2022] Open
Abstract
5-methylcytosine (5mC) is the best understood DNA modification and is generally believed to be associated with repression of gene expression. Over the last decade, sequentially oxidized forms of 5mC (oxi-mCs) have been discovered within the genomes of vertebrates. Their discovery was accompanied by that of the ten-eleven translocation (TET) methylcytosine dioxygenases, the enzymes that catalyze the formation of the oxi-mCs. Although a number of studies performed on different vertebrate models and embryonic stem cells demonstrated that both TET enzymes and oxi-mCs are likely to be important for several developmental processes it is currently unclear whether their developmental roles are conserved among vertebrates. Here, we summarize recent developments in this field suggesting that biological roles of TETs/oxi-mCs may significantly differ between mice and zebrafish. Thus, although the role of TET proteins in late organogenesis has been documented for both these systems; unlike in mice the enzymatic oxidation of 5mC does not seem to be involved in zygotic reprogramming or gastrulation in zebrafish. Our analysis may provide an insight into the general principles of epigenetic regulation of animal development and cellular differentiation.
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Affiliation(s)
- Peter Jessop
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Alexey Ruzov
- Division of Cancer and Stem Cells, Centre for Biomolecular Sciences, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin Gering
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, United Kingdom
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22
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Kasper DM, Nicoli S. Epigenetic and Epitranscriptomic Factors Make a Mark on Hematopoietic Stem Cell Development. CURRENT STEM CELL REPORTS 2018; 4:22-32. [PMID: 29910999 PMCID: PMC5999335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF THE REVIEW Blood specification is a highly dynamic process, whereby committed hemogenic endothelial cells (ECs) progressively transdifferentiate into multipotent, self-renewing hematopoietic stem cells (HSCs). Massive changes in gene expression must occur to switch cell identity, however the factors that mediate such an effect were a mystery until recently. This review summarizes the higher-order mechanisms involved in endothelial to hematopoietic reprogramming identified thus far. RECENT FINDINGS Accumulating evidence from mouse and zebrafish studies reveal that numerous chromatin-modifying (epigenetic) and RNA-modifying (epitranscriptomic) factors are required for the formation of HSCs from hemogenic endothelium. These genes function throughout the endothelial-hematopoietic transition, suggesting a dynamic interplay between 'epi'-machineries. SUMMARY Epigenetic and epitranscriptomic regulation are key mechanisms for reshaping global EC gene expression patterns to those that support HSC production. Future studies that capture modification dynamics should bring us closer to a complete understanding of how HSCs transition from hemogenic endothelium at the molecular level.
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Affiliation(s)
- Dionna M. Kasper
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA,Corresponding author:, ; Mailing address: Yale Cardiovascular Research Center, 300 George St., Room 773K, New Haven, CT 06511
| | - Stefania Nicoli
- Yale Cardiovascular Research Center, Department of Internal Medicine, Section of Cardiology, Yale University School of Medicine, New Haven, CT 06511, USA,Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA,Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06510, USA
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23
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Gore AV, Pillay LM, Venero Galanternik M, Weinstein BM. The zebrafish: A fintastic model for hematopoietic development and disease. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 7:e312. [PMID: 29436122 DOI: 10.1002/wdev.312] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 11/30/2017] [Accepted: 12/03/2017] [Indexed: 12/19/2022]
Abstract
Hematopoiesis is a complex process with a variety of different signaling pathways influencing every step of blood cell formation from the earliest precursors to final differentiated blood cell types. Formation of blood cells is crucial for survival. Blood cells carry oxygen, promote organ development and protect organs in different pathological conditions. Hematopoietic stem and progenitor cells (HSPCs) are responsible for generating all adult differentiated blood cells. Defects in HSPCs or their downstream lineages can lead to anemia and other hematological disorders including leukemia. The zebrafish has recently emerged as a powerful vertebrate model system to study hematopoiesis. The developmental processes and molecular mechanisms involved in zebrafish hematopoiesis are conserved with higher vertebrates, and the genetic and experimental accessibility of the fish and the optical transparency of its embryos and larvae make it ideal for in vivo analysis of hematopoietic development. Defects in zebrafish hematopoiesis reliably phenocopy human blood disorders, making it a highly attractive model system to screen small molecules to design therapeutic strategies. In this review, we summarize the key developmental processes and molecular mechanisms of zebrafish hematopoiesis. We also discuss recent findings highlighting the strengths of zebrafish as a model system for drug discovery against hematopoietic disorders. This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cell Differentiation and Reversion Vertebrate Organogenesis > Musculoskeletal and Vascular Nervous System Development > Vertebrates: Regional Development Comparative Development and Evolution > Organ System Comparisons Between Species.
