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Mi J, Ren L, Andersson O. Leveraging zebrafish to investigate pancreatic development, regeneration, and diabetes. Trends Mol Med 2024:S1471-4914(24)00124-2. [PMID: 38825440 DOI: 10.1016/j.molmed.2024.05.002] [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: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024]
Abstract
The zebrafish has become an outstanding model for studying organ development and tissue regeneration, which is prominently leveraged for studies of pancreatic development, insulin-producing β-cells, and diabetes. Although studied for more than two decades, many aspects remain elusive and it has only recently been possible to investigate these due to technical advances in transcriptomics, chemical-genetics, genome editing, drug screening, and in vivo imaging. Here, we review recent findings on zebrafish pancreas development, β-cell regeneration, and how zebrafish can be used to provide novel insights into gene functions, disease mechanisms, and therapeutic targets in diabetes, inspiring further use of zebrafish for the development of novel therapies for diabetes.
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Affiliation(s)
- Jiarui Mi
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Gastroenterology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, China.
| | - Lipeng Ren
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden
| | - Olov Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden; Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden.
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Lavergne A, Tarifeño-Saldivia E, Pirson J, Reuter AS, Flasse L, Manfroid I, Voz ML, Peers B. Pancreatic and intestinal endocrine cells in zebrafish share common transcriptomic signatures and regulatory programmes. BMC Biol 2020; 18:109. [PMID: 32867764 PMCID: PMC7457809 DOI: 10.1186/s12915-020-00840-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 08/04/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Endocrine cells of the zebrafish digestive system play an important role in regulating metabolism and include pancreatic endocrine cells (PECs) clustered in the islets of Langerhans and the enteroendocrine cells (EECs) scattered in the intestinal epithelium. Despite EECs and PECs are being located in distinct organs, their differentiation involves shared molecular mechanisms and transcription factors. However, their degree of relatedness remains unexplored. In this study, we investigated comprehensively the similarity of EECs and PECs by defining their transcriptomic landscape and comparing the regulatory programmes controlled by Pax6b, a key player in both EEC and PEC differentiations. RESULTS RNA sequencing was performed on EECs and PECs isolated from wild-type and pax6b mutant zebrafish. Data mining of wild-type zebrafish EEC data confirmed the expression of orthologues for most known mammalian EEC hormones, but also revealed the expression of three additional neuropeptide hormones (Proenkephalin-a, Calcitonin-a and Adcyap1a) not previously reported to be expressed by EECs in any species. Comparison of transcriptomes from EECs, PECs and other zebrafish tissues highlights a very close similarity between EECs and PECs, with more than 70% of genes being expressed in both endocrine cell types. Comparison of Pax6b-regulated genes in EECs and PECs revealed a significant overlap. pax6b loss-of-function does not affect the total number of EECs and PECs but instead disrupts the balance between endocrine cell subtypes, leading to an increase of ghrelin- and motilin-like-expressing cells in both the intestine and pancreas at the expense of other endocrine cells such as beta and delta cells in the pancreas and pyyb-expressing cells in the intestine. Finally, we show that the homeodomain of Pax6b is dispensable for its action in both EECs and PECs. CONCLUSION We have analysed the transcriptomic landscape of wild-type and pax6b mutant zebrafish EECs and PECs. Our study highlights the close relatedness of EECs and PECs at the transcriptomic and regulatory levels, supporting the hypothesis of a common phylogenetic origin and underscoring the potential implication of EECs in metabolic diseases such as type 2 diabetes.
