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Wnt-PLC-IP 3-Connexin-Ca 2+ axis maintains ependymal motile cilia in zebrafish spinal cord. Nat Commun 2020; 11:1860. [PMID: 32312952 PMCID: PMC7170879 DOI: 10.1038/s41467-020-15248-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 02/28/2020] [Indexed: 12/31/2022] Open
Abstract
Ependymal cells (ECs) are multiciliated neuroepithelial cells that line the ventricles of the brain and the central canal of the spinal cord (SC). How ependymal motile cilia are maintained remains largely unexplored. Here we show that zebrafish embryos deficient in Wnt signaling have defective motile cilia, yet harbor intact basal bodies. With respect to maintenance of ependymal motile cilia, plcδ3a is a target gene of Wnt signaling. Lack of Connexin43 (Cx43), especially its channel function, decreases motile cilia and intercellular Ca2+ wave (ICW) propagation. Genetic ablation of cx43 in zebrafish and mice diminished motile cilia. Finally, Cx43 is also expressed in ECs of the human SC. Taken together, our findings indicate that gap junction mediated ICWs play an important role in the maintenance of ependymal motile cilia, and suggest that the enhancement of functional gap junctions by pharmacological or genetic manipulations may be adopted to ameliorate motile ciliopathy. Ependymal cells are supporting cells in the central nervous system. Here the authors elucidate a signalling axis in zebrafish spinal cord ependymal cells that is important for motile cilia assembly and maintenance, demonstrating that it depends on intercellular propagation of calcium ions via connexin 43.
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52
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Conant GC. The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PLoS One 2020; 15:e0231356. [PMID: 32298330 PMCID: PMC7161988 DOI: 10.1371/journal.pone.0231356] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/20/2020] [Indexed: 12/20/2022] Open
Abstract
The ancestor of most teleost fishes underwent a whole-genome duplication event three hundred million years ago. Despite its antiquity, the effects of this event are evident both in the structure of teleost genomes and in how the surviving duplicated genes still operate to drive form and function. I inferred a set of shared syntenic regions that survive from the teleost genome duplication (TGD) using eight teleost genomes and the outgroup gar genome (which lacks the TGD). I then phylogenetically modeled the TGD's resolution via shared and independent gene losses and applied a new simulation-based statistical test for the presence of bias toward the preservation of genes from one parental subgenome. On the basis of that test, I argue that the TGD was likely an allopolyploidy. I find that duplicate genes surviving from this duplication in zebrafish are less likely to function in early embryo development than are genes that have returned to single copy at some point in this species' history. The tissues these ohnologs are expressed in, as well as their biological functions, lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina. Surviving duplicates also appear less likely to be essential than singletons, despite the fact that their single-copy orthologs in mouse are no less essential than other genes.
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Affiliation(s)
- Gavin C. Conant
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States of America
- Program in Genetics, North Carolina State University, Raleigh, NC, United States of America
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
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53
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Olender T, Jones TEM, Bruford E, Lancet D. A unified nomenclature for vertebrate olfactory receptors. BMC Evol Biol 2020; 20:42. [PMID: 32295537 PMCID: PMC7160942 DOI: 10.1186/s12862-020-01607-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 03/27/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Olfactory receptors (ORs) are G protein-coupled receptors with a crucial role in odor detection. A typical mammalian genome harbors ~ 1000 OR genes and pseudogenes; however, different gene duplication/deletion events have occurred in each species, resulting in complex orthology relationships. While the human OR nomenclature is widely accepted and based on phylogenetic classification into 18 families and further into subfamilies, for other mammals different and multiple nomenclature systems are currently in use, thus concealing important evolutionary and functional insights. RESULTS Here, we describe the Mutual Maximum Similarity (MMS) algorithm, a systematic classifier for assigning a human-centric nomenclature to any OR gene based on inter-species hierarchical pairwise similarities. MMS was applied to the OR repertoires of seven mammals and zebrafish. Altogether, we assigned symbols to 10,249 ORs. This nomenclature is supported by both phylogenetic and synteny analyses. The availability of a unified nomenclature provides a framework for diverse studies, where textual symbol comparison allows immediate identification of potential ortholog groups as well as species-specific expansions/deletions; for example, Or52e5 and Or52e5b represent a rat-specific duplication of OR52E5. Another example is the complete absence of OR subfamily OR6Z among primate OR symbols. In other mammals, OR6Z members are located in one genomic cluster, suggesting a large deletion in the great ape lineage. An additional 14 mammalian OR subfamilies are missing from the primate genomes. While in chimpanzee 87% of the symbols were identical to human symbols, this number decreased to ~ 50% in dog and cow and to ~ 30% in rodents, reflecting the adaptive changes of the OR gene superfamily across diverse ecological niches. Application of the proposed nomenclature to zebrafish revealed similarity to mammalian ORs that could not be detected from the current zebrafish olfactory receptor gene nomenclature. CONCLUSIONS We have consolidated a unified standard nomenclature system for the vertebrate OR superfamily. The new nomenclature system will be applied to cow, horse, dog and chimpanzee by the Vertebrate Gene Nomenclature Committee and its implementation is currently under consideration by other relevant species-specific nomenclature committees.
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Affiliation(s)
- Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, 76100, Rehovot, Israel.
| | - Tamsin E M Jones
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Elspeth Bruford
- HUGO Gene Nomenclature Committee, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.,Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, 76100, Rehovot, Israel
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54
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Ye C, Chen Z, Liu Z, Wang F, He X. Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish. J Genet Genomics 2020; 47:85-91. [PMID: 32173285 DOI: 10.1016/j.jgg.2019.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/14/2019] [Accepted: 11/25/2019] [Indexed: 12/26/2022]
Abstract
There is a growing interest in developing experimental methods for tracking the developmental cell lineages of a complex organism. The recently developed CRISPR/Cas9-based barcoding method is, although highly promising, difficult to scale up because it relies on exogenous barcoding sequences that are engineered into the genome. In this study, we characterized 78 high-quality endogenous sites in the zebrafish genome that can be used as CRISPR/Cas9-based barcoding sites. The 78 sites are all highly expressed in most of the cell types according to single-cell RNA sequencing (scRNA-seq) data. Hence, the barcoding information of the 78 endogenous sites is recovered by the available scRNA-seq platforms, enabling simultaneous characterization of cell type and cell lineage information.
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Affiliation(s)
- Chang Ye
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhuoxin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Zhan Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Feng Wang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xionglei He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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55
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Harjula SKE, Saralahti AK, Ojanen MJT, Rantapero T, Uusi-Mäkelä MIE, Nykter M, Lohi O, Parikka M, Rämet M. Characterization of immune response against Mycobacterium marinum infection in the main hematopoietic organ of adult zebrafish (Danio rerio). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 103:103523. [PMID: 31626817 DOI: 10.1016/j.dci.2019.103523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/09/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Tuberculosis remains a major global health challenge. To gain information about genes important for defense against tuberculosis, we used a well-established tuberculosis model; Mycobacterium marinum infection in adult zebrafish. To characterize the immunological response to mycobacterial infection at 14 days post infection, we performed a whole-genome level transcriptome analysis using cells from kidney, the main hematopoietic organ of adult zebrafish. Among the upregulated genes, those associated with immune signaling and regulation formed the largest category, whereas the largest group of downregulated genes had a metabolic role. We also performed a forward genetic screen in adult zebrafish and identified a fish line with severely impaired survival during chronic mycobacterial infection. Based on transcriptome analysis, these fish have decreased expression of several immunological genes. Taken together, these results give new information about the genes involved in the defense against mycobacterial infection in zebrafish.
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Affiliation(s)
- Sanna-Kaisa E Harjula
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Anni K Saralahti
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Markus J T Ojanen
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Laboratory of Immunoregulation, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Tommi Rantapero
- Laboratory of Computational Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Meri I E Uusi-Mäkelä
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Matti Nykter
- Laboratory of Computational Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland.
| | - Olli Lohi
- Tampere Center for Child Health Research, Tampere University and Tays Cancer Center, Tampere University Hospital, FI-33014, Tampere University, Finland.
| | - Mataleena Parikka
- Laboratory of Infection Biology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Oral and Maxillofacial Unit, Tampere University Hospital, P.O. Box 2000, FI-33521, Tampere, Finland.
| | - Mika Rämet
- Laboratory of Experimental Immunology, BioMediTech, Faculty of Medicine and Health Technology, FI-33014, Tampere University, Finland; Department of Pediatrics, Tampere University Hospital, P.O. Box 2000, FI-33521, Tampere, Finland; PEDEGO Research Unit, Medical Research Center Oulu, P.O. Box 8000, FI-90014, University of Oulu, Finland; Department of Children and Adolescents, Oulu University Hospital, P.O. Box 10, FI-90029, OYS, Finland.
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56
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Spoor S, Cheng CH, Sanderson LA, Condon B, Almsaeed A, Chen M, Bretaudeau A, Rasche H, Jung S, Main D, Bett K, Staton M, Wegrzyn JL, Feltus FA, Ficklin SP. Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5532788. [PMID: 31328773 PMCID: PMC6643302 DOI: 10.1093/database/baz077] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/12/2019] [Accepted: 05/22/2019] [Indexed: 12/20/2022]
Abstract
Community biological databases provide an important online resource for both public and private data, analysis tools and community engagement. These sites house genomic, transcriptomic, genetic, breeding and ancillary data for specific species, families or clades. Due to the complexity and increasing quantities of these data, construction of online resources is increasingly difficult especially with limited funding and access to technical expertise. Furthermore, online repositories are expected to promote FAIR data principles (findable, accessible, interoperable and reusable) that presents additional challenges. The open-source Tripal database toolkit seeks to mitigate these challenges by creating both the software and an interactive community of developers for construction of online community databases. Additionally, through coordinated, distributed co-development, Tripal sites encourage community-wide sustainability. Here, we report the release of Tripal version 3 that improves data accessibility and data sharing through systematic use of controlled vocabularies (CVs). Tripal uses the community-developed Chado database as a default data store, but now provides tools to support other data stores, while ensuring that CVs remain the central organizational structure for the data. A new site developer can use Tripal to develop a basic site with little to no programming, with the ability to integrate other data types using extension modules and the Tripal application programming interface. A thorough online User’s Guide and Developer’s Handbook are available at http://tripal.info, providing download, installation and step-by-step setup instructions.
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Affiliation(s)
- Shawna Spoor
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Chun-Huai Cheng
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | | | - Bradford Condon
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Abdullah Almsaeed
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Ming Chen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Anthony Bretaudeau
- INRA, UMR IGEPP, BIPAA/GenOuest, INRIA/Irisa - Campus de Beaulieu, Rennes Cedex, France
| | - Helena Rasche
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg im Breisgau, Germany
| | - Sook Jung
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA, USA
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Computational Biology Core, Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | - F Alex Feltus
- Dept. of Genetics and Biochemistry, Clemson University, Clemson, USA
| | - Stephen P Ficklin
- Department of Horticulture, Washington State University, Pullman, WA, USA
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57
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Abstract
The number of fishes exceeds that of all other vertebrates both in terms of species numbers and in their morphological and phylogenetic diversity. They are an ecologically and economically important group and play an essential role as a resource for humans. This makes the genomic exploration of fishes an important area of research, both from an applied and a basic research perspective. Fish genomes can vary greatly in complexity, which is partially due to differences in size and content of repetitive DNA, a history of genome duplication events and because fishes may be polyploid, all of which complicate the assembly and analysis of genome sequences. However, the advent of modern sequencing techniques now facilitates access to genomic data that permit genome-wide exploration of genetic information even for previously unexplored species. The development of genomic resources for fishes is spearheaded by model organisms that have been subject to genetic analysis and genome sequencing projects for a long time. These offer a great potential for the exploration of new species through the transfer of genomic information in comparative analyses. A growing number of genome sequencing projects and the increasing availability of tools to assemble and access genomic information now move boundaries between model and nonmodel species and promises progress in many interesting but unexplored species that remain to be studied.
