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Fang F, Chen D, Basharat AR, Poulos W, Wang Q, Cibelli JB, Liu X, Sun L. Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during the maternal-to-zygotic transition. iScience 2024; 27:109944. [PMID: 38784018 PMCID: PMC11111832 DOI: 10.1016/j.isci.2024.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 08/23/2023] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Maternal-to-zygotic transition (MZT) is central to early embryogenesis. However, its underlying molecular mechanisms are still not well described. Here, we revealed the expression dynamics of 5,000 proteins across four stages of zebrafish embryos during MZT, representing one of the most systematic surveys of proteome landscape of the zebrafish embryos during MZT. Nearly 700 proteins were differentially expressed and were divided into six clusters according to their expression patterns. The proteome expression profiles accurately reflect the main events that happen during the MZT, i.e., zygotic genome activation (ZGA), clearance of maternal mRNAs, and initiation of cellular differentiation and organogenesis. MZT is modulated by many proteins at multiple levels in a collaborative fashion, i.e., transcription factors, histones, histone-modifying enzymes, RNA helicases, and P-body proteins. Significant discrepancies were discovered between zebrafish proteome and transcriptome profiles during the MZT. The proteome dynamics database will be a valuable resource for bettering our understanding of MZT.
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Affiliation(s)
- Fei Fang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Daoyang Chen
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Abdul Rehman Basharat
- Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN 46202, USA
| | - William Poulos
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
| | - Qianyi Wang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
| | - Jose B. Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI 48824, USA
- Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Xiaowen Liu
- Deming Department of Medicine, School of Medicine, Tulane University, 1441 Canal Street, New Orleans, LA 70112, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA
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2
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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional regulators with broad expression in the zebrafish spinal cord. Dev Dyn 2024. [PMID: 38850245 DOI: 10.1002/dvdy.717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/12/2024] [Accepted: 05/15/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. RESULTS We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. CONCLUSIONS Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
| | - Paul C Campbell
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, New York, USA
| | - Richard L Bates
- Department of Biology, Syracuse University, Syracuse, New York, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, Syracuse, New York, USA
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3
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England SJ, Campbell PC, Banerjee S, Bates RL, Grieb G, Fancher WF, Lewis KE. Transcriptional Regulators with Broad Expression in the Zebrafish Spinal Cord. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580357. [PMID: 38405913 PMCID: PMC10888778 DOI: 10.1101/2024.02.14.580357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The spinal cord is a crucial part of the vertebrate CNS, controlling movements and receiving and processing sensory information from the trunk and limbs. However, there is much we do not know about how this essential organ develops. Here, we describe expression of 21 transcription factors and one transcriptional regulator in zebrafish spinal cord. Results We analyzed the expression of aurkb, foxb1a, foxb1b, her8a, homeza, ivns1abpb, mybl2b, myt1a, nr2f1b, onecut1, sall1a, sall3a, sall3b, sall4, sox2, sox19b, sp8b, tsc22d1, wdhd1, zfhx3b, znf804a, and znf1032 in wild-type and MIB E3 ubiquitin protein ligase 1 zebrafish embryos. While all of these genes are broadly expressed in spinal cord, they have distinct expression patterns from one another. Some are predominantly expressed in progenitor domains, and others in subsets of post-mitotic cells. Given the conservation of spinal cord development, and the transcription factors and transcriptional regulators that orchestrate it, we expect that these genes will have similar spinal cord expression patterns in other vertebrates, including mammals and humans. Conclusions Our data identify 22 different transcriptional regulators that are strong candidates for playing different roles in spinal cord development. For several of these genes, this is the first published description of their spinal cord expression.
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Affiliation(s)
- Samantha J. England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Paul C. Campbell
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Santanu Banerjee
- Biological Sciences Department, SUNY-Cortland, Cortland, NY 13045, USA
| | - Richard L. Bates
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - William F. Fancher
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
| | - Katharine E. Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY 13244, USA
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4
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Novakovsky G, Sasaki S, Fornes O, Omur ME, Huang H, Bayly CL, Zhang D, Lim N, Cherkasov A, Pavlidis P, Mostafavi S, Lynn FC, Wasserman WW. In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm. Stem Cell Reports 2023; 18:765-781. [PMID: 36801003 PMCID: PMC10031281 DOI: 10.1016/j.stemcr.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/18/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Improving methods for human embryonic stem cell differentiation represents a challenge in modern regenerative medicine research. Using drug repurposing approaches, we discover small molecules that regulate the formation of definitive endoderm. Among them are inhibitors of known processes involved in endoderm differentiation (mTOR, PI3K, and JNK pathways) and a new compound, with an unknown mechanism of action, capable of inducing endoderm formation in the absence of growth factors in the media. Optimization of the classical protocol by inclusion of this compound achieves the same differentiation efficiency with a 90% cost reduction. The presented in silico procedure for candidate molecule selection has broad potential for improving stem cell differentiation protocols.
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Affiliation(s)
- Gherman Novakovsky
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Shugo Sasaki
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Oriol Fornes
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Meltem E Omur
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Helen Huang
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
| | - Carmen L Bayly
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada
| | - Dahai Zhang
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Nathaniel Lim
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada; Department of Psychiatry, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Artem Cherkasov
- Department of Urological Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Paul Pavlidis
- Department of Psychiatry, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Sara Mostafavi
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Department of Statistics, University of British Columbia, Vancouver, BC, Canada; Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Francis C Lynn
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Department of Surgery, University of British Columbia, Vancouver, BC, Canada; School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada.
