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Vöcking O, Famulski JK. Single cell transcriptome analyses of the developing zebrafish eye- perspectives and applications. Front Cell Dev Biol 2023; 11:1213382. [PMID: 37457291 PMCID: PMC10346855 DOI: 10.3389/fcell.2023.1213382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/18/2023] Open
Abstract
Within a relatively short period of time, single cell transcriptome analyses (SCT) have become increasingly ubiquitous with transcriptomic research, uncovering plentiful details that boost our molecular understanding of various biological processes. Stemming from SCT analyses, the ever-growing number of newly assigned genetic markers increases our understanding of general function and development, while providing opportunities for identifying genes associated with disease. SCT analyses have been carried out using tissue from numerous organisms. However, despite the great potential of zebrafish as a model organism, other models are still preferably used. In this mini review, we focus on eye research as an example of the advantages in using zebrafish, particularly its usefulness for single cell transcriptome analyses of developmental processes. As studies have already shown, the unique opportunities offered by zebrafish, including similarities to the human eye, in combination with the possibility to analyze and extract specific cells at distinct developmental time points makes the model a uniquely powerful one. Particularly the practicality of collecting large numbers of embryos and therefore isolation of sufficient numbers of developing cells is a distinct advantage compared to other model organisms. Lastly, the advent of highly efficient genetic knockouts methods offers opportunities to characterize target gene function in a more cost-efficient way. In conclusion, we argue that the use of zebrafish for SCT approaches has great potential to further deepen our molecular understanding of not only eye development, but also many other organ systems.
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Affiliation(s)
| | - Jakub K. Famulski
- Department of Biology, University of Kentucky, Lexington, KY, United States
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52
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Inge Schytz Andersen-Civil A, Anjan Sawale R, Claude Vanwalleghem G. Zebrafish (Danio rerio) as a translational model for neuro-immune interactions in the enteric nervous system in autism spectrum disorders. Brain Behav Immun 2023:S0889-1591(23)00142-3. [PMID: 37301234 DOI: 10.1016/j.bbi.2023.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 04/28/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023] Open
Abstract
Autism spectrum disorders (ASD) affect about 1% of the population and are strongly associated with gastrointestinal diseases creating shortcomings in quality of life. Multiple factors contribute to the development of ASD and although neurodevelopmental deficits are central, the pathogenesis of the condition is complex and the high prevalence of intestinal disorders is poorly understood. In agreement with the prominent research establishing clear bidirectional interactions between the gut and the brain, several studies have made it evident that such a relation also exists in ASD. Thus, dysregulation of the gut microbiota and gut barrier integrity may play an important role in ASD. However, only limited research has investigated how the enteric nervous system (ENS) and intestinal mucosal immune factors may impact on the development of ASD-related intestinal disorders. This review focuses on the mechanistic studies that elucidate the regulation and interactions between enteric immune cells, residing gut microbiota and the ENS in models of ASD. Especially the multifaceted properties and applicability of zebrafish (Danio rerio) for the study of ASD pathogenesis are assessed in comparison to studies conducted in rodent models and humans. Advances in molecular techniques and in vivo imaging, combined with genetic manipulation and generation of germ-free animals in a controlled environment, appear to make zebrafish an underestimated model of choice for the study of ASD. Finally, we establish the research gaps that remain to be explored to further our understanding of the complexity of ASD pathogenesis and associated mechanisms that may lead to intestinal disorders.
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Affiliation(s)
- Audrey Inge Schytz Andersen-Civil
- Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark.
| | - Rajlakshmi Anjan Sawale
- Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Gilles Claude Vanwalleghem
- Department of Molecular Biology and Genetics, Universitetsbyen 81, 8000 Aarhus C, Denmark; Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
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53
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Fields C, Levin M. Regulative development as a model for origin of life and artificial life studies. Biosystems 2023; 229:104927. [PMID: 37211257 DOI: 10.1016/j.biosystems.2023.104927] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 05/23/2023]
Abstract
Using the formal framework of the Free Energy Principle, we show how generic thermodynamic requirements on bidirectional information exchange between a system and its environment can generate complexity. This leads to the emergence of hierarchical computational architectures in systems that operate sufficiently far from thermal equilibrium. In this setting, the environment of any system increases its ability to predict system behavior by "engineering" the system towards increased morphological complexity and hence larger-scale, more macroscopic behaviors. When seen in this light, regulative development becomes an environmentally-driven process in which "parts" are assembled to produce a system with predictable behavior. We suggest on this basis that life is thermodynamically favorable and that, when designing artificial living systems, human engineers are acting like a generic "environment".