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Affiliation(s)
- Arne W Nolte
- AG Ökologische Genomik, Institut für Biologie und Umweltwissenschaften, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany.
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58
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Ahi EP, Brunel M, Tsakoumis E, Schmitz M. Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling. Sci Rep 2019; 9:20166. [PMID: 31882937 PMCID: PMC6934527 DOI: 10.1038/s41598-019-56779-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/10/2019] [Indexed: 12/26/2022] Open
Abstract
The hormone leptin is a key regulator of body weight, food intake and metabolism. In mammals, leptin acts as an anorexigen and inhibits food intake centrally by affecting the appetite centres in the hypothalamus. In teleost fish, the regulatory connections between leptin and other appetite-regulating genes are largely unknown. In the present study, we used a zebrafish mutant with a loss of function leptin receptor to investigate brain expression patterns of 12 orexigenic and 24 anorexigenic genes under different feeding conditions (normal feeding, 7-day fasting, 2 and 6-hours refeeding). Expression patterns were compared to wild-type zebrafish, in order to identify leptin-dependent differentially expressed genes under different feeding conditions. We provide evidence that the transcription of certain orexigenic and anorexigenic genes is influenced by leptin signalling in the zebrafish brain. We found that the expression of orexigenic genes was not affected by impaired leptin signalling under normal feeding conditions; however, several orexigenic genes showed increased transcription during fasting and refeeding, including agrp, apln, galr1a and cnr1. This suggests an inhibitory effect of leptin signal on the transcription of these orexigenic genes during short-term fasting and refeeding in functional zebrafish. Most pronounced effects were observed in the group of anorexigenic genes, where the impairment of leptin signalling resulted in reduced gene expression in several genes, including cart family, crhb, gnrh2, mc4r, pomc and spx, in the control group. This suggests a stimulatory effect of leptin signal on the transcription of these anorexigenic genes under normal feeding condition. In addition, we found multiple gain and loss in expression correlations between the appetite-regulating genes, in zebrafish with impaired leptin signal, suggesting the presence of gene regulatory networks downstream of leptin signal in zebrafish brain. The results provide the first evidence for the effects of leptin signal on the transcription of various appetite-regulating genes in zebrafish brain, under different feeding conditions. Altogether, these transcriptional changes suggest an anorexigenic role for leptin signal, which is likely to be mediated through distinct set of appetite-regulating genes under different feeding conditions.
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Affiliation(s)
- Ehsan Pashay Ahi
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36, Uppsala, Sweden
| | - Mathilde Brunel
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, BioCentrum, Allmas Allé 5, SE-750 07 Uppsala, Sweden
| | - Emmanouil Tsakoumis
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36, Uppsala, Sweden
| | - Monika Schmitz
- Department of Organismal Biology, Comparative Physiology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18A, SE-752 36, Uppsala, Sweden.
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59
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A systems biology approach reveals neuronal and muscle developmental defects after chronic exposure to ionising radiation in zebrafish. Sci Rep 2019; 9:20241. [PMID: 31882844 PMCID: PMC6934629 DOI: 10.1038/s41598-019-56590-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/13/2019] [Indexed: 11/11/2022] Open
Abstract
Contamination of the environment after the Chernobyl and Fukushima Daiichi nuclear power plant (NPP) disasters led to the exposure of a large number of humans and wild animals to radioactive substances. However, the sub-lethal consequences induced by these absorbed radiological doses remain understudied and the long-term biological impacts largely unknown. We assessed the biological effects of chronic exposure to ionizing radiation (IR) on embryonic development by exposing zebrafish embryo from fertilization and up to 120 hours post-fertilization (hpf) at dose rates of 0.5 mGy/h, 5 mGy/h and 50 mGy/h, thereby encompassing the field of low dose rates defined at 6 mGy/h. Chronic exposure to IR altered larval behaviour in a light-dark locomotor test and affected cardiac activity at a dose rate as low as 0.5 mGy/h. The multi-omics analysis of transcriptome, proteome and transcription factor binding sites in the promoters of the deregulated genes, collectively points towards perturbations of neurogenesis, muscle development, and retinoic acid (RA) signaling after chronic exposure to IR. Whole-mount RNA in situ hybridization confirmed the impaired expression of the transcription factors her4.4 in the central nervous system and myogenin in the developing muscles of exposed embryos. At the organ level, the assessment of muscle histology by transmission electron microscopy (TEM) demonstrated myofibers disruption and altered neuromuscular junctions in exposed larvae at 5 mGy/h and 50 mGy/h. The integration of these multi-level data demonstrates that chronic exposure to low dose rates of IR has an impact on neuronal and muscle progenitor cells, that could lead to motility defects in free swimming larvae at 120 hpf. The mechanistic understanding of these effects allows us to propose a model where deregulation of RA signaling by chronic exposure to IR has pleiotropic effects on neurogenesis and muscle development.
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60
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Rissone A, Jimenez E, Bishop K, Carrington B, Slevin C, Wincovitch SM, Sood R, Candotti F, Burgess SM. A model for reticular dysgenesis shows impaired sensory organ development and hair cell regeneration linked to cellular stress. Dis Model Mech 2019; 12:dmm040170. [PMID: 31727854 PMCID: PMC6955229 DOI: 10.1242/dmm.040170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/05/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in the gene AK2 are responsible for reticular dysgenesis (RD), a rare and severe form of primary immunodeficiency in children. RD patients have a severely shortened life expectancy and without treatment die, generally from sepsis soon after birth. The only available therapeutic option for RD is hematopoietic stem cell transplantation (HSCT). To gain insight into the pathophysiology of RD, we previously created zebrafish models for Ak2 deficiencies. One of the clinical features of RD is hearing loss, but its pathophysiology and causes have not been determined. In adult mammals, sensory hair cells of the inner ear do not regenerate; however, their regeneration has been observed in several non-mammalian vertebrates, including zebrafish. Therefore, we used our RD zebrafish models to determine whether Ak2 deficiency affects sensory organ development and/or hair cell regeneration. Our studies indicated that Ak2 is required for the correct development, survival and regeneration of sensory hair cells. Interestingly, Ak2 deficiency induces the expression of several oxidative stress markers and it triggers an increased level of cell death in the hair cells. Finally, we show that glutathione treatment can partially rescue hair cell development in the sensory organs in our RD models, pointing to the potential use of antioxidants as a therapeutic treatment supplementing HSCT to prevent or ameliorate sensorineural hearing deficits in RD patients.
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Affiliation(s)
- Alberto Rissone
- Translational and Functional Genomics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Erin Jimenez
- Translational and Functional Genomics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kevin Bishop
- NHGRI Zebrafish Core, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Blake Carrington
- NHGRI Zebrafish Core, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Claire Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Raman Sood
- Translational and Functional Genomics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA
- NHGRI Zebrafish Core, Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, MD, USA
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA
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61
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Vacca F, Barca A, Gomes AS, Mazzei A, Piccinni B, Cinquetti R, Del Vecchio G, Romano A, Rønnestad I, Bossi E, Verri T. The peptide transporter 1a of the zebrafish Danio rerio, an emerging model in nutrigenomics and nutrition research: molecular characterization, functional properties, and expression analysis. GENES AND NUTRITION 2019; 14:33. [PMID: 31890051 PMCID: PMC6923934 DOI: 10.1186/s12263-019-0657-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 12/03/2019] [Indexed: 12/20/2022]
Abstract
Background Peptide transporter 1 (PepT1, alias Slc15a1) mediates the uptake of dietary di/tripeptides in all vertebrates. However, in teleost fish, more than one PepT1-type transporter might function, due to specific whole genome duplication event(s) that occurred during their evolution leading to a more complex paralogue gene repertoire than in higher vertebrates (tetrapods). Results Here, we describe a novel di/tripeptide transporter in the zebrafish (Danio rerio), i.e., the zebrafish peptide transporter 1a (PepT1a; also known as Solute carrier family 15 member a1, Slc15a1a), which is a paralogue (78% similarity, 62% identity at the amino acid level) of the previously described zebrafish peptide transporter 1b (PepT1b, alias PepT1; also known as Solute carrier family 15 member 1b, Slc15a1b). Also, we report a basic analysis of the pept1a (slc15a1a) mRNA expression levels in zebrafish adult tissues/organs and embryonic/early larval developmental stages. As assessed by expression in Xenopus laevis oocytes and two-electrode voltage clamp measurements, zebrafish PepT1a, as PepT1b, is electrogenic, Na+-independent, and pH-dependent and functions as a low-affinity system, with K0.5 values for Gly-Gln at − 60 mV of 6.92 mmol/L at pH 7.6 and 0.24 mmol/L at pH 6.5 and at − 120 mV of 3.61 mmol/L at pH 7.6 and 0.45 mmol/L at pH 6.5. Zebrafish pept1a mRNA is highly expressed in the intestine and ovary of the adult fish, while its expression in early development undergoes a complex trend over time, with pept1a mRNA being detected 1 and 2 days post-fertilization (dpf), possibly due to its occurrence in the RNA maternal pool, decreasing at 3 dpf (~ 0.5-fold) and increasing above the 1–2 dpf levels at 4 to 7 dpf, with a peak (~ 7-fold) at 6 dpf. Conclusions We show that the zebrafish PepT1a-type transporter is functional and co-expressed with pept1b (slc15a1b) in the adult fish intestine. Its expression is also confirmed during the early phases of development when the yolk syncytial layer is present and yolk protein resorption processes are active. While completing the missing information on PepT1-type transporters function in the zebrafish, these results open to future investigations on the similar/differential role(s) of PepT1a/PepT1b in zebrafish and teleost fish physiology.
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Affiliation(s)
- Francesca Vacca
- 1Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Amilcare Barca
- 2Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, I-73100 Lecce, Italy
| | - Ana S Gomes
- 3Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | - Aurora Mazzei
- 2Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, I-73100 Lecce, Italy
| | - Barbara Piccinni
- 2Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, I-73100 Lecce, Italy.,Present address: Physiopathology of Reproduction and IVF Unit, Nardò Hospital, Nardò Health and Social Care District, Lecce Local Health Agency, I-73048 Nardò, Lecce Italy
| | - Raffaella Cinquetti
- 1Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Gianmarco Del Vecchio
- 2Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, I-73100 Lecce, Italy
| | - Alessandro Romano
- 5Division of Neuroscience, Institute of Experimental Neurology, IRCCS San Raffaele Scientific Institute, I-20132 Milan, Italy
| | - Ivar Rønnestad
- 3Department of Biological Sciences, University of Bergen, P.O. Box 7803, NO-5020 Bergen, Norway
| | - Elena Bossi
- 1Department of Biotechnology and Life Sciences, University of Insubria, via J.H. Dunant 3, 21100 Varese, Italy
| | - Tiziano Verri
- 2Department of Biological and Environmental Sciences and Technologies, University of Salento, via Provinciale Lecce-Monteroni, I-73100 Lecce, Italy
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62
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A new evolutionary model for the vertebrate actin family including two novel groups. Mol Phylogenet Evol 2019; 141:106632. [DOI: 10.1016/j.ympev.2019.106632] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/19/2019] [Accepted: 09/23/2019] [Indexed: 02/06/2023]
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63
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Farnsworth DR, Saunders LM, Miller AC. A single-cell transcriptome atlas for zebrafish development. Dev Biol 2019; 459:100-108. [PMID: 31782996 DOI: 10.1016/j.ydbio.2019.11.008] [Citation(s) in RCA: 149] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/27/2022]
Abstract
The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge, we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap, we produced an atlas using single-cell RNA-sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single-cell transcriptome atlas encompasses transcriptional profiles from 44,102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single-cell resolution. Furthermore, we highlight the power of this analysis to assign new cell-type or developmental stage-specific expression information to many genes, including those that are currently known only by sequence and/or that lack expression information altogether. The resulting atlas is a resource for biologists to generate hypotheses for functional analysis, which we hope integrates with existing efforts to define the diversity of cell-types during zebrafish organogenesis, and to examine the transcriptional profiles that produce each cell type over developmental time.