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Affiliation(s)
- Arnaud Lavergne
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
| | - Estefania Tarifeño-Saldivia
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
- Present Address: Gene Expression and Regulation Laboratory, Department of Biochemistry and Molecular Biology, University of Concepción, Concepción, Chile
| | - Justine Pirson
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
| | - Anne-Sophie Reuter
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
| | - Lydie Flasse
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
| | - Isabelle Manfroid
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
| | - Marianne L. Voz
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
| | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA, University of Liège, Avenue de l’Hôpital 1, B34, Sart Tilman, 4000 Liège, Belgium
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Lu CJ, Fan XY, Guo YF, Cheng ZC, Dong J, Chen JZ, Li LY, Wang MW, Wu ZK, Wang F, Tong XJ, Luo LF, Tang FC, Zhu ZY, Zhang B. Single-cell analyses identify distinct and intermediate states of zebrafish pancreatic islet development. J Mol Cell Biol 2020; 11:435-447. [PMID: 30407522 PMCID: PMC6604604 DOI: 10.1093/jmcb/mjy064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/13/2022] Open
Abstract
Pancreatic endocrine islets are vital for glucose homeostasis. However, the islet developmental trajectory and its regulatory network are not well understood. To define the features of these specification and differentiation processes, we isolated individual islet cells from TgBAC(neurod1:EGFP) transgenic zebrafish and analyzed islet developmental dynamics across four different embryonic stages using a single-cell RNA-seq strategy. We identified proliferative endocrine progenitors, which could be further categorized by different cell cycle phases with the G1/S subpopulation displaying a distinct differentiation potential. We identified endocrine precursors, a heterogeneous intermediate-state population consisting of lineage-primed alpha, beta and delta cells that were characterized by the expression of lineage-specific transcription factors and relatively low expression of terminally differentiation markers. The terminally differentiated alpha, beta, and delta cells displayed stage-dependent differentiation states, which were related to their functional maturation. Our data unveiled distinct states, events and molecular features during the islet developmental transition, and provided resources to comprehensively understand the lineage hierarchy of islet development at the single-cell level.
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Affiliation(s)
- Chong-Jian Lu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Xiao-Ying Fan
- Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Yue-Feng Guo
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Zhen-Chao Cheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ji Dong
- Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Jin-Zi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China
| | - Lian-Yan Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Mei-Wen Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ze-Kai Wu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Fei Wang
- National Center for Protein Sciences, Peking University, Beijing, China
| | - Xiang-Jun Tong
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Ling-Fei Luo
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, Laboratory of Molecular Developmental Biology, School of Life Sciences, Southwest University, Chongqing, China
| | - Fu-Chou Tang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics (ICG), College of Life Sciences, Peking University, Beijing, China
| | - Zuo-Yan Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
| | - Bo Zhang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, College of Life Sciences, Peking University, Beijing, China
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Abstract
The zebrafish pancreas shares its basic organization and cell types with the mammalian pancreas. In addition, the developmental pathways that lead to the establishment of the pancreatic islets of Langherhans are generally conserved from fish to mammals. Zebrafish provides a powerful tool to probe the mechanisms controlling establishment of the pancreatic endocrine cell types from early embryonic progenitor cells, as well as the regeneration of endocrine cells after damage. This knowledge is, in turn, applicable to refining protocols to generate renewable sources of human pancreatic islet cells that are critical for regulation of blood sugar levels. Here, we review how previous and ongoing studies in zebrafish and beyond are influencing the understanding of molecular mechanisms underlying various forms of diabetes and efforts to develop cell-based approaches to cure this increasingly widespread disease.
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Mayran A, Pelletier A, Drouin J. Pax factors in transcription and epigenetic remodelling. Semin Cell Dev Biol 2015; 44:135-44. [PMID: 26234816 DOI: 10.1016/j.semcdb.2015.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/25/2022]
Abstract
The nine Pax transcription factors that constitute the mammalian family of paired domain (PD) factors play key roles in many developmental processes. As DNA binding transcription factors, they exhibit tremendous variability and complexity in their DNA recognition patterns. This is ascribed to the presence of multiple DNA binding structural domains, namely helix-turn-helix (HTH) domains. The PD contains two HTH subdomains and four of the nine Pax factors have an additional HTH domain, the homeodomain (HD). We now review these diverse DNA binding modalities together with their properties as transcriptional activators and repressors. The action of Pax factors on gene expression is also exerted through recruitment of chromatin remodelling complexes that introduce either activating or repressive chromatin marks. Interestingly, the recent demonstration that Pax7 has pioneer activity, the unique property to "open" chromatin, further underlines the mechanistic versatility and the developmental importance of these factors.