| | - Wyeth W Wasserman
- BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada; Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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5
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Normal embryonic development and neonatal digit regeneration in mice overexpressing a stem cell factor, Sall4. PLoS One 2022; 17:e0267273. [PMID: 35482646 PMCID: PMC9049339 DOI: 10.1371/journal.pone.0267273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/05/2022] [Indexed: 01/29/2023] Open
Abstract
Sall4 encodes a transcription factor and is known to participate in the pluripotency network of embryonic stem cells. Sall4 expression is known to be high in early stage post-implantation mouse embryos. During early post-gastrulation stages, Sall4 is highly expressed in the tail bud and distal limb buds, where progenitor cells are maintained in an undifferentiated status. The expression of Sall4 is rapidly downregulated during embryonic development. We previously demonstrated that Sall4 is required for limb and posterior axial skeleton development by conditional deletion of Sall4 in the T (Brachyury) lineage. To gain insight into Sall4 functions in embryonic development and postnatal digit regeneration, we genetically overexpressed Sall4 in the mesodermal lineage by the TCre transgene and a novel knockin allele of Rosa26-loxP-stop-loxP-Sall4. In significant contrast to severe defects by Sall4 loss of function reported in previous studies, overexpression of Sall4 resulted in normal morphology and pattern in embryos and neonates. The length of limb long bones showed subtle reduction in Sall4-overexpression mice. It is known that the digit tip of neonatal mice has level-specific regenerative ability after experimental amputation. We observed Sall4 expression in the digit tip by using a sensitive Sall4-LacZ knock-in reporter expression. Sall4 overexpression did not alter the regenerative ability of the terminal phalange that normally regenerates after amputation. Moreover, Sall4 overexpression did not confer regenerative ability to the second phalange that normally does not regenerate after amputation. These genetic experiments show that overexpression of Sall4 does not alter the development of the appendicular and axial skeleton, or neonatal digit regeneration. The results suggest that Sall4 acts as a permissive factor rather than playing an instructive role.
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6
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López-Pérez AR, Balwierz PJ, Lenhard B, Muller F, Wardle FC, Manfroid I, Voz ML, Peers B. Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics. Sci Rep 2021; 11:22717. [PMID: 34811400 PMCID: PMC8608873 DOI: 10.1038/s41598-021-02039-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/27/2021] [Indexed: 11/09/2022] Open
Abstract
Retinoic acid (RA) is a key signal for the specification of the pancreas. Still, the gene regulatory cascade triggered by RA in the endoderm remains poorly characterized. In this study, we investigated this regulatory network in zebrafish by combining RNA-seq, RAR ChIP-seq and ATAC-seq assays. By analysing the effect of RA and of the RA receptor (RAR) inverse-agonist BMS493 on the transcriptome and on the chromatin accessibility of endodermal cells, we identified a large set of genes and regulatory regions regulated by RA signalling. RAR ChIP-seq further defined the direct RAR target genes in zebrafish, including hox genes as well as several pancreatic regulators like mnx1, insm1b, hnf1ba and gata6. Comparison of zebrafish and murine RAR ChIP-seq data highlighted the conserved direct target genes and revealed that some RAR sites are under strong evolutionary constraints. Among them, a novel highly conserved RAR-induced enhancer was identified downstream of the HoxB locus and driving expression in the nervous system and in the gut in a RA-dependent manner. Finally, ATAC-seq data unveiled the role of the RAR-direct targets Hnf1ba and Gata6 in opening chromatin at many regulatory loci upon RA treatment.
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Affiliation(s)
- Ana R López-Pérez
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Avenue de l'Hôpital 1, B34, 4000, Liège, Belgium.,Umeå Centre for Molecular Medicine (UCMM), Umeå University, Umeå, Sweden
| | - Piotr J Balwierz
- Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Boris Lenhard
- Institute of Clinical Sciences and MRC Clinical Sciences Centre, Faculty of Medicine, Imperial College London, London, W12 0NN, UK
| | - Ferenc Muller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Fiona C Wardle
- Randall Centre for Cell and Molecular Biophysics, New Hunt's House, Guy's Campus, King's College London, London, SE1 1UL, UK
| | - Isabelle Manfroid
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Avenue de l'Hôpital 1, B34, 4000, Liège, Belgium
| | - Marianne L Voz
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Avenue de l'Hôpital 1, B34, 4000, Liège, Belgium
| | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Avenue de l'Hôpital 1, B34, 4000, Liège, Belgium.
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7
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Zebrafish Cdx4 regulates neural crest cell specification and migratory behaviors in the posterior body. Dev Biol 2021; 480:25-38. [PMID: 34389276 DOI: 10.1016/j.ydbio.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/17/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023]
Abstract
The neural crest (NC) is a transient multipotent cell population that migrates extensively to produce a remarkable array of vertebrate cell types. NC cell specification progresses in an anterior to posterior fashion, resulting in distinct, axial-restricted subpopulations. The anterior-most, cranial, population of NC is specified as gastrulation concludes and neurulation begins, while more posterior populations become specified as the body elongates. The mechanisms that govern development of the more posterior NC cells remain incompletely understood. Here, we report a key role for zebrafish Cdx4, a homeodomain transcription factor, in the development of posterior NC cells. We demonstrate that cdx4 is expressed in trunk NC cell progenitors, directly binds NC cell-specific enhancers in the NC GRN, and regulates expression of the key NC development gene foxd3 in the posterior body. Moreover, cdx4 mutants show disruptions to the segmental pattern of trunk NC cell migration due to loss of normal leader/follower cell dynamics. Finally, using cell transplantation to generate chimeric specimens, we show that Cdx4 does not function in the paraxial mesoderm-the environment adjacent to which crest migrates-to influence migratory behaviors. We conclude that cdx4 plays a critical, and likely tissue autonomous, role in the establishment of trunk NC migratory behaviors. Together, our results indicate that cdx4 functions as an early NC specifier gene in the posterior body of zebrafish embryos.