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Affiliation(s)
| | - Lauren M Saunders
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
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64
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Taler K, Weiss O, Rotem-Bamberger S, Rubinstein AM, Seritrakul P, Gross JM, Inbal A. Lysyl hydroxylase 3 is required for normal lens capsule formation and maintenance of lens epithelium integrity and fate. Dev Biol 2019; 458:177-188. [PMID: 31669351 DOI: 10.1016/j.ydbio.2019.10.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/03/2019] [Accepted: 10/20/2019] [Indexed: 02/06/2023]
Abstract
Lens abnormalities are a major cause of reduced vision and blindness. One mechanism that can lead to reduced lens transparency, i.e. cataract, is abnormal behavior of lens epithelial cells (LECs), the precursors of the transparent lens fiber cells. Here we describe a zebrafish mutation causing the embryonic lens epithelium to generate cellular masses comprising partially differentiated lens fiber cells. We identify the mutant gene as plod3, which encodes for Lysyl hydroxylase 3 (Lh3), an enzyme essential for modification of collagens, including Collagen IV, a main component of the lens capsule. We show that plod3-deficient lenses have abnormal lens epithelium from an early developmental stage, as well as abnormal lens capsules. Subsequently, upregulation of TGFβ signaling takes place, which drives the formation of lens epithelial cellular masses. We identify a similar phenotype in Collagen IVα5-deficient embryos, suggesting a key role for the defective lens capsule in the pathogenesis. We propose that plod3 and col4a5 mutant zebrafish can serve as useful models for better understanding the biology of LECs during embryonic development and in formation of lens epithelium-derived cataract.
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Affiliation(s)
- Kineret Taler
- Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Omri Weiss
- Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Shahar Rotem-Bamberger
- Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ariel M Rubinstein
- Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Pawat Seritrakul
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jeffrey M Gross
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Adi Inbal
- Department of Medical Neurobiology, Institute for Medical Research - Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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65
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Phylogenetic Reclassification of Vertebrate Melatonin Receptors To Include Mel1d. G3-GENES GENOMES GENETICS 2019; 9:3225-3238. [PMID: 31416806 PMCID: PMC6778780 DOI: 10.1534/g3.119.400170] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The circadian and seasonal actions of melatonin are mediated by high affinity G-protein coupled receptors (melatonin receptors, MTRs), classified into phylogenetically distinct subtypes based on sequence divergence and pharmacological characteristics. Three vertebrate MTR subtypes are currently described: MT1 (MTNR1A), MT2 (MTNR1B), and Mel1c (MTNR1C / GPR50), which exhibit distinct affinities, tissue distributions and signaling properties. We present phylogenetic and comparative genomic analyses supporting a revised classification of the vertebrate MTR family. We demonstrate four ancestral vertebrate MTRs, including a novel molecule hereafter named Mel1d. We reconstructed the evolution of each vertebrate MTR, detailing genetic losses in addition to gains resulting from whole genome duplication events in teleost fishes. We show that Mel1d was lost separately in mammals and birds and has been previously mistaken for an MT1 paralogue. The genetic and functional diversity of vertebrate MTRs is more complex than appreciated, with implications for our understanding of melatonin actions in different taxa. The significance of our findings, including the existence of Mel1d, are discussed in an evolutionary and functional context accommodating a robust phylogenetic assignment of MTR gene family structure.
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66
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Marques IJ, Lupi E, Mercader N. Model systems for regeneration: zebrafish. Development 2019; 146:146/18/dev167692. [DOI: 10.1242/dev.167692] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/19/2019] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Tissue damage can resolve completely through healing and regeneration, or can produce permanent scarring and loss of function. The response to tissue damage varies across tissues and between species. Determining the natural mechanisms behind regeneration in model organisms that regenerate well can help us develop strategies for tissue recovery in species with poor regenerative capacity (such as humans). The zebrafish (Danio rerio) is one of the most accessible vertebrate models to study regeneration. In this Primer, we highlight the tools available to study regeneration in the zebrafish, provide an overview of the mechanisms underlying regeneration in this system and discuss future perspectives for the field.
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Affiliation(s)
- Ines J. Marques
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
| | - Eleonora Lupi
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Acquifer, Ditabis, Digital Biomedical Imaging Systems, Pforzheim, Germany
| | - Nadia Mercader
- Institute of Anatomy, University of Bern, Bern 3012, Switzerland
- Centro Nacional de Investigaciones Cardiovasculares CNIC, Madrid 2029, Spain
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67
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Mehta AS, Singh A. Insights into regeneration tool box: An animal model approach. Dev Biol 2019; 453:111-129. [PMID: 30986388 PMCID: PMC6684456 DOI: 10.1016/j.ydbio.2019.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/20/2022]
Abstract
For ages, regeneration has intrigued countless biologists, clinicians, and biomedical engineers. In recent years, significant progress made in identification and characterization of a regeneration tool kit has helped the scientific community to understand the mechanism(s) involved in regeneration across animal kingdom. These mechanistic insights revealed that evolutionarily conserved pathways like Wnt, Notch, Hedgehog, BMP, and JAK/STAT are involved in regeneration. Furthermore, advancement in high throughput screening approaches like transcriptomic analysis followed by proteomic validations have discovered many novel genes, and regeneration specific enhancers that are specific to highly regenerative species like Hydra, Planaria, Newts, and Zebrafish. Since genetic machinery is highly conserved across the animal kingdom, it is possible to engineer these genes and regeneration specific enhancers in species with limited regeneration properties like Drosophila, and mammals. Since these models are highly versatile and genetically tractable, cross-species comparative studies can generate mechanistic insights in regeneration for animals with long gestation periods e.g. Newts. In addition, it will allow extrapolation of regenerative capabilities from highly regenerative species to animals with low regeneration potential, e.g. mammals. In future, these studies, along with advancement in tissue engineering applications, can have strong implications in the field of regenerative medicine and stem cell biology.
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Affiliation(s)
- Abijeet S Mehta
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, OH, 45469, USA; Premedical Program, University of Dayton, Dayton, OH, 45469, USA; Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, OH, 45469, USA; The Integrative Science and Engineering Center, University of Dayton, Dayton, OH, 45469, USA; Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, IN, USA.
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68
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Aleström P, D'Angelo L, Midtlyng PJ, Schorderet DF, Schulte-Merker S, Sohm F, Warner S. Zebrafish: Housing and husbandry recommendations. Lab Anim 2019; 54:213-224. [PMID: 31510859 PMCID: PMC7301644 DOI: 10.1177/0023677219869037] [Citation(s) in RCA: 286] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
This article provides recommendations for the care of laboratory zebrafish (Danio rerio) as part of the further implementation of Annex A to the European Convention on the protection of vertebrate animals used for experimental and other scientific purposes, EU Commission Recommendation 2007/526/EC and the fulfilment of Article 33 of EU Directive 2010/63, both concerning the housing and care of experimental animals. The recommendations provide guidance on best practices and ranges of husbandry parameters within which zebrafish welfare, as well as reproducibility of experimental procedures, are assured. Husbandry procedures found today in zebrafish facilities are numerous. While the vast majority of these practices are perfectly acceptable in terms of zebrafish physiology and welfare, the reproducibility of experimental results could be improved by further standardisation of husbandry procedures and exchange of husbandry information between laboratories. Standardisation protocols providing ranges of husbandry parameters are likely to be more successful and appropriate than the implementation of a set of fixed guidance values neglecting the empirically successful daily routines of many facilities and will better reflect the wide range of environmental parameters that characterise the natural habitats occupied by zebrafish. A joint working group on zebrafish housing and husbandry recommendations, with members of the European Society for Fish Models in Biology and Medicine (EUFishBioMed) and of the Federation of European Laboratory Animal Science Associations (FELASA) has been given a mandate to provide guidelines based on a FELASA list of parameters, ‘Terms of Reference’.
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Affiliation(s)
- Peter Aleström
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Livia D'Angelo
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy; Italian Association of Laboratory Animal Sciences (AISAL); Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Paul J Midtlyng
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Daniel F Schorderet
- Institute for Research in Ophthalmology, University of Lausanne and Ecole Polytechnique Fédérale of Lausanne, Sion, Switzerland
| | - Stefan Schulte-Merker
- Institute for Cardiovascular Organogenesis and Regeneration, WWU Münster, Faculty of Medicine, Münster, Germany.,CiM Cluster of Excellence, Faculty of Medicine, Münster, WWU Münster, Münster, Germany
| | - Frederic Sohm
- UMS AMAGEN, CNRS, INRA, Université Paris-Saclay, Gif sur Yvette, France
| | - Susan Warner
- Karolinska Institutet, Comparative Medicine, Stockholm, Sweden
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69
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Martínez R, Herrero-Nogareda L, Van Antro M, Campos MP, Casado M, Barata C, Piña B, Navarro-Martín L. Morphometric signatures of exposure to endocrine disrupting chemicals in zebrafish eleutheroembryos. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 214:105232. [PMID: 31271907 DOI: 10.1016/j.aquatox.2019.105232] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 06/09/2023]
Abstract
Understanding the mode of action of the different pollutants in human and wildlife health is a key step in environmental risk assessment. The aim of this study was to determine signatures that could link morphological phenotypes to the toxicity mechanisms of four Endocrine Disrupting Chemicals (EDCs): bisphenol A (BPA), perfluorooctanesulfonate potassium salt (PFOS), tributyltin chloride (TBT), and 17-ß-estradiol (E2). Zebrafish (Danio rerio) eleutheroembryos were exposed from 2 to 5 dpf to a wide range of BPA, PFOS, TBT and E2 concentrations. At the end of the exposures several morphometric features were assessed. Common and non-specific effects on larvae pigmentation or swim bladder area were observed after exposures to all compounds. BPA specifically induced yolk sac malabsorption syndrome and altered craniofacial parameters, whereas PFOS had specific effects on the notochord formation presenting higher rates of scoliosis and kyphosis. The main effect of E2 was an increase in the body length of the exposed eleutheroembryos. In the case of TBT, main alterations on the morphological traits were related to developmental delays. When integrating all morphometrical parameters, BPA showed the highest rates of malformations in terms of equilethality, followed by PFOS and, distantly, by TBT and E2. In the case of BPA and PFOS, we were able to relate our results with effects on the transcriptome and metabolome, previously reported. We propose that methodized morphometric analyses in zebrafish embryo model can be used as an inexpensive and easy screening tool to predict modes of action of a wide-range number of contaminants.