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Affiliation(s)
- Aniket V Gore
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Laura M Pillay
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Marina Venero Galanternik
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland
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24
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Kasper DM, Nicoli S. Epigenetic and Epitranscriptomic Factors Make a Mark on Hematopoietic Stem Cell Development. CURRENT STEM CELL REPORTS 2018. [DOI: 10.1007/s40778-018-0113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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25
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Seritrakul P, Gross JM. Tet-mediated DNA hydroxymethylation regulates retinal neurogenesis by modulating cell-extrinsic signaling pathways. PLoS Genet 2017; 13:e1006987. [PMID: 28926578 PMCID: PMC5621703 DOI: 10.1371/journal.pgen.1006987] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/29/2017] [Accepted: 08/18/2017] [Indexed: 12/28/2022] Open
Abstract
DNA hydroxymethylation has recently been shown to play critical roles in regulating gene expression and terminal differentiation events in a variety of developmental contexts. However, little is known about its function during eye development. Methylcytosine dioxygenases of the Tet family convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), an epigenetic mark thought to serve as a precursor for DNA demethylation and as a stable mark in neurons. Here, we report a requirement for Tet activity during zebrafish retinal neurogenesis. In tet2-/-;tet3-/- mutants, retinal neurons are specified but most fail to terminally differentiate. While differentiation of the first born retinal neurons, the retinal ganglion cells (RGCs), is less affected in tet2-/-;tet3-/- mutants than other retinal cell types, the majority of RGCs do not undergo terminal morphogenesis and form axons. Moreover, the few photoreceptors that differentiate in tet2-/-;tet3-/- mutants fail to form outer segments, suggesting that Tet function is also required for terminal morphogenesis of differentiated retinal neurons. Mosaic analyses revealed a surprising cell non-autonomous requirement for tet2 and tet3 activity in facilitating retinal neurogenesis. Through a combination of candidate gene analysis, transcriptomics and pharmacological manipulations, we identified the Notch and Wnt pathways as cell-extrinsic pathways regulated by tet2 and tet3 activity during RGC differentiation and morphogenesis. Transcriptome analyses also revealed the ectopic expression of non-retinal genes in tet2-/-;tet3-/- mutant retinae, and this correlated with locus-specific reduction in 5hmC. These data provide the first evidence that Tet-dependent regulation of 5hmC formation is critical for retinal neurogenesis, and highlight an additional layer of complexity in the progression from retinal progenitor cell to differentiated retinal neuron during development of the vertebrate retina.
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Affiliation(s)
- Pawat Seritrakul
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States of America
- Departments of Ophthalmology, and Developmental Biology, The Louis J. Fox Center for Vision Restoration, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Jeffrey M. Gross
- Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States of America
- Departments of Ophthalmology, and Developmental Biology, The Louis J. Fox Center for Vision Restoration, The McGowan Institute for Regenerative Medicine, The University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
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26
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Firmino J, Carballo C, Armesto P, Campinho MA, Power DM, Manchado M. Phylogeny, expression patterns and regulation of DNA Methyltransferases in early development of the flatfish, Solea senegalensis. BMC DEVELOPMENTAL BIOLOGY 2017; 17:11. [PMID: 28716037 PMCID: PMC5513168 DOI: 10.1186/s12861-017-0154-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/12/2022]
Abstract
Background The identification of DNA methyltransferases (Dnmt) expression patterns during development and their regulation is important to understand the epigenetic mechanisms that modulate larval plasticity in marine fish. In this study, dnmt1 and dnmt3 paralogs were identified in the flatfish Solea senegalensis and expression patterns in early developmental stages and juveniles were determined. Additionally, the regulation of Dnmt transcription by a specific inhibitor (5-aza-2′-deoxycytidine) and temperature was evaluated. Results Five paralog genes of dnmt3, namely dnmt3aa, dnmt3ab, dnmt3ba, dnmt3bb.1 and dnmt3bb.2 and one gene for dnmt1 were identified. Phylogenetic analysis revealed that the dnmt gene family was highly conserved