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Ferrari L, Bragato C, Brioschi L, Spreafico M, Esposito S, Pezzotta A, Pizzetti F, Moreno‐Fortuny A, Bellipanni G, Giordano A, Riva P, Frabetti F, Viani P, Cossu G, Mora M, Marozzi A, Pistocchi A. HDAC8 regulates canonical Wnt pathway to promote differentiation in skeletal muscles. J Cell Physiol 2018; 234:6067-6076. [DOI: 10.1002/jcp.27341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Affiliation(s)
- Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Cinzia Bragato
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta Milano Italy
- PhD Program in Neuroscience, University of Milano‐Bicocca Milano Italy
| | - Loredana Brioschi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Marco Spreafico
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Simona Esposito
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Alex Pezzotta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Fabrizio Pizzetti
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Artal Moreno‐Fortuny
- Division of Cell Matrix Biology and Regenerative Medicine Faculty of Biology, Medicine and Health, University of Manchester Manchester UK
- Developmental Genetics, Department of Biomedicine University of Basel Basel Switzerland
| | - Gianfranco Bellipanni
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University Philadelphia
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Department of Biology, Center for Biotechnology, College of Science and Technology, Temple University Philadelphia
- Department of Medicine Surgery & Neuroscience, University of Siena Siena Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Flavia Frabetti
- Department of Experimental, Diagnostic and Specialty Medicine University of Bologna Bologna Italy
| | - Paola Viani
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Giulio Cossu
- Division of Cell Matrix Biology and Regenerative Medicine Faculty of Biology, Medicine and Health, University of Manchester Manchester UK
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico C. Besta Milano Italy
| | - Anna Marozzi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale Università degli Studi di Milano Milano Italy
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Huang B, Li X, Tu X, Zhao W, Zhu D, Feng Y, Si X, Chen JG. OTX1 regulates cell cycle progression of neural progenitors in the developing cerebral cortex. J Biol Chem 2017; 293:2137-2148. [PMID: 29273633 DOI: 10.1074/jbc.ra117.001249] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Indexed: 01/01/2023] Open
Abstract
The progenitor cells in the cerebral cortex coordinate proliferation and mitotic exit to generate the correct number of neurons and glial cells during development. However, mechanisms for regulating the mitotic cycle of cortical progenitors are not fully understood. Otx1 is one of the homeobox-containing transcription factors frequently implicated in the development of the central nervous system. Mice bearing a targeted deletion of Otx1 exhibit brain hypoplasia and a decrease in the number of cortical neurons. We hypothesized that Otx1 might be crucial to the proliferation and differentiation of cortical progenitors. Otx1 knockdown by in utero electroporation in the mouse brain reduced the proportion of the G1 phase while increasing the S and M phases of progenitor cells. The knockdown diminished Tbr1+ neurons but increased GFAP+ astrocytes in the early postnatal cortex as revealed by lineage tracing study. Tbr2+ basal progenitors lacking Otx1 were held at the transit-amplifying stage. In contrast, overexpression of wildtype Otx1 but not an astrocytoma-related mutant Y320C inhibited proliferation of the progenitor cells in embryonic cortex. This study demonstrates that Otx1 is one of the key elements regulating cortical neurogenesis, and a loss-of-function in Otx1 may contribute to the overproduction of astrocytes in vivo.