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Affiliation(s)
- Rubén Martínez
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain; Universitat de Barcelona (UB), Barcelona, Catalunya, 08007, Spain.
| | - Laia Herrero-Nogareda
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Morgane Van Antro
- Laboratory of Evolutionary and Adaptive Physiology, Institute of Life, Earth and Environment, University of Namur, 61 Rue de Bruxelles, B5000, Namur, Belgium.
| | - Maria Pilar Campos
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Marta Casado
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Carlos Barata
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Benjamin Piña
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
| | - Laia Navarro-Martín
- Institute of Environmental Assessment and Water Research, IDAEA-CSIC, Barcelona, Catalunya, 08034, Spain.
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70
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Mehta AS, Luz-Madrigal A, Li JL, Tsonis PA, Singh A. Comparative transcriptomic analysis and structure prediction of novel Newt proteins. PLoS One 2019; 14:e0220416. [PMID: 31419228 PMCID: PMC6697330 DOI: 10.1371/journal.pone.0220416] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 07/15/2019] [Indexed: 01/25/2023] Open
Abstract
Notophthalmus viridescens (Red-spotted Newt) possess amazing capabilities to regenerate their organs and other tissues. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of five protein members expressed in adult tissues during regeneration in Notophthalmus viridescens. The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate three-dimensional structure of these novel Newt proteins and predicted their function. Our data suggests that these proteins could act as ion transporters, and be involved in redox reaction(s). Due to absence of transgenic approaches in N. viridescens, and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster to misexpress these genes. Expression of 2775 transcripts were compared between these five newly identified Newt genes. We found that genes involved in the developmental process, cell cycle, apoptosis, and immune response are among those that are highly enriched. To validate the RNA Seq. data, expression of six highly regulated genes were verified using real time Quantitative Polymerase Chain Reaction (RT-qPCR). These graded gene expression patterns provide insight into the function of novel protein family identified in Newt, and layout a map for future studies in the field.
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Affiliation(s)
- Abijeet Singh Mehta
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Agustin Luz-Madrigal
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Jian-Liang Li
- Sanford Burnham Prebys Medical Discovery Institute at Lake Nona, Orlando, Florida, United States of America
| | - Panagiotis A Tsonis
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Amit Singh
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
- Premedical Program, University of Dayton, Dayton, Ohio, United States of America
- Center for Tissue Regeneration and Engineering at Dayton (TREND), University of Dayton, Dayton, Ohio, United States of America
- The Integrative Science and Engineering Center, University of Dayton, Dayton, Ohio, United States of America
- Center for Genomic Advocacy (TCGA), Indiana State University, Terre Haute, Indiana, United States of America
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71
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Tang M, Lu Y, Xiong Z, Chen M, Qin Y. The Grass Carp Genomic Visualization Database (GCGVD): an informational platform for genome biology of grass carp. Int J Biol Sci 2019; 15:2119-2127. [PMID: 31592084 PMCID: PMC6775296 DOI: 10.7150/ijbs.32860] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 05/27/2019] [Indexed: 11/25/2022] Open
Abstract
With the release of the draft genome of the grass carp, researches on the grass carp from the genetic level and the further molecular mechanisms of economically valuable physiological behaviors have gained great attention. In this paper, we integrated a large number of genomic, genetic and some other data resources and established a web-based grass carp genomic visualization database (GCGVD). To view these data more effectively, we visualized grass carp and zebrafish gene collinearity and genetic linkage map using Scalable Vector Graphics (SVG) format in the browser, and genomic annotations by JBrowse. Furthermore, we carried out some preliminary study on a whole-genome alternative splicing (AS)of the grass carp. The RNA-seq reads of 15 samples were aligned to the reference genome of the grass carp by Bowtie2 software. RNA-seq reads of each sample and density map of reads were also exhibited in JBrowse. Additionally, we designed a universal grass carp genome annotation data model to improve the retrieval speed and scalability. Compared with the published database GCGD previously, we newly added the visualization of some more genomic annotations, conserved domain and RNA-seq reads aligned to the reference genome. GCGVD can be accessed at http://122.112.216.104.
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Affiliation(s)
- Min Tang
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Ying Lu
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhongmin Xiong
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Ming Chen
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
| | - Yufang Qin
- College of Information Technology, Shanghai Ocean University, Shanghai, 201306, China.,Key Laboratory of Fisheries Information Ministry of Agriculture, Shanghai, 201306, China
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72
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Balik-Meisner MR, Mav D, Phadke DP, Everett LJ, Shah RR, Tal T, Shepard PJ, Merrick BA, Paules RS. Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. Zebrafish 2019; 16:331-347. [PMID: 31188086 PMCID: PMC6685209 DOI: 10.1089/zeb.2018.1720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sentinel gene sets have been developed with the purpose of maximizing the information from targeted transcriptomic platforms. We recently described the development of an S1500+ sentinel gene set, which was built for the human transcriptome, utilizing a data- and knowledge-driven hybrid approach to select a small subset of genes that optimally capture transcriptional diversity, correlation with other genes based on large-scale expression profiling, and known pathway annotation within the human genome. While this detailed bioinformatics approach for gene selection can in principle be applied to other species, the reliability of the resulting gene set depends on availability of a large body of transcriptomics data. For the model organism zebrafish, we aimed to create a similar sentinel gene set (Zf S1500+ gene set); however, there is insufficient standardized expression data in the public domain to train the gene correlation model. Therefore, our strategy was to use human-zebrafish ortholog mapping of the human S1500+ genes and nominations from experts in the zebrafish scientific community. In this study, we present the bioinformatics curation and refinement process to produce the final Zf S1500+ gene set, explore whole transcriptome extrapolation using this gene set, and assess pathway-level inference. This gene set will add value to targeted high-throughput transcriptomics in zebrafish for toxicogenomic screening and other research domains.
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Affiliation(s)
| | - Deepak Mav
- Sciome, LLC, Research Triangle Park, North Carolina
| | | | | | | | - Tamara Tal
- National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | - B. Alex Merrick
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Richard S. Paules
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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73
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Redox Signaling via Lipid Peroxidation Regulates Retinal Progenitor Cell Differentiation. Dev Cell 2019; 50:73-89.e6. [DOI: 10.1016/j.devcel.2019.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/07/2019] [Accepted: 05/03/2019] [Indexed: 12/31/2022]
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74
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Morgan R, Sundin J, Finnøen MH, Dresler G, Vendrell MM, Dey A, Sarkar K, Jutfelt F. Are model organisms representative for climate change research? Testing thermal tolerance in wild and laboratory zebrafish populations. CONSERVATION PHYSIOLOGY 2019; 7:coz036. [PMID: 31249690 PMCID: PMC6589993 DOI: 10.1093/conphys/coz036] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/29/2019] [Accepted: 05/24/2019] [Indexed: 05/31/2023]
Abstract
Model organisms can be useful for studying climate change impacts, but it is unclear whether domestication to laboratory conditions has altered their thermal tolerance and therefore how representative of wild populations they are. Zebrafish in the wild live in fluctuating thermal environments that potentially reach harmful temperatures. In the laboratory, zebrafish have gone through four decades of domestication and adaptation to stable optimal temperatures with few thermal extremes. If maintaining thermal tolerance is costly or if genetic traits promoting laboratory fitness at optimal temperature differ from genetic traits for high thermal tolerance, the thermal tolerance of laboratory zebrafish could be hypothesized to be lower than that of wild zebrafish. Furthermore, very little is known about the thermal environment of wild zebrafish and how close to their thermal limits they live. Here, we compared the acute upper thermal tolerance (critical thermal maxima; CTmax) of wild zebrafish measured on-site in West Bengal, India, to zebrafish at three laboratory acclimation/domestication levels: wild-caught, F1 generation wild-caught and domesticated laboratory AB-WT line. We found that in the wild, CTmax increased with increasing site temperature. Yet at the warmest site, zebrafish lived very close to their thermal limit, suggesting that they may currently encounter lethal temperatures. In the laboratory, acclimation temperature appeared to have a stronger effect on CTmax than it did in the wild. The fish in the wild also had a 0.85-1.01°C lower CTmax compared to all laboratory populations. This difference between laboratory-held and wild populations shows that environmental conditions can affect zebrafish's thermal tolerance. However, there was no difference in CTmax between the laboratory-held populations regardless of the domestication duration. This suggests that thermal tolerance is maintained during domestication and highlights that experiments using domesticated laboratory-reared model species can be appropriate for addressing certain questions on thermal tolerance and global warming impacts.
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Affiliation(s)
- Rachael Morgan
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Josefin Sundin
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Mette H Finnøen
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Gunnar Dresler
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Marc Martínez Vendrell
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
- Department of Biology, University of Barcelona, Barcelona, Spain
| | - Arpita Dey
- Department of Zoology, University of North Bengal, Darjeeling, Siliguri, West Bengal, India
| | - Kripan Sarkar
- Rainbow Ornamental Fish Farm, Baxipara, Raninagar, Mohitnagar, Jalpaiguri, West Bengal, India
| | - Fredrik Jutfelt
- Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
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75
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On the traces of tcf12: Investigation of the gene expression pattern during development and cranial suture patterning in zebrafish (Danio rerio). PLoS One 2019; 14:e0218286. [PMID: 31188878 PMCID: PMC6561585 DOI: 10.1371/journal.pone.0218286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022] Open
Abstract
The transcription factor 12 (tcf12) is a basic Helix-Loop-Helix protein (bHLH) of the E-protein family, proven to play an important role in developmental processes like neurogenesis, mesoderm formation, and cranial vault development. In humans, mutations in TCF12 lead to craniosynostosis, a congenital birth disorder characterized by the premature fusion of one or several of the cranial sutures. Current research has been primarily focused on functional studies of TCF12, hence the cellular expression profile of this gene during embryonic development and early stages of ossification remains poorly understood. Here we present the establishment and detailed analysis of two transgenic tcf12:EGFP fluorescent zebrafish (Danio rerio) reporter lines. Using these transgenic lines, we analyzed the general spatiotemporal expression pattern of tcf12 during different developmental stages and put emphasis on skeletal development and cranial suture patterning. We identified robust tcf12 promoter-driven EGFP expression in the central nervous system (CNS), the heart, the pronephros, and the somites of zebrafish embryos. Additionally, expression was observed inside the muscles and bones of the viscerocranium in juvenile and adult fish. During cranial vault development, the transgenic fish show a high amount of tcf12 expressing cells at the growth fronts of the ossifying frontal and parietal bones and inside the emerging cranial sutures. Subsequently, we tested the transcriptional activity of three evolutionary conserved non-coding elements (CNEs) located in the tcf12 locus by transient transgenic assays and compared their in vivo activity to the expression pattern determined in the transgenic tcf12:EGFP lines. We could validate two of them as tcf12 enhancer elements driving specific gene expression in the CNS during embryogenesis. Our newly established transgenic lines enhance the understanding of tcf12 gene regulation and open up the possibilities for further functional investigation of these novel tcf12 enhancer elements in zebrafish.