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Affiliation(s)
- Chris Fields
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA.
| | - Michael Levin
- Allen Discovery Center at Tufts University, Medford, MA, 02155, USA; Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, 02115, USA
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54
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Jain N, Sonawane PM, Liu H, Roychaudhury A, Lee Y, An J, Kim D, Kim D, Kim Y, Kim YC, Cho KB, Park HS, Kim CH, Churchill DG. "Lighting up" fluoride: cellular imaging and zebrafish model interrogations using a simple ESIPT-based mycophenolic acid precursor-based probe. Analyst 2023; 148:2609-2615. [PMID: 37190984 DOI: 10.1039/d3an00646h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The discovery and implementation of media that derive from bioinspired designs and bear optical readouts featuring large Stokes shifts are of continued interest to a wide variety of researchers and clinicians. Myco-F, a novel mycophenolic acid precursor-based probe features a cleavable tert-butyldimethylsiloxy group to allow for fluoride detection. Myco-F exhibits high selectivity and specificity towards F- (Stokes shift = 120 nm). All measurements were performed in complete aqueous media (LOD=0.38 μM). Myco-F enables detection of fluoride ions in living HEK293 cells and localizes in the eye region (among other regions) of the zebrafish. DFT calculations support the proposed ESIPT working photomechanism.
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Affiliation(s)
- Neha Jain
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Prasad M Sonawane
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Haoyan Liu
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | | | - Youngseob Lee
- Department of Chemistry, Jeonbuk National University and Research Institute for Physics and Chemistry, Jeonju 54896, Republic of Korea
| | - Jongkeol An
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Donghyeon Kim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Dongwook Kim
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science. (IBS), Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Yunsu Kim
- KAIST Institute for Health Science and Technology (KIHST) (Therapeutic Bioengineering Section), Daejeon 34141, Republic of Korea
| | - Yeu-Chun Kim
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyung-Bin Cho
- Department of Chemistry, Jeonbuk National University and Research Institute for Physics and Chemistry, Jeonju 54896, Republic of Korea
| | - Hee-Sung Park
- KAIST Institute for Health Science and Technology (KIHST) (Therapeutic Bioengineering Section), Daejeon 34141, Republic of Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, Republic of Korea
| | - David G Churchill
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
- Department of Chemical & Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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55
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Teefy BB, Lemus AJ, Adler A, Xu A, Bhala R, Hsu K, Benayoun BA. Widespread sex-dimorphism across single-cell transcriptomes of adult African turquoise killifish tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.05.539616. [PMID: 37214847 PMCID: PMC10197525 DOI: 10.1101/2023.05.05.539616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The African turquoise killifish (Nothobranchius furzeri), the shortest-lived vertebrate that can be bred in captivity, is an emerging model organism to study vertebrate aging. Here we describe the first multi-tissue, single-cell gene expression atlas of female and male turquoise killifish tissues comprising immune and metabolic cells from the blood, kidney, liver, and spleen. We were able to annotate 22 distinct cell types, define associated marker genes, and infer differentiation trajectories. Using this dataset, we found pervasive sex-dimorphic gene expression across cell types, especially in the liver. Sex-dimorphic genes tended to be involved in processes related to lipid metabolism, and indeed, we observed clear differences in lipid storage in female vs. male turquoise killifish livers. Importantly, we use machine-learning to predict sex using single-cell gene expression in our atlas and identify potential transcriptional markers for molecular sex identity in this species. As proof-of-principle, we show that our atlas can be used to deconvolute existing liver bulk RNA-seq data in this species to obtain accurate estimates of cell type proportions across biological conditions. We believe that this single-cell atlas can be a resource to the community that could notably be leveraged to identify cell type-specific genes for cell type-specific expression in transgenic animals.