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Affiliation(s)
- Alexandre Mayran
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Audrey Pelletier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
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Mussar K, Tucker A, McLennan L, Gearhart A, Jimenez-Caliani AJ, Cirulli V, Crisa L. Macrophage/epithelium cross-talk regulates cell cycle progression and migration in pancreatic progenitors. PLoS One 2014; 9:e89492. [PMID: 24586821 PMCID: PMC3929706 DOI: 10.1371/journal.pone.0089492] [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: 12/24/2013] [Accepted: 01/21/2014] [Indexed: 01/06/2023] Open
Abstract
Macrophages populate the mesenchymal compartment of all organs during embryogenesis and have been shown to support tissue organogenesis and regeneration by regulating remodeling of the extracellular microenvironment. Whether this mesenchymal component can also dictate select developmental decisions in epithelia is unknown. Here, using the embryonic pancreatic epithelium as model system, we show that macrophages drive the epithelium to execute two developmentally important choices, i.e. the exit from cell cycle and the acquisition of a migratory phenotype. We demonstrate that these developmental decisions are effectively imparted by macrophages activated toward an M2 fetal-like functional state, and involve modulation of the adhesion receptor NCAM and an uncommon "paired-less" isoform of the transcription factor PAX6 in the epithelium. Over-expression of this PAX6 variant in pancreatic epithelia controls both cell motility and cell cycle progression in a gene-dosage dependent fashion. Importantly, induction of these phenotypes in embryonic pancreatic transplants by M2 macrophages in vivo is associated with an increased frequency of endocrine-committed cells emerging from ductal progenitor pools. These results identify M2 macrophages as key effectors capable of coordinating epithelial cell cycle withdrawal and cell migration, two events critical to pancreatic progenitors' delamination and progression toward their differentiated fates.
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Affiliation(s)
- Kristin Mussar
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Andrew Tucker
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Linsey McLennan
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Addie Gearhart
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Antonio J. Jimenez-Caliani
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Vincenzo Cirulli
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Laura Crisa
- Department of Medicine, Institute of Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, United States of America
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Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by a Marek's disease virus oncoprotein, Meq. J Virol 2013; 87:9016-29. [PMID: 23740999 DOI: 10.1128/jvi.01163-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marek's disease (MD) is an economically significant disease in chickens that is caused by the highly oncogenic Marek's disease virus (MDV). A major unanswered question is the mechanism of MDV-induced tumor formation. Meq, a bZIP transcription factor discovered in the 1990s, is critically involved in viral oncogenicity, but only a few of its host target genes have been described, impeding our understanding of MDV-induced tumorigenesis. Using chromatin immunoprecipitation-sequencing (ChIP-seq) and microarray analysis, a high-confidence list of Meq binding sites in the chicken genome and a global transcriptome of Meq-responsive genes were generated. Meq binding sites were found to be enriched in the promoter regions of upregulated genes but not in those of downregulated genes. ChIP-seq was also performed for c-Jun, a known heterodimeric partner of Meq. The close location of binding sites of Meq and c-Jun was noted, suggesting cooperativity between these two factors in modulating transcription. Pathway analysis indicated that Meq transcriptionally regulates many genes that are part of several signaling pathways including the extracellular signal-regulated kinase /mitogen-activated protein kinase (ERK/MAPK), Jak-STAT, and ErbB pathways, which are critical for oncogenesis and/or include signaling mediators involved in apoptosis. Meq activates oncogenic signaling cascades by transcriptionally activating major kinases in the ERK/MAPK pathway and simultaneously repressing phosphatases, as verified using inhibitors of MEK and ERK1/2 in a cell proliferation assay. This study provides significant insights into the mechanistic basis of Meq-dependent cell transformation.