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Schüttler A, Altenburger R, Ammar M, Bader-Blukott M, Jakobs G, Knapp J, Krüger J, Reiche K, Wu GM, Busch W. Map and model-moving from observation to prediction in toxicogenomics. Gigascience 2019; 8:giz057. [PMID: 31140561 PMCID: PMC6539241 DOI: 10.1093/gigascience/giz057] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/13/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Chemicals induce compound-specific changes in the transcriptome of an organism (toxicogenomic fingerprints). This provides potential insights about the cellular or physiological responses to chemical exposure and adverse effects, which is needed in assessment of chemical-related hazards or environmental health. In this regard, comparison or connection of different experiments becomes important when interpreting toxicogenomic experiments. Owing to lack of capturing response dynamics, comparability is often limited. In this study, we aim to overcome these constraints. RESULTS We developed an experimental design and bioinformatic analysis strategy to infer time- and concentration-resolved toxicogenomic fingerprints. We projected the fingerprints to a universal coordinate system (toxicogenomic universe) based on a self-organizing map of toxicogenomic data retrieved from public databases. Genes clustering together in regions of the map indicate functional relation due to co-expression under chemical exposure. To allow for quantitative description and extrapolation of the gene expression responses we developed a time- and concentration-dependent regression model. We applied the analysis strategy in a microarray case study exposing zebrafish embryos to 3 selected model compounds including 2 cyclooxygenase inhibitors. After identification of key responses in the transcriptome we could compare and characterize their association to developmental, toxicokinetic, and toxicodynamic processes using the parameter estimates for affected gene clusters. Furthermore, we discuss an association of toxicogenomic effects with measured internal concentrations. CONCLUSIONS The design and analysis pipeline described here could serve as a blueprint for creating comparable toxicogenomic fingerprints of chemicals. It integrates, aggregates, and models time- and concentration-resolved toxicogenomic data.
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Affiliation(s)
- Andreas Schüttler
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Institute for Environmental Research, RWTH Aachen, Worringerweg 1, 52074 Aachen, Germany
| | - Rolf Altenburger
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
- Institute for Environmental Research, RWTH Aachen, Worringerweg 1, 52074 Aachen, Germany
| | - Madeleine Ammar
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Marcella Bader-Blukott
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Gianina Jakobs
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Johanna Knapp
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Janet Krüger
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Kristin Reiche
- Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstr. 1, 04103 Leipzig, Germany
| | - Gi-Mick Wu
- DEVELOP, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
| | - Wibke Busch
- Department Bioanalytical Ecotoxicology, Helmholtz-Centre for Environmental Research – UFZ, Permoserstr. 15, 04318 Leipzig, Germany
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77
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Otten C, Knox J, Boulday G, Eymery M, Haniszewski M, Neuenschwander M, Radetzki S, Vogt I, Hähn K, De Luca C, Cardoso C, Hamad S, Igual Gil C, Roy P, Albiges-Rizo C, Faurobert E, von Kries JP, Campillos M, Tournier-Lasserve E, Derry WB, Abdelilah-Seyfried S. Systematic pharmacological screens uncover novel pathways involved in cerebral cavernous malformations. EMBO Mol Med 2019; 10:emmm.201809155. [PMID: 30181117 PMCID: PMC6180302 DOI: 10.15252/emmm.201809155] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cerebral cavernous malformations (CCMs) are vascular lesions in the central nervous system causing strokes and seizures which currently can only be treated through neurosurgery. The disease arises through changes in the regulatory networks of endothelial cells that must be comprehensively understood to develop alternative, non-invasive pharmacological therapies. Here, we present the results of several unbiased small-molecule suppression screens in which we applied a total of 5,268 unique substances to CCM mutant worm, zebrafish, mouse, or human endothelial cells. We used a systems biology-based target prediction tool to integrate the results with the whole-transcriptome profile of zebrafish CCM2 mutants, revealing signaling pathways relevant to the disease and potential targets for small-molecule-based therapies. We found indirubin-3-monoxime to alleviate the lesion burden in murine preclinical models of CCM2 and CCM3 and suppress the loss-of-CCM phenotypes in human endothelial cells. Our multi-organism-based approach reveals new components of the CCM regulatory network and foreshadows novel small-molecule-based therapeutic applications for suppressing this devastating disease in patients.
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Affiliation(s)
- Cécile Otten
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Jessica Knox
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Gwénola Boulday
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France
| | - Mathias Eymery
- INSERM U1209, Grenoble, France.,Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, Grenoble, France
| | - Marta Haniszewski
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Silke Radetzki
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Ingo Vogt
- German Center for Diabetes Research, Neuherberg, Germany.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Kristina Hähn
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Coralie De Luca
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France
| | - Cécile Cardoso
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France
| | - Sabri Hamad
- German Center for Diabetes Research, Neuherberg, Germany.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Carla Igual Gil
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Peter Roy
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Corinne Albiges-Rizo
- INSERM U1209, Grenoble, France.,Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, Grenoble, France
| | - Eva Faurobert
- INSERM U1209, Grenoble, France.,Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France.,CNRS UMR 5309, Grenoble, France
| | - Jens P von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Mónica Campillos
- German Center for Diabetes Research, Neuherberg, Germany.,Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Elisabeth Tournier-Lasserve
- INSERM UMR-1161, Génétique et physiopathologie des maladies cérébro-vasculaires, Université Paris Diderot, Paris, France.,AP-HP, Groupe hospitalier Saint-Louis, Lariboisière, Fernand-Widal, Service de génétique moléculaire neuro-vasculaire, Paris, France
| | - W Brent Derry
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Developmental and Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Salim Abdelilah-Seyfried
- Institute of Biochemistry and Biology, Potsdam University, Potsdam, Germany .,Institute of Molecular Biology, Hannover Medical School, Hannover, Germany
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78
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Baxter LL, Watkins-Chow DE, Pavan WJ, Loftus SK. A curated gene list for expanding the horizons of pigmentation biology. Pigment Cell Melanoma Res 2019; 32:348-358. [PMID: 30339321 PMCID: PMC10413850 DOI: 10.1111/pcmr.12743] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/01/2018] [Accepted: 09/29/2018] [Indexed: 12/27/2022]
Abstract
Over the past century, studies of human pigmentary disorders along with mouse and zebrafish models have shed light on the many cellular functions associated with visible pigment phenotypes. This has led to numerous genes annotated with the ontology term "pigmentation" in independent human, mouse, and zebrafish databases. Comparisons among these datasets revealed that each is individually incomplete in documenting all genes involved in integument-based pigmentation phenotypes. Additionally, each database contained inherent species-specific biases in data annotation, and the term "pigmentation" did not solely reflect integument pigmentation phenotypes. This review presents a comprehensive, cross-species list of 650 genes involved in pigmentation phenotypes that was compiled with extensive manual curation of genes annotated in OMIM, MGI, ZFIN, and GO. The resulting cross-species list of genes both intrinsic and extrinsic to integument pigment cells provides a valuable tool that can be used to expand our knowledge of complex, pigmentation-associated pathways.
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Affiliation(s)
- Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Dawn E Watkins-Chow
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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79
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Gould CJ, Saldanha CJ, Connaughton VP. Acute exposure to 4-OH-A, not PCB 1254, alters brain aromatase activity but does not adversely affect growth in zebrafish. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2019; 68:133-140. [PMID: 30889543 PMCID: PMC6516860 DOI: 10.1016/j.etap.2019.02.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Acute developmental exposure to pharmaceuticals or environmental contaminants can have deleterious, long lasting effects. Many of these compounds are endocrine disruptors (EDCs) that target estrogen signaling, with effects on reproductive and non-reproductive tissues. We recently reported that zebrafish larvae transiently exposed to the pharmaceutical EDC 4-OH-A display visual deficits as adults. Here, we examine whether these long-term effects are due to compound-induced morphological and/or cellular changes. Zebrafish aged 24 h, 48 h, 72 h, or 7 days post-fertilization (larvae) or 3-4mos (adults) were exposed to either 4-OH-A or PCB1254 for 24 h. After that time, notochord length, eye diameter, inter-eye distance, and heart rate were measured from larvae; and aromatase (estrogen synthase) activity was measured in homogenates of adult brain tissue. In general, indices of larval growth and development were not altered by 24 h exposure to either compound. 4-OH-A potently inhibited aromatase activity, while PCB1254 did not, with inhibition continuing even after removal from treatment. These results support differential function of EDCs and indicate that developmental exposure to 4-OH-A causes sustained inhibition of aromatase, which could be associated with altered adult behaviors.
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Affiliation(s)
- Cassie J Gould
- Department of Biology, American University, Washington, DC, United States; Behavior, Cognition & Neuroscience Program, American University, Washington, DC, United States; Center for Behavioral Neuroscience, American University, Washington, DC, United States.
| | - Colin J Saldanha
- Department of Biology, American University, Washington, DC, United States; Behavior, Cognition & Neuroscience Program, American University, Washington, DC, United States; Center for Behavioral Neuroscience, American University, Washington, DC, United States
| | - Victoria P Connaughton
- Department of Biology, American University, Washington, DC, United States; Behavior, Cognition & Neuroscience Program, American University, Washington, DC, United States; Center for Behavioral Neuroscience, American University, Washington, DC, United States
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80
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Huckins LM, Dobbyn A, Ruderfer DM, Hoffman G, Wang W, Pardiñas AF, Rajagopal VM, Als TD, T Nguyen H, Girdhar K, Boocock J, Roussos P, Fromer M, Kramer R, Domenici E, Gamazon ER, Purcell S, Demontis D, Børglum AD, Walters JTR, O'Donovan MC, Sullivan P, Owen MJ, Devlin B, Sieberts SK, Cox NJ, Im HK, Sklar P, Stahl EA. Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. Nat Genet 2019; 51:659-674. [PMID: 30911161 PMCID: PMC7034316 DOI: 10.1038/s41588-019-0364-4] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/30/2019] [Indexed: 01/23/2023]
Abstract
Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.
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Affiliation(s)
- Laura M Huckins
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Amanda Dobbyn
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Gabriel Hoffman
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weiqing Wang
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Antonio F Pardiñas
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Veera M Rajagopal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Thomas D Als
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Hoang T Nguyen
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kiran Girdhar
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - James Boocock
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Panos Roussos
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Menachem Fromer
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robin Kramer
- Human Brain Collection Core, National Institute of Mental Health, Bethesda, MD, USA
| | - Enrico Domenici
- Laboratory of Neurogenomic Biomarkers, Centre for Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Eric R Gamazon
- Vanderbilt University Medical Center, Nashville, TN, USA
- Clare Hall, University of Cambridge, Cambridge, UK
| | - Shaun Purcell
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ditte Demontis
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - Anders D Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Denmark
- Center for Integrative Sequencing, Aarhus University, Aarhus, Denmark
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Patrick Sullivan
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Karolinska Institutet, Stockholm, Sweden
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Nancy J Cox
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Pamela Sklar
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eli A Stahl
- Pamela Sklar Division of Psychiatric Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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81
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Model systems inform rare disease diagnosis, therapeutic discovery and pre-clinical efficacy. Emerg Top Life Sci 2019; 3:1-10. [DOI: 10.1042/etls20180057] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/15/2019] [Indexed: 01/12/2023]
Abstract
Abstract
Model systems have played a large role in understanding human diseases and are instrumental in taking basic research findings to the clinic; however, for rare diseases, model systems play an even larger role. Here, we outline how model organisms are crucial for confirming causal associations, understanding functional mechanisms and developing therapies for disease. As diseases that have been studied extensively through genetics and molecular biology, cystic fibrosis and Rett syndrome are portrayed as primary examples of how genetic diagnosis, model organism development and therapies have led to improved patient health. Considering which model to use, yeast, worms, flies, fish, mice or larger animals requires a careful evaluation of experimental genetic tools and gene pathway conservation. Recent advances in genome editing will aid in confirming diagnoses and developing model systems for rare disease. Genetic or chemical screening for disease suppression may reveal functional pathway members and provide candidate entry points for developing therapies. Model organisms may also be used in drug discovery and as preclinical models as a prelude to testing treatments in patient populations. Now, model organisms will increasingly be used as platforms for understanding variation in rare disease severity and onset, thereby informing therapeutic intervention.