in teleosts and three fish-specific genes, dnmt3aa, dnmt3ba and dnmt3bb.2 have evolved. The spatio-temporal expression patterns of four dnmts (dnmt1, dnmt3aa, dnmt3ab and dnmt3bb.1) were different in early larval stages although all of them reduced expression with the age and were detected in neural organs and dnmt3aa appeared specific to somites. In juveniles, the four dnmt genes were expressed in brain and hematopoietic tissues such as kidney, spleen and gills. Treatment of sole embryos with 5-aza-2′-deoxycytidine down-regulated dntm1 and up-regulated dntm3aa. Moreover, in lecithotrophic larval stages, dnmt3aa and dnmt3ab were temperature sensitive and their expression was higher in larvae incubated at 16 °C relative to 20 °C. Conclusion Five dnmt3 and one dnmt1 paralog were identified in sole and their distinct developmental and tissue-specific expression patterns indicate that they may have different roles during development. The inhibitor 5-aza-2′-deoxycytidine modified the transcript abundance of dntm1 and dntm3aa in embryos, which suggests that a regulatory feedback mechanism exists for these genes. The impact of thermal regime on expression levels of dnmt3aa and dnmt3ab in lecithotrophic larval stages suggests that these paralogs might be involved in thermal programing. Electronic supplementary material The online version of this article (doi:10.1186/s12861-017-0154-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joana Firmino
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain.,Comparative Molecular Endocrinology Group, Marine Science Centre (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Carlos Carballo
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
| | - Paula Armesto
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain
| | - Marco A Campinho
- Comparative Molecular Endocrinology Group, Marine Science Centre (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Deborah M Power
- Comparative Molecular Endocrinology Group, Marine Science Centre (CCMAR), Universidade do Algarve, 8005-139, Faro, Portugal
| | - Manuel Manchado
- IFAPA Centro El Toruño, Junta de Andalucía, Camino Tiro Pichón s/n, 11500 El Puerto de Santa María, Cádiz, Spain.
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27
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Abstract
Zebrafish have been extensively used for studying vertebrate development and modeling human diseases such as cancer. In the last two decades, they have also emerged as an important model for developmental toxicology research and, more recently, for studying the developmental origins of health and disease (DOHaD). It is widely recognized that epigenetic mechanisms mediate the persistent effects of exposure to chemicals during sensitive windows of development. There is considerable interest in understanding the epigenetic mechanisms associated with DOHaD using zebrafish as a model system. This review summarizes our current knowledge on the effects of environmental chemicals on DNA methylation, histone modifications and noncoding RNAs in the context of DOHaD, and suggest some key considerations in designing experiments for characterizating the mechanisms of action.
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Affiliation(s)
- Neelakanteswar Aluru
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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28
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Venero Galanternik M, Castranova D, Gore AV, Blewett NH, Jung HM, Stratman AN, Kirby MR, Iben J, Miller MF, Kawakami K, Maraia RJ, Weinstein BM. A novel perivascular cell population in the zebrafish brain. eLife 2017; 6. [PMID: 28395729 PMCID: PMC5423774 DOI: 10.7554/elife.24369] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/28/2017] [Indexed: 12/12/2022] Open
Abstract
The blood-brain barrier is essential for the proper homeostasis and function of the CNS, but its mechanism of function is poorly understood. Perivascular cells surrounding brain blood vessels are thought to be important for blood-brain barrier establishment, but their roles are not well defined. Here, we describe a novel perivascular cell population closely associated with blood vessels on the zebrafish brain. Based on similarities in their morphology, location, and scavenger behavior, these cells appear to be the zebrafish equivalent of cells variably characterized as Fluorescent Granular Perithelial cells (FGPs), perivascular macrophages, or 'Mato Cells' in mammals. Despite their macrophage-like morphology and perivascular location, zebrafish FGPs appear molecularly most similar to lymphatic endothelium, and our imaging studies suggest that these cells emerge by differentiation from endothelium of the optic choroidal vascular plexus. Our findings provide the first report of a perivascular cell population in the brain derived from vascular endothelium.