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8
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Yang H, Luan Y, Liu T, Lee HJ, Fang L, Wang Y, Wang X, Zhang B, Jin Q, Ang KC, Xing X, Wang J, Xu J, Song F, Sriranga I, Khunsriraksakul C, Salameh T, Li D, Choudhary MNK, Topczewski J, Wang K, Gerhard GS, Hardison RC, Wang T, Cheng KC, Yue F. A map of cis-regulatory elements and 3D genome structures in zebrafish. Nature 2020; 588:337-343. [PMID: 33239788 DOI: 10.1038/s41586-020-2962-9] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 09/17/2020] [Indexed: 01/08/2023]
Abstract
The zebrafish (Danio rerio) has been widely used in the study of human disease and development, and about 70% of the protein-coding genes are conserved between the two species1. However, studies in zebrafish remain constrained by the sparse annotation of functional control elements in the zebrafish genome. Here we performed RNA sequencing, assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation with sequencing, whole-genome bisulfite sequencing, and chromosome conformation capture (Hi-C) experiments in up to eleven adult and two embryonic tissues to generate a comprehensive map of transcriptomes, cis-regulatory elements, heterochromatin, methylomes and 3D genome organization in the zebrafish Tübingen reference strain. A comparison of zebrafish, human and mouse regulatory elements enabled the identification of both evolutionarily conserved and species-specific regulatory sequences and networks. We observed enrichment of evolutionary breakpoints at topologically associating domain boundaries, which were correlated with strong histone H3 lysine 4 trimethylation (H3K4me3) and CCCTC-binding factor (CTCF) signals. We performed single-cell ATAC-seq in zebrafish brain, which delineated 25 different clusters of cell types. By combining long-read DNA sequencing and Hi-C, we assembled the sex-determining chromosome 4 de novo. Overall, our work provides an additional epigenomic anchor for the functional annotation of vertebrate genomes and the study of evolutionarily conserved elements of 3D genome organization.
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Affiliation(s)
- Hongbo Yang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Yu Luan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Hyung Joo Lee
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Li Fang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Xiaotao Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Bo Zhang
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Khai Chung Ang
- Department of Pathology and Penn State Zebrafish Functional Genomics Core, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Xiaoyun Xing
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Jie Xu
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Iyyanki Sriranga
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | | | - Tarik Salameh
- Bioinformatics and Genomics Program, The Pennsylvania State University, State College, PA, USA
| | - Daofeng Li
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Mayank N K Choudhary
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Jacek Topczewski
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Stanley Manne Children's Research Institute, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Glenn S Gerhard
- Department of Medical Genetics and Molecular Biochemistry, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Ross C Hardison
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Ting Wang
- Department of Genetics, The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
| | - Keith C Cheng
- Department of Pathology and Penn State Zebrafish Functional Genomics Core, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA. .,Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA.
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The Cdx transcription factors and retinoic acid play parallel roles in antero-posterior position of the pectoral fin field during gastrulation. Mech Dev 2020; 164:103644. [PMID: 32911082 DOI: 10.1016/j.mod.2020.103644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/27/2022]
Abstract
The molecular regulators that determine the precise position of the vertebrate limb along the anterio-posterior axis have not been identified. One model suggests that a combination of hox genes in the lateral plate mesoderm (LPM) promotes formation of the limb field, however redundancy among duplicated paralogs has made this model difficult to confirm. In this study, we identify an optimal window during mid-gastrulation stages when transient mis-regulation of retinoic acid signaling or the caudal related transcription factor, Cdx4, both known regulators of hox genes, can alter the position of the pectoral fin field. We show that increased levels of either RA or Cdx4 during mid-gastrulation are sufficient to rostrally shift the position of the pectoral fin field at the expense of surrounding gene expression in the anterior lateral plate mesoderm (aLPM). Alternatively, embryos deficient for both Cdx4 and Cdx1a (Cdx-deficient) form pectoral fins that are shifted towards the posterior and reveal an additional effect on size of the pectoral fin buds. Prior to formation of the pectoral fin buds, the fin field in Cdx-deficient embryos is visibly expanded into the posterior LPM (pLPM) region at the expense of surrounding gene expression. The effects on gene expression immediately post-gastrulation and during somitogenesis support a model where RA and Cdx4 act in parallel to regulate the position of the pectoral fin. Our transient method is a potentially useful model for studying the mechanisms of limb positioning along the AP axis.
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10
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Gong G, Kam H, Tse Y, Lee SM. Cardiotoxicity of forchlorfenuron (CPPU) in zebrafish (Danio rerio) and H9c2 cardiomyocytes. CHEMOSPHERE 2019; 235:153-162. [PMID: 31255755 DOI: 10.1016/j.chemosphere.2019.06.027] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/01/2019] [Accepted: 06/03/2019] [Indexed: 06/09/2023]
Abstract
Forchlorfenuron (CPPU), as a plant growth regulator or herbicide/pesticide, is widely used in agriculture worldwide. It is adopted by most farmers due to its high efficacy for boosting size and improving the quality of fruit. However, CPPU was implicated in, and gained notoriety due to an incident of exploding watermelon that occurred in 2011. Subsequently, the wider community became aware of the potential risks it posed to living organisms and the ecosystem. In this study, we evaluated the effects of CPPU on the survival, cardiac morphology and function, as well as hematopoietic system, of zebrafish (Danio rerio). Notably, CPPU (2.5-12.5 μg/ml) induced cardiac morphology deformation, cardiac contractile dysfunction and erythrocyte reduction in zebrafish. Consistently, the mRNA expression levels of several cardiac and hematopoietic gene markers (myl7, gata4, mef2c, amhc, vmhc and gata1) were altered by CPPU treatment. In addition, CPPU caused cytotoxicity, cytoskeleton destruction and reduced corresponding proteins (Myl7, Gata4 and Mef2c) expression in H9c2 cardiomyocytes in vitro. Taken together, this study has identified the cardiotoxicity of CPPU in different experimental models and enhanced our understanding on the mechanism underlying the toxicity of CPPU to living organisms.