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82
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Chang H, Yeo J, Kim JG, Kim H, Lim J, Lee M, Kim HH, Ohk J, Jeon HY, Lee H, Jung H, Kim KW, Kim VN. Terminal Uridylyltransferases Execute Programmed Clearance of Maternal Transcriptome in Vertebrate Embryos. Mol Cell 2019; 70:72-82.e7. [PMID: 29625039 DOI: 10.1016/j.molcel.2018.03.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 02/07/2018] [Accepted: 03/01/2018] [Indexed: 12/26/2022]
Abstract
During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3' modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.
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Affiliation(s)
- Hyeshik Chang
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jinah Yeo
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jeong-Gyun Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - Hyunjoon Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Jaechul Lim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Mihye Lee
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea
| | - Hyun Ho Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - Jiyeon Ohk
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Hee-Yeon Jeon
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hyunsook Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hosung Jung
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Kyu-Won Kim
- Department of Molecular Medicine and Biopharmaceutical Science, Seoul National University, Seoul 08826, Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Korea.
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83
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Schulz A, Brendler J, Blaschuk O, Landgraf K, Krueger M, Ricken AM. Non-pathological Chondrogenic Features of Valve Interstitial Cells in Normal Adult Zebrafish. J Histochem Cytochem 2019; 67:361-373. [PMID: 30620237 DOI: 10.1369/0022155418824083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In the heart, unidirectional blood flow depends on proper heart valve function. As, in mammals, regulatory mechanisms of early heart valve and bone development are shown to contribute to adult heart valve pathologies, we used the animal model zebrafish (ZF, Danio rerio) to investigate the microarchitecture and differentiation of cardiac valve interstitial cells in the transition from juvenile (35 days) to end of adult breeding (2.5 years) stages. Of note, light microscopy and immunohistochemistry revealed major differences in ZF heart valve microarchitecture when compared with adult mice. We demonstrate evidence for rather chondrogenic features of valvular interstitial cells by histological staining and immunodetection of SOX-9, aggrecan, and type 2a1 collagen. Collagen depositions are enriched in a thin layer at the atrial aspect of atrioventricular valves and the ventricular aspect of bulboventricular valves, respectively. At the ultrastructural level, the collagen fibrils are lacking obvious periodicity and orientation throughout the entire valve.
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Affiliation(s)
- Alina Schulz
- Institute of Anatomy, Faculty of Medicine.,University of Leipzig, Leipzig, Germany
| | - Jana Brendler
- Institute of Anatomy, Faculty of Medicine.,University of Leipzig, Leipzig, Germany
| | - Orest Blaschuk
- Division of Urology, Department of Surgery, McGill University, Montreal, Québec, Canada.,University of Leipzig, Leipzig, Germany
| | - Kathrin Landgraf
- Center for Pediatric Research Leipzig, University Hospital for Children & Adolescents and Integrated Research and Treatment Centre Adiposity Diseases.,University of Leipzig, Leipzig, Germany
| | - Martin Krueger
- Institute of Anatomy, Faculty of Medicine.,University of Leipzig, Leipzig, Germany
| | - Albert M Ricken
- Institute of Anatomy, Faculty of Medicine.,University of Leipzig, Leipzig, Germany
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84
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Putman T, Hybiske K, Jow D, Afrasiabi C, Lelong S, Cano MA, Stupp GS, Waagmeester A, Good BM, Wu C, Su AI. ChlamBase: a curated model organism database for the Chlamydia research community. Database (Oxford) 2019; 2019:baz041. [PMID: 30985891 PMCID: PMC6463448 DOI: 10.1093/database/baz041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/22/2019] [Accepted: 03/07/2019] [Indexed: 02/06/2023]
Abstract
The accelerating growth of genomic and proteomic information for Chlamydia species, coupled with unique biological aspects of these pathogens, necessitates bioinformatic tools and features that are not provided by major public databases. To meet these growing needs, we developed ChlamBase, a model organism database for Chlamydia that is built upon the WikiGenomes application framework, and Wikidata, a community-curated database. ChlamBase was designed to serve as a central access point for genomic and proteomic information for the Chlamydia research community. ChlamBase integrates information from numerous external databases, as well as important data extracted from the literature that are otherwise not available in structured formats that are easy to use. In addition, a key feature of ChlamBase is that it empowers users in the field to contribute new annotations and data as the field advances with continued discoveries. ChlamBase is freely and publicly available at chlambase.org.
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Affiliation(s)
- Tim Putman
- Ontology Development Group, Library, Oregon Health and Science University, Portland, OR, USA
| | - Kevin Hybiske
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Derek Jow
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Cyrus Afrasiabi
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sebastien Lelong
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Marco Alvarado Cano
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gregory S Stupp
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Benjamin M Good
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Chunlei Wu
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew I Su
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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85
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Abstract
Variably expressive copy-number variants (CNVs) are characterized by extensive phenotypic heterogeneity of neuropsychiatric phenotypes. Approaches to identify single causative genes for these phenotypes within each CNV have not been successful. Here, we posit using multiple lines of evidence, including pathogenicity metrics, functional assays of model organisms, and gene expression data, that multiple genes within each CNV region are likely responsible for the observed phenotypes. We propose that candidate genes within each region likely interact with each other through shared pathways to modulate the individual gene phenotypes, emphasizing the genetic complexity of CNV-associated neuropsychiatric features.
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Affiliation(s)
- Matthew Jensen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Bioinformatics and Genomics Program, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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86
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Abstract
Humoral regulation by ligand/receptor interactions is a fundamental feature of vertebrate hematopoiesis. Zebrafish are an established vertebrate animal model of hematopoiesis, sharing with mammals conserved genetic, molecular and cell biological regulatory mechanisms. This comprehensive review considers zebrafish hematopoiesis from the perspective of the hematopoietic growth factors (HGFs), their receptors and their actions. Zebrafish possess multiple HGFs: CSF1 (M-CSF) and CSF3 (G-CSF), kit ligand (KL, SCF), erythropoietin (EPO), thrombopoietin (THPO/TPO), and the interleukins IL6, IL11, and IL34. Some ligands and/or receptor components have been duplicated by various mechanisms including the teleost whole genome duplication, adding complexity to the ligand/receptor interactions possible, but also providing examples of several different outcomes of ligand and receptor subfunctionalization or neofunctionalization. CSF2 (GM-CSF), IL3 and IL5 and their receptors are absent from zebrafish. Overall the humoral regulation of hematopoiesis in zebrafish displays considerable similarity with mammals, which can be applied in biological and disease modelling research.
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Affiliation(s)
- Vahid Pazhakh
- a Australian Regenerative Medicine Institute, Monash University , Clayton , Australia
| | - Graham J Lieschke
- a Australian Regenerative Medicine Institute, Monash University , Clayton , Australia
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87
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Benoit CR, Stanton AE, Tartanian AC, Motzer AR, McGaughey DM, Bond SR, Brody LC. Functional and phylogenetic characterization of noncanonical vitamin B 12-binding proteins in zebrafish suggests involvement in cobalamin transport. J Biol Chem 2018; 293:17606-17621. [PMID: 30237171 PMCID: PMC6231144 DOI: 10.1074/jbc.ra118.005323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
In humans, transport of food-derived cobalamin (vitamin B12) from the digestive system into the bloodstream involves three paralogous proteins: transcobalamin (TC), haptocorrin (HC), and intrinsic factor (IF). Each of these proteins contains two domains, an α-domain and a β-domain, which together form a cleft in which cobalamin binds. Zebrafish (Danio rerio) are thought to possess only a single cobalamin transport protein, referred to as Tcn2, which is a transcobalamin homolog. Here, we used CRISPR/Cas9 mutagenesis to create null alleles of tcn2 in zebrafish. Fish homozygous for tcn2-null alleles were viable and exhibited no obvious developmentally or behaviorally abnormal phenotypes. For this reason, we hypothesized that previously unidentified cobalamin-carrier proteins encoded in the zebrafish genome may provide an additional pathway for cobalamin transport. We identified genes predicted to code for two such proteins, Tcn-beta-a (Tcnba) and Tcn-beta-b (Tcnbb), which differ from all previously characterized cobalamin transport proteins as they lack the α-domain. These β-domain-only proteins are representative of an undescribed class of cobalamin-carrier proteins that are highly conserved throughout the ray-finned fishes. We observed that the genes encoding the three cobalamin transport homologs, tcn2, tcnba, and tcnbb, are expressed in unique spatial and temporal patterns in the developing zebrafish. Moreover, exogenously expressed recombinant Tcnba and Tcnbb bound cobalamin with high affinity, comparable with binding by full-length Tcn2. Taken together, our results suggest that this noncanonical protein structure has evolved to fully function as a cobalamin-carrier protein, thereby allowing for a compensatory cobalamin transport mechanism in the tcn2-/- zebrafish.
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Affiliation(s)
- Courtney R Benoit
- From the Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Abigail E Stanton
- From the Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Aileen C Tartanian
- From the Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Andrew R Motzer
- From the Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 and
| | - David M McGaughey
- From the Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 and
| | - Stephen R Bond
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Lawrence C Brody
- From the Gene and Environment Interaction Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892 and
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88
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Shaw CH, Gao G, Wiens GD. Differential expression and evolution of three tandem, interleukin-1 receptor-like 1 genes in rainbow trout (Oncorhynchus mykiss). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:193-203. [PMID: 29886053 DOI: 10.1016/j.dci.2018.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/06/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Interleukin-1 receptor-like 1 (Il1rl1 or ST2), a member of the interleukin-1 receptor family, has pleiotropic roles including tissue homeostasis, inflammation, immune polarization, and disease resistance in mammals. A single orthologue was previously described in salmonid fish; however, a recently improved genome assembly of rainbow trout (Oncorhynchus mykiss) revealed three adjacent, tandem il1rl1 orthologues on chromosome Omy 03. Here, we report the genomic organization and evolution of the three il1rl1 genes (il1rl1α, il1rl1β, il1rl1γ), and use both RNA-seq and gene-specific qPCR methods to quantify expression patterns. Nucleotide sequence homology between the three genes is >95% and each predicted protein contains three IG/IG-like domains, a transmembrane region and a TIR domain. The amino acid sequence homology of the rainbow trout il1rl1 genes are highly related to two functional copies in Atlantic and Coho salmon (∼94%) but relatively low (22-26%) with avian and mammalian species. Transcript abundance measured by RNA-seq in 15 tissues of healthy adult rainbow trout indicate constitutive expression of each gene. In whole body lysates, il1rl1α was shown to have >20 fold mRNA expression compared to il1rl1β and il1rl1γ as measured by qPCR assays specific to il1rl1α or il1rl1γ, as well as a multi-gene qPCR assay (il1rl1α,β,γ). Unrooted phylogenetic trees grouped the rainbow trout il1rl1 genes apart from other interleukin-1 receptor family genes and genomic comparisons identify preserved synteny between mammals, birds and salmonids albeit a pseudogene is present in both Atlantic salmon and Coho salmon. Phylogenetic analyses suggest that the three genes arose by tandem duplication but are inconclusive whether these events occurred prior-to or after salmonid speciation. These findings further the understanding of interleukin receptor family evolution and their contribution to teleost immune function.