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Affiliation(s)
- Baoshan Huang
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xue Li
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiaomeng Tu
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Wei Zhao
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Dan Zhu
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Yue Feng
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Xiang Si
- From the School of Ophthalmology and Optometry and Eye Hospital.,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Jie-Guang Chen
- From the School of Ophthalmology and Optometry and Eye Hospital, .,the State Key Laboratory of Optometry, Ophthalmology and Vision Science, and.,the Zhejiang Provincial Key Laboratory of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
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3
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Fazio G, Gaston-Massuet C, Bettini LR, Graziola F, Scagliotti V, Cereda A, Ferrari L, Mazzola M, Cazzaniga G, Giordano A, Cotelli F, Bellipanni G, Biondi A, Selicorni A, Pistocchi A, Massa V. CyclinD1 Down-Regulation and Increased Apoptosis Are Common Features of Cohesinopathies. J Cell Physiol 2016. [PMID: 26206533 DOI: 10.1002/jcp.25106] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetic variants within components of the cohesin complex (NIPBL, SMC1A, SMC3, RAD21, PDS5, ESCO2, HDAC8) are believed to be responsible for a spectrum of human syndromes known as "cohesinopathies" that includes Cornelia de Lange Syndrome (CdLS). CdLS is a multiple malformation syndrome affecting almost any organ and causing severe developmental delay. Cohesinopathies seem to be caused by dysregulation of specific developmental pathways downstream of mutations in cohesin components. However, it is still unclear how mutations in different components of the cohesin complex affect the output of gene regulation. In this study, zebrafish embryos and SMC1A-mutated patient-derived fibroblasts were used to analyze abnormalities induced by SMC1A loss of function. We show that the knockdown of smc1a in zebrafish impairs neural development, increases apoptosis, and specifically down-regulates Ccnd1 levels. The same down-regulation of cohesin targets is observed in SMC1A-mutated patient fibroblasts. Previously, we have demonstrated that haploinsufficiency of NIPBL produces similar effects in zebrafish and in patients fibroblasts indicating a possible common feature for neurological defects and mental retardation in cohesinopathies. Interestingly, expression analysis of Smc1a and Nipbl in developing mouse embryos reveals a specific pattern in the hindbrain, suggesting a role for cohesins in neural development in vertebrates.
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Affiliation(s)
- Grazia Fazio
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Carles Gaston-Massuet
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK
| | - Laura Rachele Bettini
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Federica Graziola
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK.,Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Valeria Scagliotti
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London Medical School, Queen Mary University of London, London, UK
| | - Anna Cereda
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy
| | - Mara Mazzola
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Antonio Giordano
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Andrea Biondi
- Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy.,Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Angelo Selicorni
- Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milano, Italy.,Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Valentina Massa
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
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4
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Valenti F, Ibetti J, Komiya Y, Baxter M, Lucchese AM, Derstine L, Covaciu C, Rizzo V, Vento R, Russo G, Macaluso M, Cotelli F, Castiglia D, Gottardi CJ, Habas R, Giordano A, Bellipanni G. The increase in maternal expression of axin1 and axin2 contribute to the zebrafish mutant ichabod ventralized phenotype. J Cell Biochem 2015; 116:418-30. [PMID: 25335865 DOI: 10.1002/jcb.24993] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/06/2014] [Indexed: 11/11/2022]
Abstract
β-Catenin is a central effector of the Wnt pathway and one of the players in Ca(+)-dependent cell-cell adhesion. While many wnts are present and expressed in vertebrates, only one β-catenin exists in the majority of the organisms. One intriguing exception is zebrafish that carries two genes for β-catenin. The maternal recessive mutation ichabod presents very low levels of β-catenin2 that in turn affects dorsal axis formation, suggesting that β-catenin1 is incapable to compensate for β-catenin2 loss and raising the question of whether these two β-catenins may have differential roles during early axis specification. Here we identify a specific antibody that can discriminate selectively for β-catenin1. By confocal co-immunofluorescent analysis and low concentration gain-of-function experiments, we show that β-catenin1 and 2 behave in similar modes in dorsal axis induction and cellular localization. Surprisingly, we also found that in the ich embryo the mRNAs of the components of β-catenin regulatory pathway, including β-catenin1, are more abundant than in the Wt embryo. Increased levels of β-catenin1 are found at the membrane level but not in the nuclei till high stage. Finally, we present evidence that β-catenin1 cannot revert the ich phenotype because it may be under the control of a GSK3β-independent mechanism that required Axin's RGS domain function.