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Affiliation(s)
- Guiyi Gong
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China; Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Hiotong Kam
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China
| | - Yuchung Tse
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen, 518055, China
| | - Simon Mingyuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, University of Macau, Macau, China.
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11
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Tahara N, Kawakami H, Chen KQ, Anderson A, Yamashita Peterson M, Gong W, Shah P, Hayashi S, Nishinakamura R, Nakagawa Y, Garry DJ, Kawakami Y. Sall4 regulates neuromesodermal progenitors and their descendants during body elongation in mouse embryos. Development 2019; 146:dev.177659. [PMID: 31235634 DOI: 10.1242/dev.177659] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022]
Abstract
Bi-potential neuromesodermal progenitors (NMPs) produce both neural and paraxial mesodermal progenitors in the trunk and tail during vertebrate body elongation. We show that Sall4, a pluripotency-related transcription factor gene, has multiple roles in regulating NMPs and their descendants in post-gastrulation mouse embryos. Sall4 deletion using TCre caused body/tail truncation, reminiscent of early depletion of NMPs, suggesting a role of Sall4 in NMP maintenance. This phenotype became significant at the time of the trunk-to-tail transition, suggesting that Sall4 maintenance of NMPs enables tail formation. Sall4 mutants exhibit expanded neural and reduced mesodermal tissues, indicating a role of Sall4 in NMP differentiation balance. Mechanistically, we show that Sall4 promotion of WNT/β-catenin signaling contributes to NMP maintenance and differentiation balance. RNA-Seq and SALL4 ChIP-Seq analyses support the notion that Sall4 regulates both mesodermal and neural development. Furthermore, in the mesodermal compartment, genes regulating presomitic mesoderm differentiation are downregulated in Sall4 mutants. In the neural compartment, we show that differentiation of NMPs towards post-mitotic neuron is accelerated in Sall4 mutants. Our results collectively provide evidence supporting the role of Sall4 in regulating NMPs and their descendants.
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Affiliation(s)
- Naoyuki Tahara
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Katherine Q Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Aaron Anderson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Malina Yamashita Peterson
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Wuming Gong
- Lillehei Heart Institute, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
| | - Pruthvi Shah
- Lillehei Heart Institute, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA
| | - Shinichi Hayashi
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan 860-0811
| | - Yasushi Nakagawa
- Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Department of Neuroscience, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
| | - Daniel J Garry
- Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA.,Lillehei Heart Institute, University of Minnesota, 2231 6th St. SE, Minneapolis, MN 55455, USA.,Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA .,Stem Cell Institute, University of Minnesota, 2001 6th St. SE, Minneapolis, MN 55455, USA.,Developmental Biology Center, University of Minnesota, 321 Church St. SE, Minneapolis, MN 55455, USA
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12
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Joshi P, Darr AJ, Skromne I. CDX4 regulates the progression of neural maturation in the spinal cord. Dev Biol 2019; 449:132-142. [PMID: 30825428 DOI: 10.1016/j.ydbio.2019.02.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 11/17/2022]
Abstract
The progression of cells down different lineage pathways is a collaborative effort between networks of extracellular signals and intracellular transcription factors. In the vertebrate spinal cord, FGF, Wnt and Retinoic Acid signaling pathways regulate the progressive caudal-to-rostral maturation of neural progenitors by regulating a poorly understood gene regulatory network of transcription factors. We have mapped out this gene regulatory network in the chicken pre-neural tube, identifying CDX4 as a dual-function core component that simultaneously regulates gradual loss of cell potency and acquisition of differentiation states: in a caudal-to-rostral direction, CDX4 represses the early neural differentiation marker Nkx1.2 and promotes the late neural differentiation marker Pax6. Significantly, CDX4 prevents premature PAX6-dependent neural differentiation by blocking Ngn2 activation. This regulation of CDX4 over Pax6 is restricted to the rostral pre-neural tube by Retinoic Acid signaling. Together, our results show that in the spinal cord, CDX4 is part of the gene regulatory network controlling the sequential and progressive transition of states from high to low potency during neural progenitor maturation. Given CDX well-known involvement in Hox gene regulation, we propose that CDX factors coordinate the maturation and axial specification of neural progenitor cells during spinal cord development.
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Affiliation(s)
- Piyush Joshi
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, United States; Cancer and Blood Disorders Institute, Johns Hopkins All Children's Hospital, 600 5th St S, St. Petersburg, FL 33701, United States
| | - Andrew J Darr
- Department of Health Sciences Education, University of Illinois College of Medicine, 1 Illini Drive, Peoria, IL 61605, United States
| | - Isaac Skromne
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, Florida, 33146, United States; Department of Biology, University of Richmond, 138 UR Drive B322, Richmond, VA, 23173, United States.