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Affiliation(s)
- Cassidy H Shaw
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, WV 25430, USA.
| | - Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, WV 25430, USA
| | - Gregory D Wiens
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, USDA, Kearneysville, WV 25430, USA.
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89
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Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C. Model organism data evolving in support of translational medicine. Lab Anim (NY) 2018; 47:277-289. [PMID: 30224793 PMCID: PMC6322546 DOI: 10.1038/s41684-018-0150-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Model organism databases (MODs) have been collecting and integrating biomedical research data for 30 years and were designed to meet specific needs of each model organism research community. The contributions of model organism research to understanding biological systems would be hard to overstate. Modern molecular biology methods and cost reductions in nucleotide sequencing have opened avenues for direct application of model organism research to elucidating mechanisms of human diseases. Thus, the mandate for model organism research and databases has now grown to include facilitating use of these data in translational applications. Challenges in meeting this opportunity include the distribution of research data across many databases and websites, a lack of data format standards for some data types, and sustainability of scale and cost for genomic database resources like MODs. The issues of widely distributed data and application of data standards are some of the challenges addressed by FAIR (Findable, Accessible, Interoperable, and Re-usable) data principles. The Alliance of Genome Resources is now moving to address these challenges by bringing together expertly curated research data from fly, mouse, rat, worm, yeast, zebrafish, and the Gene Ontology consortium. Centralized multi-species data access, integration, and format standardization will lower the data utilization barrier in comparative genomics and translational applications and will provide a framework in which sustainable scale and cost can be addressed. This article presents a brief historical perspective on how the Alliance model organisms are complementary and how they have already contributed to understanding the etiology of human diseases. In addition, we discuss four challenges for using data from MODs in translational applications and how the Alliance is working to address them, in part by applying FAIR data principles. Ultimately, combined data from these animal models are more powerful than the sum of the parts.
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Affiliation(s)
- Douglas G Howe
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA.
| | | | - Yvonne M Bradford
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | | | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Stacia R Engel
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | | | | | - Ranjana Kishore
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Stanley J F Laulederkind
- Department of Biomedical Engineering, Medical College of Wisconsin and Marquette University, Milwaukee, WI, USA
| | - Suzanna E Lewis
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sierra A T Moxon
- The Institute of Neuroscience, University of Oregon, Eugene, OR, USA
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90
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Komissarov A, Vij S, Yurchenko A, Trifonov V, Thevasagayam N, Saju J, Sridatta PSR, Purushothaman K, Graphodatsky A, Orbán L, Kuznetsova I. B Chromosomes of the Asian Seabass ( Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations. Genes (Basel) 2018; 9:E464. [PMID: 30241368 PMCID: PMC6211105 DOI: 10.3390/genes9100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 12/01/2022] Open
Abstract
The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.
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Affiliation(s)
- Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
| | - Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- School of Applied Science, Republic Polytechnic 9 Woodlands Avenue 9, Singapore 738964, Singapore.
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Natascha Thevasagayam
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | - Jolly Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | | | - Kathiresan Purushothaman
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
| | - Alexander Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Department of Animal Sciences, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Hungary.
- Center for Comparative Genomics, Murdoch University, 6150 Murdoch, Australia.
| | - Inna Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
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91
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Somorjai IML, Martí-Solans J, Diaz-Gracia M, Nishida H, Imai KS, Escrivà H, Cañestro C, Albalat R. Wnt evolution and function shuffling in liberal and conservative chordate genomes. Genome Biol 2018; 19:98. [PMID: 30045756 PMCID: PMC6060547 DOI: 10.1186/s13059-018-1468-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 06/22/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND What impact gene loss has on the evolution of developmental processes, and how function shuffling has affected retained genes driving essential biological processes, remain open questions in the fields of genome evolution and EvoDevo. To investigate these problems, we have analyzed the evolution of the Wnt ligand repertoire in the chordate phylum as a case study. RESULTS We conduct an exhaustive survey of Wnt genes in genomic databases, identifying 156 Wnt genes in 13 non-vertebrate chordates. This represents the most complete Wnt gene catalog of the chordate subphyla and has allowed us to resolve previous ambiguities about the orthology of many Wnt genes, including the identification of WntA for the first time in chordates. Moreover, we create the first complete expression atlas for the Wnt family during amphioxus development, providing a useful resource to investigate the evolution of Wnt expression throughout the radiation of chordates. CONCLUSIONS Our data underscore extraordinary genomic stasis in cephalochordates, which contrasts with the liberal and dynamic evolutionary patterns of gene loss and duplication in urochordate genomes. Our analysis has allowed us to infer ancestral Wnt functions shared among all chordates, several cases of function shuffling among Wnt paralogs, as well as unique expression domains for Wnt genes that likely reflect functional innovations in each chordate lineage. Finally, we propose a potential relationship between the evolution of WntA and the evolution of the mouth in chordates.
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Affiliation(s)
- Ildikó M L Somorjai
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, North Haugh, St Andrews, KY16 9ST, Scotland, UK.
- Scottish Oceans Institute, School of Biology, University of St Andrews, East Sands, St Andrews, KY16 8LB, Scotland, UK.
| | - Josep Martí-Solans
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Miriam Diaz-Gracia
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Hiroki Nishida
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Kaoru S Imai
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, 560-0043, Japan
| | - Hector Escrivà
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Cristian Cañestro
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
| | - Ricard Albalat
- Departament de Genètica, , Microbiologia i Estadística, and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain.
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92
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Marques DA, Jones FC, Di Palma F, Kingsley DM, Reimchen TE. Experimental evidence for rapid genomic adaptation to a new niche in an adaptive radiation. Nat Ecol Evol 2018; 2:1128-1138. [PMID: 29942074 PMCID: PMC6519129 DOI: 10.1038/s41559-018-0581-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/17/2018] [Indexed: 12/20/2022]
Abstract
A substantial part of biodiversity is thought to have arisen from adaptive radiations in which one lineage rapidly diversified into multiple lineages adapted to many different niches. However, selection and drift reduce genetic variation during adaptation to new niches and may thus prevent or slow down further niche shifts. We tested whether rapid adaptation is still possible from a highly derived ecotype in the adaptive radiation of threespine stickleback on the Haida Gwaii archipelago, Western Canada. In a 19-years selection experiment, we let giant stickleback from a large blackwater lake evolve in a small clearwater pond without vertebrate predators. 56 whole genomes from the experiment and 26 natural populations revealed that adaptive genomic change was rapid in many small genomic regions and encompassed 75% of the adaptive genomic change between 12,000 years old ecotypes. Adaptive genomic change was as fast as phenotypic change in defence and trophic morphology and both were largely parallel between the short-term selection experiment and long-term natural adaptive radiation. Our results show that functionally relevant standing genetic variation can persist in derived adaptive radiation members, allowing adaptive radiations to unfold very rapidly.
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Affiliation(s)
- David A Marques
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada. .,Aquatic Ecology & Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland. .,Department of Fish Ecology and Evolution, Eawag: Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland.
| | - Felicity C Jones
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Federica Di Palma
- Earlham Institute, Norwich Research Park, Norwich, UK.,Department of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - David M Kingsley
- Department of Developmental Biology, HHMI and Stanford University School of Medicine, Stanford, CA, USA
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada
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93
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Porseryd T, Reyhanian Caspillo N, Volkova K, Elabbas L, Källman T, Dinnétz P, Olsson PE, Porsch-Hällström I. Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol. Gen Comp Endocrinol 2018. [PMID: 29526718 DOI: 10.1016/j.ygcen.2018.03.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
17α-Ethinylestradiol (EE2) is a ubiquitous aquatic contaminant shown to decrease fish fertility at low concentrations, especially in fish exposed during development. The mechanisms of the decreased fertility are not fully understood. In this study, we perform transcriptome analysis by RNA sequencing of testes from zebrafish with previously reported lowered fertility due to exposure to low concentrations of EE2 during development. Fish were exposed to 1.2 and 1.6 ng/L (measured concentration; nominal concentrations 3 and 10 ng/L) of EE2 from fertilization to 80 days of age, followed by 82 days of remediation in clean water. RNA sequencing analysis revealed 249 and 16 genes to be differentially expressed after exposure to 1.2 and 1.6 ng/L, respectively; a larger inter-sample variation was noted in the latter. Expression of 11 genes were altered by both exposures and in the same direction. The coding sequences most affected could be categorized to the putative functions cell signalling, proteolysis, protein metabolic transport and lipid metabolic process. Several homeobox transcription factors involved in development and differentiation showed increased expression in response to EE2 and differential expression of genes related to cell death, differentiation and proliferation was observed. In addition, several genes related to steroid synthesis, testis development and function were differentially expressed. A number of genes associated with spermatogenesis in zebrafish and/or mouse were also found to be differentially expressed. Further, differences in non-coding sequences were observed, among them several differentially expressed miRNA that might contribute to testis gene regulation at post-transcriptional level. This study has generated insights of changes in gene expression that accompany fertility alterations in zebrafish males that persist after developmental exposure to environmental relevant concentrations of EE2 that persist followed by clean water to adulthood. Hopefully, this will generate hypotheses to test in search for mechanistic explanations.
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Affiliation(s)
- T Porseryd
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden.
| | - N Reyhanian Caspillo
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden; Örebro Life Science Center, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - K Volkova
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden; Örebro Life Science Center, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - L Elabbas
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden
| | - T Källman
- National Bioinformatics Infrastructure Sweden, Uppsala University, 75124 Uppsala, Sweden; Science for Life Laboratory and Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden
| | - P Dinnétz
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden
| | - P-E Olsson
- Örebro Life Science Center, School of Science and Technology, Örebro University, SE-701 82 Örebro, Sweden
| | - I Porsch-Hällström
- School of Natural Sciences, Technology and Environmental Studies, Södertörn University, SE-141 89 Huddinge, Sweden
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94
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Matern MS, Beirl A, Ogawa Y, Song Y, Paladugu N, Kindt KS, Hertzano R. Transcriptomic Profiling of Zebrafish Hair Cells Using RiboTag. Front Cell Dev Biol 2018; 6:47. [PMID: 29765956 PMCID: PMC5939014 DOI: 10.3389/fcell.2018.00047] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 04/13/2018] [Indexed: 01/27/2023] Open
Abstract
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging. Cell sorting methods, as well as single-cell RNA-Seq, have proved to be very informative in studying hair cell-specific gene expression. However, these methods require that tissues are dissociated, the processing for which can lead to changes in gene expression prior to RNA extraction. To bypass this problem, we have developed a transgenic zebrafish model to evaluate the translatome of the inner ear and lateral line hair cells in their native tissue environment; the Tg(myo6b:RiboTag) zebrafish. This model expresses both GFP and a hemagglutinin (HA) tagged rpl10a gene under control of the myo6b promoter (myo6b:GFP-2A-rpl10a-3xHA), resulting in HA-tagged ribosomes expressed specifically in hair cells. Consequently, intact zebrafish larvae can be used to enrich for actively translated hair cell mRNA via an immunoprecipitation protocol using an antibody for the HA-tag (similar to the RiboTag mice). We demonstrate that this model can be used to reliably enrich for actively translated zebrafish hair cell mRNA. Additionally, we perform a global hair cell translatome analysis using RNA-Seq and show enrichment of known hair cell expressed transcripts and depletion of non-hair cell expressed transcripts in the immunoprecipitated material compared with mRNA extracted from whole fish (input). Our results show that our model can identify novel hair cell expressed genes in intact zebrafish, without inducing changes to gene expression that result from tissue dissociation and delays during cell sorting. Overall, we believe that this model will be highly useful for studying changes in zebrafish hair cell-specific gene expression in response to developmental progression, mutations, as well as hair cell damage by noise or ototoxic drug exposure.