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8
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Go W, Korzh V. Plasma membrane Ca(2+) ATPase Atp2b1a regulates bone mineralization in zebrafish. Bone 2013; 54:48-57. [PMID: 23353107 DOI: 10.1016/j.bone.2013.01.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 12/07/2012] [Accepted: 01/07/2013] [Indexed: 01/11/2023]
Abstract
The zebrafish transgenic lines provide a possibility to observe the development of tissues and organs in real time. Using the reporter line for the zebrafish plasma membrane Ca(2+) ATPase (SqET4), we detected its expression in the epithelium of pharyngeal teeth and analyzed its role in their calcification and that of cranial bones. atp2b1a's expression in the pharyngeal epithelium is faithfully recapitulated in the SqET4 transgenics by GFP expression. We showed by morpholino knockdown of Atp2b1a translations as well as chemical inhibition of Atp2b1a pump activity using carboxyeosin, that its activity is required to facilitate calcification of the developing pharyngeal teeth by the dental epithelium. Atp2b1a could be required during calcification of endochondral bones, where it acts at two levels: 1) by exporting Ca(2+) from ameloblasts, it provides raw material for calcifying the pharyngeal teeth by adjacent odontoblasts; and 2) by regulating terminal differentiation of pharyngeal epithelial cells, including ameloblasts required for tissue hyper-mineralization. atp2b1a's expression in the pharyngeal epithelium is regulated by the homeodomain transcription factor dlx2b.
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Affiliation(s)
- William Go
- Institute of Molecular and Cell Biology, A-STAR, Singapore
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Djiotsa J, Verbruggen V, Giacomotto J, Ishibashi M, Manning E, Rinkwitz S, Manfroid I, Voz ML, Peers B. Pax4 is not essential for beta-cell differentiation in zebrafish embryos but modulates alpha-cell generation by repressing arx gene expression. BMC DEVELOPMENTAL BIOLOGY 2012; 12:37. [PMID: 23244389 PMCID: PMC3563606 DOI: 10.1186/1471-213x-12-37] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Accepted: 12/14/2012] [Indexed: 01/03/2023]
Abstract
BACKGROUND Genetic studies in mouse have demonstrated the crucial function of PAX4 in pancreatic cell differentiation. This transcription factor specifies β- and δ-cell fate at the expense of α-cell identity by repressing Arx gene expression and ectopic expression of PAX4 in α-cells is sufficient to convert them into β-cells. Surprisingly, no Pax4 orthologous gene can be found in chicken and Xenopus tropicalis raising the question of the function of pax4 gene in lower vertebrates such as in fish. In the present study, we have analyzed the expression and the function of the orthologous pax4 gene in zebrafish. RESULTS pax4 gene is transiently expressed in the pancreas of zebrafish embryos and is mostly restricted to endocrine precursors as well as to some differentiating δ- and ε-cells but was not detected in differentiating β-cells. pax4 knock-down in zebrafish embryos caused a significant increase in α-cells number while having no apparent effect on β- and δ-cell differentiation. This rise of α-cells is due to an up-regulation of the Arx transcription factor. Conversely, knock-down of arx caused to a complete loss of α-cells and a concomitant increase of pax4 expression but had no effect on the number of β- and δ-cells. In addition to the mutual repression between Arx and Pax4, these two transcription factors negatively regulate the transcription of their own gene. Interestingly, disruption of pax4 RNA splicing or of arx RNA splicing by morpholinos targeting exon-intron junction sites caused a blockage of the altered transcripts in cell nuclei allowing an easy characterization of the arx- and pax4-deficient cells. Such analyses demonstrated that arx knock-down in zebrafish does not lead to a switch of cell fate, as reported in mouse, but rather blocks the cells in their differentiation process towards α-cells. CONCLUSIONS In zebrafish, pax4 is not required for the generation of the first β- and δ-cells deriving from the dorsal pancreatic bud, unlike its crucial role in the differentiation of these cell types in mouse. On the other hand, the mutual repression between Arx and Pax4 is observed in both mouse and zebrafish. These data suggests that the main original function of Pax4 during vertebrate evolution was to modulate the number of pancreatic α-cells and its role in β-cells differentiation appeared later in vertebrate evolution.