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Affiliation(s)
- Bryan B. Teefy
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Aaron J.J. Lemus
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Ari Adler
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan Xu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Quantitative & Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Rajyk Bhala
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
| | - Katelyn Hsu
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
| | - Bérénice A. Benayoun
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA 90089, USA
- Molecular and Computational Biology Department, USC Dornsife College of Letters, Arts and Sciences, Los Angeles, CA 90089, USA
- Biochemistry and Molecular Medicine Department, USC Keck School of Medicine, Los Angeles, CA 90089, USA
- USC Norris Comprehensive Cancer Center, Epigenetics and Gene Regulation, Los Angeles, CA 90089, USA
- USC Stem Cell Initiative, Los Angeles, CA 90089, USA
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56
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Olson HM, Maxfield A, Calistri NL, Heiser LM, Nechiporuk AV. RhoA GEF Mcf2lb regulates rosette integrity during collective cell migration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537573. [PMID: 37131612 PMCID: PMC10153259 DOI: 10.1101/2023.04.19.537573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During development, multicellular rosettes serve as important cellular intermediates in the formation of diverse organ systems. Multicellular rosettes are transient epithelial structures that are defined by the apical constriction of cells towards the rosette center. Due to the important role these structures play during development, understanding the molecular mechanisms by which rosettes are formed and maintained is of high interest. Utilizing the zebrafish posterior lateral line primordium (pLLP) as a model system, we identify the RhoA GEF Mcf2lb as a regulator of rosette integrity. The pLLP is a group of ~150 cells that migrates along the zebrafish trunk and is organized into epithelial rosettes; these are deposited along the trunk and will differentiate into sensory organs called neuromasts (NMs). Using single-cell RNA sequencing and whole-mount in situ hybridization, we showed that mcf2lb is expressed in the pLLP during migration. Given the known role of RhoA in rosette formation, we asked whether Mcf2lb plays a role in regulating apical constriction of cells within rosettes. Live imaging and subsequent 3D analysis of mcf2lb mutant pLLP cells showed disrupted apical constriction and subsequent rosette organization. This in turn resulted in a unique posterior Lateral Line phenotype: an excess number of deposited NMs along the trunk of the zebrafish. Cell polarity markers ZO-1 and Par-3 were apically localized, indicating that pLLP cells are normally polarized. In contrast, signaling components that mediate apical constriction downstream of RhoA, Rock-2a and non-muscle Myosin II were diminished apically. Altogether our results suggest a model whereby Mcf2lb activates RhoA, which in turn activates downstream signaling machinery to induce and maintain apical constriction in cells incorporated into rosettes.
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Affiliation(s)
- Hannah M. Olson
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, The Knight Cancer Institute, Portland, Oregon, USA
- Neuroscience Graduate Program, Oregon Health & Science University, Portland, Oregon, USA
| | - Amanda Maxfield
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, The Knight Cancer Institute, Portland, Oregon, USA
| | - Nicholas L. Calistri
- Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
- Biomedical Engineering Graduate Program, Oregon Health & Science University, Portland, Oregon, USA
| | - Laura M. Heiser
- Biomedical Engineering, Oregon Health & Science University, Portland, Oregon, USA
| | - Alex V. Nechiporuk
- Department of Cell, Developmental & Cancer Biology, Oregon Health & Science University, The Knight Cancer Institute, Portland, Oregon, USA
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57
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Fishman L, Nechooshtan G, Erhard F, Regev A, Farrell JA, Rabani M. Single-cell temporal dynamics reveals the relative contributions of transcription and degradation to cell-type specific gene expression in zebrafish embryos. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.537620. [PMID: 37131717 PMCID: PMC10153228 DOI: 10.1101/2023.04.20.537620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
During embryonic development, pluripotent cells assume specialized identities by adopting particular gene expression profiles. However, systematically dissecting the underlying regulation of mRNA transcription and degradation remains a challenge, especially within whole embryos with diverse cellular identities. Here, we collect temporal cellular transcriptomes of zebrafish embryos, and decompose them into their newly-transcribed (zygotic) and pre-existing (maternal) mRNA components by combining single-cell RNA-Seq and metabolic labeling. We introduce kinetic models capable of quantifying regulatory rates of mRNA transcription and degradation within individual cell types during their specification. These reveal different regulatory rates between thousands of genes, and sometimes between cell types, that shape spatio-temporal expression patterns. Transcription drives most cell-type restricted gene expression. However, selective retention of maternal transcripts helps to define the gene expression profiles of germ cells and enveloping layer cells, two of the earliest specified cell-types. Coordination between transcription and degradation restricts expression of maternal-zygotic genes to specific cell types or times, and allows the emergence of spatio-temporal patterns when overall mRNA levels are held relatively constant. Sequence-based analysis links differences in degradation to specific sequence motifs. Our study reveals mRNA transcription and degradation events that control embryonic gene expression, and provides a quantitative approach to study mRNA regulation during a dynamic spatio-temporal response.