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Affiliation(s)
- Maggie S. Matern
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Alisha Beirl
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Yoko Ogawa
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Yang Song
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Nikhil Paladugu
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Katie S. Kindt
- Section on Sensory Cell Development and Function, National Institute on Deafness and Other Communication Disorders, Bethesda, MD, United States
| | - Ronna Hertzano
- Department of Otorhinolaryngology Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD, United States,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States,Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States,*Correspondence: Ronna Hertzano
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95
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Nelson AC, Cutty SJ, Gasiunas SN, Deplae I, Stemple DL, Wardle FC. In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors. Cell Rep 2018; 19:2782-2795. [PMID: 28658625 PMCID: PMC5494305 DOI: 10.1016/j.celrep.2017.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/28/2017] [Accepted: 05/31/2017] [Indexed: 01/15/2023] Open
Abstract
T-box transcription factors T/Brachyury homolog A (Ta) and Tbx16 are essential for correct mesoderm development in zebrafish. The downstream transcriptional networks guiding their functional activities are poorly understood. Additionally, important contributions elsewhere are likely masked due to redundancy. Here, we exploit functional genomic strategies to identify Ta and Tbx16 targets in early embryogenesis. Surprisingly, we discovered they not only activate mesodermal gene expression but also redundantly regulate key endodermal determinants, leading to substantial loss of endoderm in double mutants. To further explore the gene regulatory networks (GRNs) governing endoderm formation, we identified targets of Ta/Tbx16-regulated homeodomain transcription factor Mixl1, which is absolutely required in zebrafish for endoderm formation. Interestingly, we find many endodermal determinants coordinately regulated through common genomic occupancy by Mixl1, Eomesa, Smad2, Nanog, Mxtx2, and Pou5f3. Collectively, these findings augment the endoderm GRN and reveal a panel of target genes underlying the Ta, Tbx16, and Mixl1 mutant phenotypes.
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Affiliation(s)
- Andrew C Nelson
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK; Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Stephen J Cutty
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Saule N Gasiunas
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Isabella Deplae
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | - Derek L Stemple
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fiona C Wardle
- Randall Division of Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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96
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Dobrzycki T, Krecsmarik M, Bonkhofer F, Patient R, Monteiro R. An optimised pipeline for parallel image-based quantification of gene expression and genotyping after in situ hybridisation. Biol Open 2018. [PMID: 29535102 PMCID: PMC5936060 DOI: 10.1242/bio.031096] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Advances in genome engineering have resulted in the generation of numerous zebrafish mutant lines. A commonly used method to assess gene expression in the mutants is in situ hybridisation (ISH). Because the embryos can be distinguished by genotype after ISH, comparing gene expression between wild-type and mutant siblings can be done blinded and in parallel. Such experimental design reduces the technical variation between samples and minimises the risk of bias. This approach, however, requires an efficient method of genomic DNA extraction from post-ISH fixed zebrafish samples to ascribe phenotype to genotype. Here we describe a method to obtain PCR-quality DNA from 95-100% of zebrafish embryos, suitable for genotyping after ISH. In addition, we provide an image analysis protocol for quantifying gene expression of ISH-probed embryos, adaptable for the analysis of different expression patterns. Finally, we show that intensity-based image analysis enables accurate representation of the variability of gene expression detected by ISH and that it can complement quantitative methods like qRT-PCR. By combining genotyping after ISH and computer-based image analysis, we have established a high-confidence, unbiased methodology to assign gene expression levels to specific genotypes, and applied it to the analysis of molecular phenotypes of newly generated lmo4a mutants. Summary: Our optimised protocol to genotype zebrafish mutant embryos after in situ hybridisation and digitally quantify the in situ signal will help to standardise existing experimental designs and methods of analysis.
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Affiliation(s)
- Tomasz Dobrzycki
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Monika Krecsmarik
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,BHF Centre of Research Excellence, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Florian Bonkhofer
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Roger Patient
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.,BHF Centre of Research Excellence, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Rui Monteiro
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK .,BHF Centre of Research Excellence, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
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97
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Spanjaard B, Hu B, Mitic N, Olivares-Chauvet P, Janjuha S, Ninov N, Junker JP. Simultaneous lineage tracing and cell-type identification using CRISPR-Cas9-induced genetic scars. Nat Biotechnol 2018; 36:469-473. [PMID: 29644996 PMCID: PMC5942543 DOI: 10.1038/nbt.4124] [Citation(s) in RCA: 324] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 03/15/2018] [Indexed: 12/12/2022]
Abstract
A key goal of developmental biology is to understand how a single cell transforms into a full-grown organism comprising many different cell types. Single-cell RNA-sequencing (scRNA-seq) is commonly used to identify cell types in a tissue or organ1. However, organizing the resulting taxonomy of cell types into lineage trees to understand developmental origin of cells remains challenging. Here we present LINNAEUS (LINeage tracing by Nuclease-Activated Editing of Ubiquitous Sequences)—a strategy for simultaneous lineage tracing and transcriptome profiling in thousands of single cells. By combining scRNA-seq with computational analysis of lineage barcodes, generated by genome editing of transgenic reporter genes, we reconstruct developmental lineage trees in zebrafish larvae, and in heart, liver, pancreas and telencephalon of adult fish. LINNAEUS provides a systematic approach for tracing the origin of novel cell types, or known cell types under different conditions.
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Affiliation(s)
- Bastiaan Spanjaard
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Bo Hu
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Nina Mitic
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Pedro Olivares-Chauvet
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Sharan Janjuha
- DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Nikolay Ninov
- DFG-Center for Regenerative Therapies Dresden, Technische Universität Dresden, Dresden, Germany
| | - Jan Philipp Junker
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
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98
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Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain. Nat Biotechnol 2018; 36:442-450. [PMID: 29608178 PMCID: PMC5938111 DOI: 10.1038/nbt.4103] [Citation(s) in RCA: 374] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 12/25/2022]
Abstract
The lineage relationships among the hundreds of cell types generated during development are difficult to reconstruct. A recent method, GESTALT, used CRISPR-Cas9 barcode editing for large-scale lineage tracing, but was restricted to early development and did not identify cell types. Here we present scGESTALT, which combines the lineage recording capabilities of GESTALT with cell-type identification by single-cell RNA sequencing. The method relies on an inducible system that enables barcodes to be edited at multiple time points, capturing lineage information from later stages of development. Sequencing of ~60,000 transcriptomes from the juvenile zebrafish brain identifies >100 cell types and marker genes. Using these data, we generate lineage trees with hundreds of branches that help uncover restrictions at the level of cell types, brain regions, and gene expression cascades during differentiation. scGESTALT can be applied to other multicellular organisms to simultaneously characterize molecular identities and lineage histories of thousands of cells during development and disease.
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99
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Schüttler A, Reiche K, Altenburger R, Busch W. The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. Toxicol Sci 2018; 157:291-304. [PMID: 28329862 PMCID: PMC5443304 DOI: 10.1093/toxsci/kfx045] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Numerous studies have been published in the past years investigating the transcriptome of the zebrafish embryo (ZFE) upon being subjected to chemical stress. Aiming at a more mechanistic understanding of the results of such studies, knowledge about commonalities of transcript regulation in response to chemical stress is needed. Thus, our goal in this study was to identify and interpret genes and gene sets constituting a general response to chemical exposure. Therefore, we aggregated and reanalyzed published toxicogenomics data obtained with the ZFE. We found that overlap of differentially transcribed genes in response to chemical stress across independent studies is generally low and the most commonly differentially transcribed genes appear in less than 50% of all treatments across studies. However, effect size analysis revealed several genes showing a common trend of differential expression, among which genes related to calcium homeostasis emerged as key, especially in exposure settings up to 24 h post-fertilization. Additionally, we found that these and other downregulated genes are often linked to anatomical regions developing during the respective exposure period. Genes showing a trend of increased expression were, among others, linked to signaling pathways (e.g., Wnt, Fgf) as well as lysosomal structures and apoptosis. The findings of this study help to increase the understanding of chemical stress responses in the developing zebrafish embryo and provide a starting point to improve experimental designs for this model system. In future, improved time- and concentration-resolved experiments should offer better understanding of stress response patterns and access to mechanistic information.
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Affiliation(s)
- Andreas Schüttler
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraβe 15, Leipig, Germany.,Institute for Environmental Research, RWTH Aachen, Worringerweg 1, Aachen, Germany
| | - Kristin Reiche
- Young Investigators Group Bioinformatics and Transcriptomics, Department Molecular Systems Biology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraβe 15, Leipig, Germany.,Bioinformatics Unit, Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraβe 1, Leipzig, Germany
| | - Rolf Altenburger
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraβe 15, Leipig, Germany.,Institute for Environmental Research, RWTH Aachen, Worringerweg 1, Aachen, Germany
| | - Wibke Busch
- Department Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipig, Germany
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100
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Olmos V, Marro M, Loza-Alvarez P, Raldúa D, Prats E, Padrós F, Piña B, Tauler R, de Juan A. Combining hyperspectral imaging and chemometrics to assess and interpret the effects of environmental stressors on zebrafish eye images at tissue level. JOURNAL OF BIOPHOTONICS 2018; 11:e201700089. [PMID: 28766927 DOI: 10.1002/jbio.201700089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/27/2017] [Accepted: 07/31/2017] [Indexed: 06/07/2023]
Abstract
Changes on an organism by the exposure to environmental stressors may be characterized by hyperspectral images (HSI), which preserve the morphology of biological samples, and suitable chemometric tools. The approach proposed allows assessing and interpreting the effect of contaminant exposure on heterogeneous biological samples monitored by HSI at specific tissue levels. In this work, the model example used consists of the study of the effect of the exposure of chlorpyrifos-oxon on zebrafish tissues. To assess this effect, unmixing of the biological sample images followed by tissue-specific classification models based on the unmixed spectral signatures is proposed. Unmixing and classification are performed by multivariate curve resolution-alternating least squares (MCR-ALS) and partial least squares-discriminant analysis (PLS-DA), respectively. Crucial aspects of the approach are: (1) the simultaneous MCR-ALS analysis of all images from 1 population to take into account biological variability and provide reliable tissue spectral signatures, and (2) the use of resolved spectral signatures from control and exposed populations obtained from resampling of pixel subsets analyzed by MCR-ALS multiset analysis as information for the tissue-specific PLS-DA classification models. Classification results diagnose the presence of a significant effect and identify the spectral regions at a tissue level responsible for the biological change.
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Affiliation(s)
- Víctor Olmos
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Mònica Marro
- Institut de Ciencies Fotòniques (ICFO), The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Pablo Loza-Alvarez
- Institut de Ciencies Fotòniques (ICFO), The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Demetrio Raldúa
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Diagnostic (IDAEA-CSIC), Barcelona, Spain
| | - Eva Prats
- Research and Development Centre (CID-CSIC), Barcelona, Spain
| | - Francesc Padrós
- Pathological Diagnostic Service in Fish, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Benjamin Piña
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Diagnostic (IDAEA-CSIC), Barcelona, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Diagnostic (IDAEA-CSIC), Barcelona, Spain
| | - Anna de Juan
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
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