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13
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Six6 and Six7 coordinately regulate expression of middle-wavelength opsins in zebrafish. Proc Natl Acad Sci U S A 2019; 116:4651-4660. [PMID: 30765521 PMCID: PMC6410792 DOI: 10.1073/pnas.1812884116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Color discrimination in the vertebrate retina is mediated by a combination of cone cell types expressing UV (SWS1), blue (SWS2), green (RH2), and red (LWS) opsins. Although the tetrachromatic cone system is retained in most nonmammalian vertebrate lineages, the transcriptional mechanism underlying gene expression of cone opsins remains elusive. Here, we found that the retinal transcription factors, sine oculis homeobox 6 (Six6b) and Six7, synergistically and positively regulate gene expression of zebrafish SWS2 and RH2 opsins. Larvae deficient for both of these transcription factors showed heavily impaired visually driven foraging behavior and were unable to compete for food when reared in a group with normal siblings. The results suggest that six6b and six7 play a pivotal role in blue- and green-light sensitivity and daylight vision. Color discrimination in the vertebrate retina is mediated by a combination of spectrally distinct cone photoreceptors, each expressing one of multiple cone opsins. The opsin genes diverged early in vertebrate evolution into four classes maximally sensitive to varying wavelengths of light: UV (SWS1), blue (SWS2), green (RH2), and red (LWS) opsins. Although the tetrachromatic cone system is retained in most nonmammalian vertebrate lineages, the transcriptional mechanism underlying gene expression of the cone opsins remains elusive, particularly for SWS2 and RH2 opsins, both of which have been lost in the mammalian lineage. In zebrafish, which have all four cone subtypes, rh2 opsin gene expression depends on a homeobox transcription factor, sine oculis homeobox 7 (Six7). However, the six7 gene is found only in the ray-finned fish lineage, suggesting the existence of another evolutionarily conserved transcriptional factor(s) controlling rh2 opsin expression in vertebrates. Here, we found that the reduced rh2 expression caused by six7 deficiency was rescued by forced expression of six6b, which is a six7-related transcription factor conserved widely among vertebrates. The compensatory role of six6b was reinforced by ChIP-sequencing analysis, which revealed a similar pattern of Six6b- and Six7-binding sites within and near the cone opsin genes. TAL effector nuclease-induced genetic ablation of six6b and six7 revealed that they coordinately regulate SWS2 opsin gene expression. Mutant larvae deficient for these transcription factors showed severely impaired visually driven foraging behavior. These results demonstrate that in zebrafish, six6b and six7 govern expression of the SWS2 and RH2 opsins responsible for middle-wavelength sensitivity, which would be physiologically important for daylight vision.
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14
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Kobayashi I, Kobayashi-Sun J, Hirakawa Y, Ouchi M, Yasuda K, Kamei H, Fukuhara S, Yamaguchi M. Dual role of Jam3b in early hematopoietic and vascular development. Development 2019; 147:dev.181040. [DOI: 10.1242/dev.181040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 12/11/2019] [Indexed: 12/23/2022]
Abstract
In order to efficiently derive hematopoietic stem cells (HSCs) from pluripotent precursors, it is crucial to understand how mesodermal cells acquire hematopoietic and endothelial identities, two divergent, but closely related cell fates. Although Npas4 has been recently identified as a conserved master regulator of hemato-vascular development, the molecular mechanisms underlying cell fate divergence between hematopoietic and vascular endothelial cells are still unclear. Here, we show in zebrafish that mesodermal cell differentiation into hematopoietic and vascular endothelial cells is regulated by Junctional adhesion molecule 3b (Jam3b) via two independent signaling pathways. Mutation of jam3b led to a reduction in npas4l expression in the posterior lateral plate mesoderm and defects in both hematopoietic and vascular development. Mechanistically, we uncover that Jam3b promotes endothelial specification by regulating npas4l expression through repression of the Rap1a-Erk signaling cascade. Jam3b subsequently promotes hematopoietic development, including HSCs, by regulating lrrc15 expression in endothelial precursors through the activation of an integrin-dependent signaling cascade. Our data provide insight into the divergent mechanisms for instructing hematopoietic or vascular fates from mesodermal cells.
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Affiliation(s)
- Isao Kobayashi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
| | - Jingjing Kobayashi-Sun
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Yuto Hirakawa
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Madoka Ouchi
- Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Ishikawa, Japan
| | - Koyuki Yasuda
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
| | - Hiroyasu Kamei
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Kanagawa, Japan
| | - Masaaki Yamaguchi
- Faculty of Biological Science and Technology, Institute of Science and Engineering, Kanazawa University, Ishikawa, Japan
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15
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Yang J. SALL4 as a transcriptional and epigenetic regulator in normal and leukemic hematopoiesis. Biomark Res 2018; 6:1. [PMID: 29308206 PMCID: PMC5751604 DOI: 10.1186/s40364-017-0115-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/22/2017] [Indexed: 02/06/2023] Open
Abstract
In recent years, there has been substantial progress in our knowledge of the molecular pathways by which stem cell factor SALL4 regulates the embryonic stem cell (ESC) properties, developmental events, and human cancers. This review summarizes recent advances in the biology of SALL4 with a focus on its regulatory functions in normal and leukemic hematopoiesis. In the normal hematopoietic system, expression of SALL4 is mainly enriched in the bone marrow hematopoietic stem/progenitor cells (HSCs/HPCs), but is rapidly silenced following lineage differentiation. In hematopoietic malignancies, however, SALL4 expression is abnormally re-activated and linked with deteriorated disease status in patients. Further, SALL4 activation participates in the pathogenesis of tumor initiation and disease progression. Thus, a better understanding of SALL4's biologic functions and mechanisms will facilitate development of advanced targeted anti-leukemia approaches in future.