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Affiliation(s)
- Joachim Djiotsa
- Molecular Biology and Genetic Engineering, Giga-Research, University of Liège, 1 avenue de l'Hôpital B34, Sart-Tilman B-4000, Belgium
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Gestri G, Link BA, Neuhauss SCF. The visual system of zebrafish and its use to model human ocular diseases. Dev Neurobiol 2012; 72:302-27. [PMID: 21595048 DOI: 10.1002/dneu.20919] [Citation(s) in RCA: 115] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Free swimming zebrafish larvae depend mainly on their sense of vision to evade predation and to catch prey. Hence, there is strong selective pressure on the fast maturation of visual function and indeed the visual system already supports a number of visually driven behaviors in the newly hatched larvae.The ability to exploit the genetic and embryonic accessibility of the zebrafish in combination with a behavioral assessment of visual system function has made the zebrafish a popular model to study vision and its diseases.Here, we review the anatomy, physiology, and development of the zebrafish eye as the basis to relate the contributions of the zebrafish to our understanding of human ocular diseases.
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Affiliation(s)
- Gaia Gestri
- Department of Cell and Developmental Biology, University College, London,UK.
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11
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Voz ML, Coppieters W, Manfroid I, Baudhuin A, Von Berg V, Charlier C, Meyer D, Driever W, Martial JA, Peers B. Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing. PLoS One 2012; 7:e34671. [PMID: 22496837 PMCID: PMC3319596 DOI: 10.1371/journal.pone.0034671] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 03/06/2012] [Indexed: 02/03/2023] Open
Abstract
Forward genetics using zebrafish is a powerful tool for studying vertebrate development through large-scale mutagenesis. Nonetheless, the identification of the molecular lesion is still laborious and involves time-consuming genetic mapping. Here, we show that high-throughput sequencing of the whole zebrafish genome can directly locate the interval carrying the causative mutation and at the same time pinpoint the molecular lesion. The feasibility of this approach was validated by sequencing the m1045 mutant line that displays a severe hypoplasia of the exocrine pancreas. We generated 13 Gb of sequence, equivalent to an eightfold genomic coverage, from a pool of 50 mutant embryos obtained from a map-cross between the AB mutant carrier and the WIK polymorphic strain. The chromosomal region carrying the causal mutation was localized based on its unique property to display high levels of homozygosity among sequence reads as it derives exclusively from the initial AB mutated allele. We developed an algorithm identifying such a region by calculating a homozygosity score along all chromosomes. This highlighted an 8-Mb window on chromosome 5 with a score close to 1 in the m1045 mutants. The sequence analysis of all genes within this interval revealed a nonsense mutation in the snapc4 gene. Knockdown experiments confirmed the assertion that snapc4 is the gene whose mutation leads to exocrine pancreas hypoplasia. In conclusion, this study constitutes a proof-of-concept that whole-genome sequencing is a fast and effective alternative to the classical positional cloning strategies in zebrafish.
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Affiliation(s)
- Marianne L Voz
- Laboratoire de Biologie Moléculaire et de Génie Génétique, Université de Liège, Sart Tilman, Belgium.
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12
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Arkhipova V, Wendik B, Devos N, Ek O, Peers B, Meyer D. Characterization and regulation of the hb9/mnx1 beta-cell progenitor specific enhancer in zebrafish. Dev Biol 2012; 365:290-302. [PMID: 22426004 PMCID: PMC3327876 DOI: 10.1016/j.ydbio.2012.03.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 02/27/2012] [Accepted: 03/01/2012] [Indexed: 11/06/2022]
Abstract
Differentiation of insulin producing beta-cells is a genetically well defined process that involves functions of various conserved transcription factors. Still, the transcriptional mechanisms underlying specification and determination of beta-cell fate are poorly defined. Here we provide the description of a beta-cell progenitor specific enhancer as a model to study initial steps of beta-cell differentiation. We show that evolutionary non-conserved upstream sequences of the zebrafish hb9 gene are required and sufficient for regulating expression in beta-cells prior to the onset of insulin expression. This enhancer contains binding sites for paired-box transcription factors and two E-boxes that in EMSA studies show interaction with Pax6b and NeuroD, respectively. We show that Pax6b is a potent activator of endodermal hb9 expression and that this activation depends on the beta-cell enhancer. Using genetic approaches we show that pax6b is crucial for maintenance but not induction of pancreatic hb9 transcription. As loss of Pax6b or Hb9 independently results in the loss of insulin expression, the data reveal a novel cross-talk between the two essential regulators of early beta-cell differentiation. While we find that the known pancreatic E-box binding proteins NeuroD and Ngn3 are not required for hb9 expression we also show that removal of both E-boxes selectively eliminates pancreatic specific reporter expression. The data provide evidence for an Ngn3 independent pathway of beta-cell specification that requires function of currently not specified E-box binding factors.