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Affiliation(s)
- Fabio Valenti
- Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, 19122, Pennsylvania; Department of Biology, College of Science and Technology, Temple University, Philadelphia, 19122, Pennsylvania
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5
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Ferrari L, Pistocchi A, Libera L, Boari N, Mortini P, Bellipanni G, Giordano A, Cotelli F, Riva P. FAS/FASL are dysregulated in chordoma and their loss-of-function impairs zebrafish notochord formation. Oncotarget 2015; 5:5712-24. [PMID: 25071022 PMCID: PMC4170636 DOI: 10.18632/oncotarget.2145] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Chordoma is a rare malignant tumor that recapitulates the notochord phenotype and is thought to derive from notochord remnants not correctly regressed during development. Apoptosis is necessary for the proper notochord development in vertebrates, and the apoptotic pathway mediated by Fas and Fasl has been demonstrated to be involved in notochord cells regression. This study was conducted to investigate the expression of FAS/FASL pathway in a cohort of skull base chordomas and to analyze the role of fas/fasl homologs in zebrafish notochord formation. FAS/FASL expression was found to be dysregulated in chordoma leading to inactivation of the downstream Caspases in the samples analyzed. Both fas and fasl were specifically expressed in zebrafish notochord sorted cells. fas and fasl loss-of-function mainly resulted in larvae with notochord multi-cell-layer jumps organization, larger vacuolated notochord cells, defects in the peri-notochordal sheath structure and in vertebral mineralization. Interestingly, we observed the persistent expression of ntla and col2a1a, the zebrafish homologs of the human T gene and COL2A1 respectively, which are specifically up-regulated in chordoma. These results demonstrate for the first time the dysregulation of FAS/FASL in chordoma and their role in notochord formation in the zebrafish model, suggesting their possible implication in chordoma onset.
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Affiliation(s)
- Luca Ferrari
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università Degli Studi di Milano, Via Viotti 3/5 20133 Milan, Italy; These authors contribute equally in this study
| | - Anna Pistocchi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università Degli Studi di Milano, Via Viotti 3/5 20133 Milan, Italy; Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26 20133 Milan, Italy; These authors contribute equally in this study
| | - Laura Libera
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università Degli Studi di Milano, Via Viotti 3/5 20133 Milan, Italy
| | - Nicola Boari
- Dipartimento di Neurochirurgia, Università Vita-Salute IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy
| | - Pietro Mortini
- Dipartimento di Neurochirurgia, Università Vita-Salute IRCCS Ospedale San Raffaele, Via Olgettina 60, 20132 Milan, Italy
| | - Gianfranco Bellipanni
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA; Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Antonio Giordano
- Department of Biology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA; Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, USA
| | - Franco Cotelli
- Dipartimento di Bioscienze, Università Degli Studi di Milano, Via Celoria 26 20133 Milan, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università Degli Studi di Milano, Via Viotti 3/5 20133 Milan, Italy
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6
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Vitale G, Gaudenzi G, Dicitore A, Cotelli F, Ferone D, Persani L. Zebrafish as an innovative model for neuroendocrine tumors. Endocr Relat Cancer 2014; 21:R67-83. [PMID: 24292602 DOI: 10.1530/erc-13-0388] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tumor models have a relevant role in furthering our understanding of the biology of malignant disease and in preclinical cancer research. Only few models are available for neuroendocrine tumors (NETs), probably due to the rarity and heterogeneity of this group of neoplasms. This review provides insights into the current state-of-the-art of zebrafish as a model in cancer research, focusing on potential applications in NETs. Zebrafish has a complex circulatory system similar to that of mammals. A novel angiogenesis assay based on the injection of human NET cell lines (TT and DMS79 cells) into the subperidermal space of the zebrafish embryos has been developed. Proangiogenic factors locally released by the tumor graft affect the normal developmental pattern of the subintestinal vessels by stimulating the migration and growth of sprouting vessels toward the implant. In addition, a description of the striking homology between zebrafish and humans of molecular targets involved in tumor angiogenesis (somatostatin receptors, dopamine receptors, mammalian target of rapamycin), and currently used as targeted therapy of NETs, is reported.