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Affiliation(s)
- Jianchang Yang
- Department of Surgery and Medicine, Baylor College of Medicine, Houston, TX 77030 USA
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16
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Dong X, Li J, He L, Gu C, Jia W, Yue Y, Li J, Zhang Q, Chu L, Zhao Q. Zebrafish Znfl1 proteins control the expression of hoxb1b gene in the posterior neuroectoderm by acting upstream of pou5f3 and sall4 genes. J Biol Chem 2017. [PMID: 28623229 DOI: 10.1074/jbc.m117.777094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Transcription factors play crucial roles in patterning posterior neuroectoderm. Previously, zinc finger transcription factor znfl1 was reported to be expressed in the posterior neuroectoderm of zebrafish embryos. However, its roles remain unknown. Here, we report that there are 13 copies of znfl1 in the zebrafish genome, and all the paralogues share highly identical protein sequences and cDNA sequences. When znfl1s are knocked down using a morpholino to inhibit their translation or dCas9-Eve to inhibit their transcription, the zebrafish gastrula displays reduced expression of hoxb1b, the marker gene for the posterior neuroectoderm. Further analyses reveal that diminishing znfl1s produces the decreased expressions of pou5f3, whereas overexpression of pou5f3 effectively rescues the reduced expression of hoxb1b in the posterior neuroectoderm. Additionally, knocking down znfl1s causes the reduced expression of sall4, a direct regulator of pou5f3, in the posterior neuroectoderm, and overexpression of sall4 rescues the expression of pou5f3 in the knockdown embryos. In contrast, knocking down either pou5f3 or sall4 does not affect the expressions of znfl1s Taken together, our results demonstrate that zebrafish znfl1s control the expression of hoxb1b in the posterior neuroectoderm by acting upstream of pou5f3 and sall4.
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Affiliation(s)
- Xiaohua Dong
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China; Institute of Genome Editing, Nanjing YSY Biotech Company, Limited, Nanjing 211812, China
| | - Jingyun Li
- Maternal and Child Health Medical Institute, Department of Plastic and Cosmetic Surgery, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Luqingqing He
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Chun Gu
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Wenshuang Jia
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Yunyun Yue
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Jun Li
- Maternal and Child Health Medical Institute, Department of Plastic and Cosmetic Surgery, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing 210004, China
| | - Qinxin Zhang
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China
| | - Lele Chu
- Institute of Genome Editing, Nanjing YSY Biotech Company, Limited, Nanjing 211812, China
| | - Qingshun Zhao
- Ministry of Education Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing 210061, China.
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17
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Creamer JP, Dege C, Ren Q, Ho JTK, Valentine MC, Druley TE, Sturgeon CM. Human definitive hematopoietic specification from pluripotent stem cells is regulated by mesodermal expression of CDX4. Blood 2017; 129:2988-2992. [PMID: 28408465 PMCID: PMC5454336 DOI: 10.1182/blood-2016-11-749382] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Accepted: 04/08/2017] [Indexed: 12/15/2022] Open
Abstract
The generation of hematopoietic stem cells from human pluripotent stem cells (hPSCs) is a major goal for regenerative medicine. Achieving this goal is complicated by our incomplete understanding of the mechanism regulating definitive hematopoietic specification. We used our stage-specific hPSC differentiation method to obtain and identify, via CD235a expression, mesoderm harboring exclusively primitive or definitive hematopoietic potential to understand the genetic regulation of definitive hematopoietic specification. Whole-transcriptome gene expression analyses on WNT-dependent KDR+CD235a- definitive hematopoietic mesoderm and WNT-independent KDR+CD235a+ primitive hematopoietic mesoderm revealed strong CDX gene expression within definitive hematopoietic mesoderm. Temporal expression analyses revealed that CDX4 was expressed exclusively within definitive hematopoietic KDR+CD235a- mesoderm in a WNT- and fibroblast growth factor-dependent manner. We found that exogenous CDX4 expression exclusively during mesoderm specification resulted in a >90% repression in primitive hematopoietic potential, but conferred fivefold greater definitive hematopoietic potential, similar to that observed following WNT stimulation. In contrast, CDX4 knockout hPSCs had intact primitive hematopoietic potential, but exhibited a fivefold decrease in multilineage definitive hematopoietic potential. Taken together, these findings indicate that CDX4 is a critical transcription factor in the regulation of human definitive hematopoietic specification, and provides a mechanistic basis for WNT-mediated definitive hematopoietic specification from hPSCs.
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Affiliation(s)
| | | | - Qihao Ren
- Division of Hematology, Department of Medicine
| | | | | | | | - Christopher M Sturgeon
- Division of Hematology, Department of Medicine
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO
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18
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Erickson JR, Gearhart MD, Honson DD, Reid TA, Gardner MK, Moriarity BS, Echeverri K. A novel role for SALL4 during scar-free wound healing in axolotl. NPJ Regen Med 2016; 1. [PMID: 28955504 PMCID: PMC5612448 DOI: 10.1038/npjregenmed.2016.16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human response to serious cutaneous damage is limited to relatively primitive wound healing, whereby collagenous scar tissue fills the wound bed. Scars assure structural integrity at the expense of functional regeneration. In contrast, axolotls have the remarkable capacity to functionally regenerate full thickness wounds. Here, we identified a novel role for SALL4 in regulating collagen transcription after injury that is essential for perfect skin regeneration in axolotl. Furthermore, we identify miR-219 as a molecular regulator of Sall4 during wound healing. Taken together, our work highlights one molecular mechanism that allows for efficient cutaneous wound healing in the axolotl.
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Affiliation(s)
- Jami R Erickson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, USA
| | - Micah D Gearhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, USA
| | - Drew D Honson
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, USA
| | - Taylor A Reid
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, USA
| | - Melissa K Gardner
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, USA
| | - Branden S Moriarity
- Department of Pediatrics, University of Minnesota, Center for Genome Engineering, University of Minnesota, Masonic Cancer Center, University of Minnesota, Minnesota, MN USA
| | - Karen Echeverri
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minnesota, MN, USA
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19
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Cui B, Ren L, Xu QH, Yin LY, Zhou XY, Liu JX. Silver_ nanoparticles inhibited erythrogenesis during zebrafish embryogenesis. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2016; 177:295-305. [PMID: 27340786 DOI: 10.1016/j.aquatox.2016.06.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 06/06/2023]
Abstract
Silver_ nanoparticles (AgNPs), for their attractive antimicrobial properties, have become one of the most commercial nanomaterials used recently. AgNPs are reported to be toxic to blood cells of aquatic organisms and humans, however, few studies related to toxic effects of AgNPs in hematopoiesis using an in vivo model were available. Firstly, microarrays were applied to reveal transcriptional responses of zebrafish embryos to AgNPs at 24h post-fertilization (hpf)in this study, and hemoglobin genes were found to be down-regulated by AgNPs and to be enriched in the top 10 categories by Gene Ontology (GO) analysis. The reduced expressions of hemoglobin were further demonstrated by qRT-PCR detection, whole-mount in situ hybridization, and O-dianisidine staining at transcriptional and translational level. Next, the commitment of mesoderm, specification of hematopoietic progenitor cells and differentiation of erythroids were detected at different developmental stages in AgNPs-exposed embryos, and erythrogenesis were found to be inhibited by AgNPs in developmental-stage-specific and cell-specific manners. Finally, it was pointed out that AgNPs affected erythrogenesis mostly by their particles other than their releasing ions.