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Affiliation(s)
- Valeriya Arkhipova
- Institute for Molecular Biology/CMBI, Technikerstr. 25, University of Innsbruck, 6020 Innsbruck, Austria.
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13
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Morris AC. The genetics of ocular disorders: insights from the zebrafish. ACTA ACUST UNITED AC 2012; 93:215-28. [PMID: 21932431 DOI: 10.1002/bdrc.20211] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Proper formation of the vertebrate eye requires a precisely coordinated sequence of morphogenetic events that integrate the developmental contributions of the skin ectoderm, neuroectoderm, and head mesenchyme. Disruptions in this process result in ocular malformations or retinal degeneration and can cause significant visual impairment. The zebrafish is an excellent vertebrate model for the study of eye development and disease due to the transparency of the embryo, its ex utero development, and its amenability to forward genetic screens. This review will present an overview of the genetic methodologies utilized in the zebrafish, a description of several zebrafish models of congenital ocular diseases, and a discussion of the utility of the zebrafish for assessing the pathogenicity of candidate disease alleles.
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Affiliation(s)
- Ann C Morris
- Department of Biology, University of Kentucky, Lexington, USA.
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14
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Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic partner for FOS protein in invasive tumors. Proc Natl Acad Sci U S A 2012; 109:2168-73. [PMID: 22308434 DOI: 10.1073/pnas.1119229109] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ecotropic viral integration site 1 (EVI1) is an oncogenic dual domain zinc finger transcription factor that plays an essential role in the regulation of hematopoietic stem cell renewal, and its overexpression in myeloid leukemia and epithelial cancers is associated with poor patient survival. Despite the discovery of EVI1 in 1988 and its emerging role as a dominant oncogene in various types of cancer, few EVI1 target genes are known. This lack of knowledge has precluded a clear understanding of exactly how EVI1 contributes to cancer. Using a combination of ChIP-Seq and microarray studies in human ovarian carcinoma cells, we show that the two zinc finger domains of EVI1 bind to DNA independently and regulate different sets of target genes. Strikingly, an enriched fraction of EVI1 target genes are cancer genes or genes associated with cancer. We also show that more than 25% of EVI1-occupied genes contain linked EVI1 and activator protein (AP)1 DNA binding sites, and this finding provides evidence for a synergistic cooperative interaction between EVI1 and the AP1 family member FOS in the regulation of cell adhesion, proliferation, and colony formation. An increased number of dual EVI1/AP1 target genes are also differentially regulated in late-stage ovarian carcinomas, further confirming the importance of the functional cooperation between EVI1 and FOS. Collectively, our data indicate that EVI1 is a multipurpose transcription factor that synergizes with FOS in invasive tumors.
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Abstract
The pancreas is a vertebrate-specific organ of endodermal origin which is responsible for production of digestive enzymes and hormones involved in regulating glucose homeostasis, in particular insulin, deficiency of which results in diabetes. Basic research on the genetic and molecular pathways regulating pancreas formation and function has gained major importance for the development of regenerative medical approaches aimed at improving diabetes treatment. Among the different model organisms that are currently used to elucidate the basic pathways of pancreas development and regeneration, the zebrafish is distinguished by its unique opportunities to combine genetic and pharmacological approaches with sophisticated live-imaging methodology, and by its ability to regenerate the pancreas within a short time. Here we review current perspectives and present methods for studying two important processes contributing to pancreas development and regeneration, namely cell migration via time-lapse micropscopy and cell proliferation via incorporation of nucleotide analog EdU, with a focus on the insulin-producing beta cells of the islet.
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Affiliation(s)
- Robin A Kimmel
- Institute of Molecular Biology, University of Innsbruck, A-6020 Innsbruck, Austria
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