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Affiliation(s)
- Marina Venero Galanternik
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Daniel Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Aniket V Gore
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Nathan H Blewett
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Hyun Min Jung
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Amber N Stratman
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Martha R Kirby
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, United States
| | - James Iben
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Mayumi F Miller
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan.,Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), Mishima, Japan
| | - Richard J Maraia
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
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29
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Goyal S, Suzuki T, Li JR, Maeda S, Kishima M, Nishimura H, Shimizu Y, Suzuki H. RUNX1 induces DNA replication independent active DNA demethylation at SPI1 regulatory regions. BMC Mol Biol 2017; 18:9. [PMID: 28376714 PMCID: PMC5381148 DOI: 10.1186/s12867-017-0087-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/28/2017] [Indexed: 11/10/2022] Open
Abstract
Background SPI1 is an essential transcription factor (TF) for the hematopoietic lineage, in which its expression is tightly controlled through a −17-kb upstream regulatory region and a promoter region. Both regulatory regions are demethylated during hematopoietic development, although how the change of DNA methylation status is performed is still unknown. Results We found that the ectopic overexpression of RUNX1 (another key TF in hematopoiesis) in HEK-293T cells induces almost complete DNA demethylation at the −17-kb upstream regulatory region and partial but significant DNA demethylation at the proximal promoter region. This DNA demethylation occurred in mitomycin-C-treated nonproliferating cells at both regulatory regions, suggesting active DNA demethylation. Furthermore, ectopic RUNX1 expression induced significant endogenous SPI1 expression, although its expression level was much lower than that of natively SPI1-expressing monocyte cells. Conclusions These results suggest the novel role of RUNX1 as an inducer of DNA demethylation at the SPI1 regulatory regions, although the mechanism of RUNX1-induced DNA demethylation remains to be explored.
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Affiliation(s)
- Shubham Goyal
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takahiro Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Jing-Ru Li
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Shiori Maeda
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Mami Kishima
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hajime Nishimura
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Yuri Shimizu
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Harukazu Suzuki
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
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30
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Robertson AL, Avagyan S, Gansner JM, Zon LI. Understanding the regulation of vertebrate hematopoiesis and blood disorders - big lessons from a small fish. FEBS Lett 2016; 590:4016-4033. [PMID: 27616157 DOI: 10.1002/1873-3468.12415] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Accepted: 09/07/2016] [Indexed: 12/12/2022]
Abstract
Hematopoietic stem cells (HSCs) give rise to all differentiated blood cells. Understanding the mechanisms that regulate self-renewal and lineage specification of HSCs is key for developing treatments for many human diseases. Zebrafish have emerged as an excellent model for studying vertebrate hematopoiesis. This review will highlight the unique strengths of zebrafish and important findings that have emerged from studies of blood development and disorders using this system. We discuss recent advances in our understanding of hematopoiesis, including the origin of HSCs, molecular control of their development, and key signaling pathways involved in their regulation. We highlight significant findings from zebrafish models of blood disorders and discuss their application for investigating stem cell dysfunction in disease and for the development of new therapeutics.
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Affiliation(s)
- Anne L Robertson
- Division of Hematology/Oncology, Boston Children's Hospital and Harvard Medical School, MA, USA
| | - Serine Avagyan
- Division of Hematology/Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, MA, USA
| | - John M Gansner
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Leonard I Zon
- Howard Hughes Medical Institute, Harvard Stem Cell Institute, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
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31
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DNA methylation in hematopoietic development and disease. Exp Hematol 2016; 44:783-790. [PMID: 27178734 DOI: 10.1016/j.exphem.2016.04.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/28/2022]
Abstract
DNA methylation is an important epigenetic modification that can have profound and widespread effects on gene expression and on cellular fate and function. Recent work has indicated that DNA methylation plays a critical role in hematopoietic development and hematopoietic disease. DNA methyltransferases and Ten-eleven translocation enzymes are required to add and remove methyl "marks" from DNA, respectively, and both sets of genes have been found necessary for proper formation and maintenance of hematopoietic stem cells and for differentiation of downstream hematopoietic lineages during development. DNA methylation and demethylation enzymes have also been implicated in hematopoietic disorders such as acute myeloid leukemia and myelodysplastic syndrome. Here, we review some of the recent literature regarding the role of DNA methylation in hematopoietic health and disease.
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