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Affiliation(s)
- Bei Cui
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Long Ren
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Qin-Han Xu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Li-Yan Yin
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, Hainan University, HaiKou, 570228, China.
| | - Xin-Ying Zhou
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Jing-Xia Liu
- College of Fisheries, Key Laboratory of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, 430070, China; Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Hunan, Changde, 415000, China.
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20
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Tatetsu H, Kong NR, Chong G, Amabile G, Tenen DG, Chai L. SALL4, the missing link between stem cells, development and cancer. Gene 2016; 584:111-9. [PMID: 26892498 DOI: 10.1016/j.gene.2016.02.019] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/10/2016] [Accepted: 02/12/2016] [Indexed: 01/01/2023]
Abstract
There is a growing body of evidence supporting that cancer cells share many similarities with embryonic stem cells (ESCs). For example, aggressive cancers and ESCs share a common gene expression signature that includes hundreds of genes. Since ESC genes are not present in most adult tissues, they could be ideal candidate targets for cancer-specific diagnosis and treatment. This is an exciting cancer-targeting model. The major hurdle to test this model is to identify the key factors/pathway(s) within ESCs that are responsible for the cancer phenotype. SALL4 is one of few genes that can establish this link. The first publication of SALL4 is on its mutation in a human inherited disorder with multiple developmental defects. Since then, over 300 papers have been published on various aspects of this gene in stem cells, development, and cancers. This review aims to summarize our current knowledge of SALL4, including a SALL4-based approach to classify and target cancers. Many questions about this important gene still remain unanswered, specifically, on how this gene regulates cell fates at a molecular level. Understanding SALL4's molecular functions will allow development of specific targeted approaches in the future.
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Affiliation(s)
- Hiro Tatetsu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, New Research Building Room 652D, Boston, MA 02115, USA
| | - Nikki R Kong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, New Research Building Room 652D, Boston, MA 02115, USA
| | - Gao Chong
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, New Research Building Room 652D, Boston, MA 02115, USA
| | | | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Centre for Translational Medicine (MD6), #12-01, 14 Medical Drive, 117599, Singapore; Harvard Stem Cell Institute, Center for Life Science Room 437, 3 Blackfan Circle Room 437, Boston, MA 02115, USA
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, New Research Building Room 652D, Boston, MA 02115, USA.
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21
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Chang J, Skromne I, Ho RK. CDX4 and retinoic acid interact to position the hindbrain-spinal cord transition. Dev Biol 2016; 410:178-189. [PMID: 26773000 DOI: 10.1016/j.ydbio.2015.12.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 12/17/2015] [Accepted: 12/23/2015] [Indexed: 12/15/2022]
Abstract
The sub-division of the posterior-most territory of the neural plate results in the formation of two distinct neural structures, the hindbrain and the spinal cord. Although many of the molecular signals regulating the development of these individual structures have been elucidated, the mechanisms involved in delineating the boundary between the hindbrain and spinal cord remain elusive. Two molecules, retinoic acid (RA) and the Cdx4 transcription factor have been previously implicated as important regulators of hindbrain and spinal cord development, respectively. Here, we provide evidence that suggests multiple regulatory interactions occur between RA signaling and the Cdx4 transcription factor to establish the anterior-posterior (AP) position of the transition between the hindbrain and spinal cord. Using chemical inhibitors to alter RA concentrations and morpholinos to knock-down Cdx4 function in zebrafish, we show that Cdx4 acts to prevent RA degradation in the presumptive spinal cord domain by suppressing expression of the RA degradation enzyme, Cyp26a1. In the hindbrain, RA signaling modulates its own concentration by activating the expression of cyp26a1 and inhibiting the expansion of cdx4. Therefore, interactions between Cyp26a1 and Cdx4 modulate RA levels along the AP axis to segregate the posterior neural plate into the hindbrain and spinal cord territories.
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Affiliation(s)
- Jessie Chang
- Committee on Developmental Biology, University of Chicago, Chicago, IL 60637, USA
| | - Isaac Skromne
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Robert K Ho
- Department of Organismal Biology and Anatomy, University of Chicago, 1027 E. 57th St, Chicago, IL 60637, USA.