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Affiliation(s)
- Giovanni Vitale
- Department of Clinical Sciences and Community Health (DISCCO), University of Milan, Milan, Italy Laboratory of Endocrine and Metabolic Research, Istituto Auxologico Italiano IRCCS, via Zucchi 18, Cusano Milanino (MI) 20095, Italy Department of Biosciences, University of Milan, Milan, Italy Endocrinology Unit, Department of Internal Medicine and Medical Specialties, Center of Excellence for Biomedical Research, IRCCS AOU San Martino-IST, University of Genoa, Genoa, Italy
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7
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Malafoglia V, Colasanti M, Raffaeli W, Balciunas D, Giordano A, Bellipanni G. Extreme thermal noxious stimuli induce pain responses in zebrafish larvae. J Cell Physiol 2014; 229:300-8. [PMID: 23929528 DOI: 10.1002/jcp.24447] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 08/01/2013] [Indexed: 11/06/2022]
Abstract
Exposing tissues to extreme high or low temperature leads to burns. Burned animals sustain several types of damage, from the disruption of the tissue to degeneration of axons projecting through muscle and skin. Such damage causes pain due to both inflammation and axonal degeneration (neuropathic-like pain). Thus, the approach to cure and alleviate the symptoms of burns must be twofold: rebuilding the tissue that has been destroyed and alleviating the pain derived from the burns. While tissue regeneration techniques have been developed, less is known on the treatment of the induced pain. Thus, appropriate animal models are necessary for the development of the best treatment for pain induced in burned tissues. We have developed a methodology in the zebrafish aimed to produce a new animal model for the study of pain induced by burns. Here, we show that two events linked to the onset of burn-induced inflammation and neuropathic-like pain in mammals, degeneration of axons innervating the affected tissues and over-expression of specific genes in sensory tissues, are conserved from zebrafish to mammals.
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Affiliation(s)
- Valentina Malafoglia
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, Pennsylvania; ISAL-Foundation, Institute for Research on Pain, Torre Pedrera (RN), Italy
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8
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Mancini P, Castelli M, Vignali R. Identification and evolution of molecular domains involved in differentiating the cement gland-promoting activity of Otx proteins in Xenopus laevis. Mech Dev 2013; 130:628-39. [DOI: 10.1016/j.mod.2013.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
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9
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Malafoglia V, Bryant B, Raffaeli W, Giordano A, Bellipanni G. The zebrafish as a model for nociception studies. J Cell Physiol 2013; 228:1956-66. [DOI: 10.1002/jcp.24379] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 03/26/2013] [Indexed: 12/18/2022]
Affiliation(s)
| | - Bruce Bryant
- Monell Chemical Senses Center; Philadelphia, Pennsylvania
| | - William Raffaeli
- Institute for Research on Pain; ISAL-Foundation; Torre Pedrera (RN); Italy
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10
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Deep mRNA sequencing analysis to capture the transcriptome landscape of zebrafish embryos and larvae. PLoS One 2013; 8:e64058. [PMID: 23700457 PMCID: PMC3659048 DOI: 10.1371/journal.pone.0064058] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 04/09/2013] [Indexed: 11/19/2022] Open
Abstract
Transcriptome analysis is a powerful tool to obtain large amount genome-scale gene expression profiles. Despite its extensive usage to diverse biological problems in the last decade, transcriptomic researches approaching the zebrafish embryonic development have been very limited. Several recent studies have made great progress in this direction, yet the large gap still exists, especially regarding to the transcriptome dynamics of embryonic stages from early gastrulation onwards. Here, we present a comprehensive analysis about the transcriptomes of 9 different stages covering 7 major periods (cleavage, blastula, gastrula, segmentation, pharyngula, hatching and early larval stage) in zebrafish development, by recruiting the RNA-sequencing technology. We detected the expression for at least 24,065 genes in at least one of the 9 stages. We identified 16,130 genes that were significantly differentially expressed between stages and were subsequently classified into six clusters. Each revealed gene cluster had distinct expression patterns and characteristic functional pathways, providing a framework for the understanding of the developmental transcriptome dynamics. Over 4000 genes were identified as preferentially expressed in one of the stages, which could be of high relevance to stage-specific developmental and molecular events. Among the 68 transcription factor families active during development, most had enhanced average expression levels and thus might be crucial for embryogenesis, whereas the inactivation of the other families was likely required by the activation of the zygotic genome. We discussed our RNA-seq data together with previous findings about the Wnt signaling pathway and some other genes with known functions, to show how our data could be used to advance our understanding about these developmental functional elements. Our study provides ample information for further study about the molecular and cellular mechanisms underlying vertebrate development.
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