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22
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Hayward AG, Joshi P, Skromne I. Spatiotemporal analysis of zebrafishhoxgene regulation by Cdx4. Dev Dyn 2015; 244:1564-73. [DOI: 10.1002/dvdy.24343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 08/07/2015] [Accepted: 08/24/2015] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Piyush Joshi
- Department of Biology; University of Miami; Coral Gables Florida
| | - Isaac Skromne
- Department of Biology; University of Miami; Coral Gables Florida
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Dhiman H, Kapoor S, Sivadas A, Sivasubbu S, Scaria V. zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs. PLoS One 2015; 10:e0129997. [PMID: 26065909 PMCID: PMC4466246 DOI: 10.1371/journal.pone.0129997] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 05/15/2015] [Indexed: 12/13/2022] Open
Abstract
Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw RNA-Seq datasets in public domain encompassing critical developmental time-points and adult tissues provides us with a unique opportunity to understand the spatiotemporal expression patterns of lncRNAs. In the present report, we created a catalog of lncRNAs in zebrafish, derived largely from the three annotation sets, as well as manual curation of literature to compile a total of 2,267 lncRNA transcripts in zebrafish. The lncRNAs were further classified based on the genomic context and relationship with protein coding gene neighbors into 4 categories. Analysis revealed a total of 86 intronic, 309 promoter associated, 485 overlapping and 1,386 lincRNAs. We created a comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion mutants. The resource also hosts a genome browser where the datasets could be browsed in the genome context. To the best of our knowledge, this is the first comprehensive resource providing a unified catalog of lncRNAs in zebrafish. The resource is freely available at URL: http://genome.igib.res.in/zflncRNApedia
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Affiliation(s)
- Heena Dhiman
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR–Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India
| | - Shruti Kapoor
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR–Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi, 110001, India
| | - Ambily Sivadas
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR–Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India
| | - Sridhar Sivasubbu
- Genomics and Molecular Medicine, CSIR Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110025, India
- * E-mail: (SS); (VS)
| | - Vinod Scaria
- GN Ramachandran Knowledge Center for Genome Informatics, CSIR–Institute of Genomics and Integrative Biology, Mathura Road, Delhi, 110020, India
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, Delhi, 110001, India
- * E-mail: (SS); (VS)
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24
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GATA family members as inducers for cellular reprogramming to pluripotency. Cell Res 2015; 25:169-80. [PMID: 25591928 DOI: 10.1038/cr.2015.6] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/18/2014] [Accepted: 11/20/2014] [Indexed: 01/21/2023] Open
Abstract
Members of the GATA protein family play important roles in lineage specification and transdifferentiation. Previous reports show that some members of the GATA protein family can also induce pluripotency in somatic cells by substituting for Oct4, a key pluripotency-associated factor. However, the mechanism linking lineage-specifying cues and the activation of pluripotency remains elusive. Here, we report that all GATA family members can substitute for Oct4 to induce pluripotency. We found that all members of the GATA family could inhibit the overrepresented ectodermal-lineage genes, which is consistent with previous reports indicating that a balance of different lineage-specifying forces is important for the restoration of pluripotency. A conserved zinc-finger DNA-binding domain in the C-terminus is critical for the GATA family to induce pluripotency. Using RNA-seq and ChIP-seq, we determined that the pluripotency-related gene Sall4 is a direct target of GATA family members during reprogramming and serves as a bridge linking the lineage-specifying GATA family to the pluripotency circuit. Thus, the GATA family is the first protein family of which all members can function as inducers of the reprogramming process and can substitute for Oct4. Our results suggest that the role of GATA family in reprogramming has been underestimated and that the GATA family may serve as an important mediator of cell fate conversion.
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25
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Chu M, Wang L, Wang H, Shen T, Yang Y, Sun Y, Tang N, Ni T, Zhu J, Mailman RB, Wang Y. A novel role of CDX1 in embryonic epicardial development. PLoS One 2014; 9:e103271. [PMID: 25068460 PMCID: PMC4113346 DOI: 10.1371/journal.pone.0103271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 06/30/2014] [Indexed: 12/26/2022] Open
Abstract
The molecular mechanism that regulates epicardial development has yet to be understood. In this study, we explored the function of CDX1, a Caudal-related family member, in epicardial epithelial-to-mesenchymal transition (EMT) and in the migration and the differentiation of epicardium-derived progenitors into vascular smooth muscle cells. We detected a transient expression of CDX1 in murine embryonic hearts at 11.5 days post coitum (dpc). Using a doxycycline-inducible CDX1 mouse model, primary epicardium, and ex vivo heart culture, we further demonstrated that ectopic expression of CDX1 promoted epicardial EMT. In addition, a low-dose CDX1 induction led to enhanced migration and differentiation of epicardium-derived cells into α-SMA+ vascular smooth muscles. In contrast, either continued high-level induction of CDX1 or CDX1 deficiency attenuated the ability of epicardium-derived cells to migrate and to mature into smooth muscles induced by TGF-β1. Further RNA-seq analyses showed that CDX1 induction altered the transcript levels of genes involved in neuronal development, angiogenesis, and cell adhesions required for EMT. Our data have revealed a previously undefined role of CDX1 during epicardial development, and suggest that transient expression of CDX1 promotes epicardial EMT, whereas subsequent down-regulation of CDX1 after 11.5 dpc in mice is necessary for further subepicardial invasion of EPDCs and contribution to coronary vascular endothelium or smooth muscle cells.
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MESH Headings
- Animals
- Cell Adhesion/genetics
- Cell Differentiation/genetics
- Cell Line
- Cell Movement/genetics
- Cells, Cultured
- Coronary Vessel Anomalies/genetics
- Embryonic Stem Cells
- Endothelium, Vascular/metabolism
- Epithelial-Mesenchymal Transition/genetics
- Gene Expression
- Gene Expression Regulation, Developmental
- Heart/embryology
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Mice
- Mice, Transgenic
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Myocytes, Smooth Muscle/cytology
- Myocytes, Smooth Muscle/metabolism
- Neurogenesis/genetics
- Organogenesis/genetics
- Pericardium/embryology
- Pericardium/metabolism
- Phenotype
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Affiliation(s)
- Min Chu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Libo Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ting Shen
- State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanqin Yang
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Yun Sun
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Nannan Tang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Ting Ni
- State Key Laboratory of Genetics Engineering & MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jun Zhu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
| | - Richard B. Mailman
- Department of Pharmacology, Penn State College of Medicine, Hershey, Pennsylvania, United States of America
| | - Yuan Wang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
- * E-mail:
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