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Affiliation(s)
- Lior Fishman
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Gal Nechooshtan
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Florian Erhard
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Aviv Regev
- Department of Biology, MIT, Cambridge MA 02139, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, 20814, USA
| | - Michal Rabani
- Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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58
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Sur A, Wang Y, Capar P, Margolin G, Farrell JA. Single-cell analysis of shared signatures and transcriptional diversity during zebrafish development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533545. [PMID: 36993555 PMCID: PMC10055256 DOI: 10.1101/2023.03.20.533545] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
During development, animals generate distinct cell populations with specific identities, functions, and morphologies. We mapped transcriptionally distinct populations across 489,686 cells from 62 stages during wild-type zebrafish embryogenesis and early larval development (3-120 hours post-fertilization). Using these data, we identified the limited catalog of gene expression programs reused across multiple tissues and their cell-type-specific adaptations. We also determined the duration each transcriptional state is present during development and suggest new long-term cycling populations. Focused analyses of non-skeletal muscle and the endoderm identified transcriptional profiles of understudied cell types and subpopulations, including the pneumatic duct, individual intestinal smooth muscle layers, spatially distinct pericyte subpopulations, and homologs of recently discovered human best4+ enterocytes. The transcriptional regulators of these populations remain unknown, so we reconstructed gene expression trajectories to suggest candidates. To enable additional discoveries, we make this comprehensive transcriptional atlas of early zebrafish development available through our website, Daniocell.
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Affiliation(s)
- Abhinav Sur
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814
| | - Yiqun Wang
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
| | - Paulina Capar
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814
| | - Gennady Margolin
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20814
| | - Jeffrey A. Farrell
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD 20814
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59
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Mattis KK, Krentz NAJ, Metzendorf C, Abaitua F, Spigelman AF, Sun H, Ikle JM, Thaman S, Rottner AK, Bautista A, Mazzaferro E, Perez-Alcantara M, Manning Fox JE, Torres JM, Wesolowska-Andersen A, Yu GZ, Mahajan A, Larsson A, MacDonald PE, Davies B, den Hoed M, Gloyn AL. Loss of RREB1 in pancreatic beta cells reduces cellular insulin content and affects endocrine cell gene expression. Diabetologia 2023; 66:674-694. [PMID: 36633628 PMCID: PMC9947029 DOI: 10.1007/s00125-022-05856-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/17/2022] [Indexed: 01/13/2023]
Abstract
AIMS/HYPOTHESIS Genome-wide studies have uncovered multiple independent signals at the RREB1 locus associated with altered type 2 diabetes risk and related glycaemic traits. However, little is known about the function of the zinc finger transcription factor Ras-responsive element binding protein 1 (RREB1) in glucose homeostasis or how changes in its expression and/or function influence diabetes risk. METHODS A zebrafish model lacking rreb1a and rreb1b was used to study the effect of RREB1 loss in vivo. Using transcriptomic and cellular phenotyping of a human beta cell model (EndoC-βH1) and human induced pluripotent stem cell (hiPSC)-derived beta-like cells, we investigated how loss of RREB1 expression and activity affects pancreatic endocrine cell development and function. Ex vivo measurements of human islet function were performed in donor islets from carriers of RREB1 type 2 diabetes risk alleles. RESULTS CRISPR/Cas9-mediated loss of rreb1a and rreb1b function in zebrafish supports an in vivo role for the transcription factor in beta cell mass, beta cell insulin expression and glucose levels. Loss of RREB1 also reduced insulin gene expression and cellular insulin content in EndoC-βH1 cells and impaired insulin secretion under prolonged stimulation. Transcriptomic analysis of RREB1 knockdown and knockout EndoC-βH1 cells supports RREB1 as a novel regulator of genes involved in insulin secretion. In vitro differentiation of RREB1KO/KO hiPSCs revealed dysregulation of pro-endocrine cell genes, including RFX family members, suggesting that RREB1 also regulates genes involved in endocrine cell development. Human donor islets from carriers of type 2 diabetes risk alleles in RREB1 have altered glucose-stimulated insulin secretion ex vivo, consistent with a role for RREB1 in regulating islet cell function. CONCLUSIONS/INTERPRETATION Together, our results indicate that RREB1 regulates beta cell function by transcriptionally regulating the expression of genes involved in beta cell development and function.
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Affiliation(s)
- Katia K Mattis
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nicole A J Krentz
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Christoph Metzendorf
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Fernando Abaitua
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Aliya F Spigelman
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Han Sun
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Jennifer M Ikle
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Swaraj Thaman
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Antje K Rottner
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Austin Bautista
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Eugenia Mazzaferro
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | | | - Jocelyn E Manning Fox
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jason M Torres
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | - Grace Z Yu
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | - Anubha Mahajan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Genentech, South San Francisco, CA, USA
| | - Anders Larsson
- Department of Medical Sciences, Clinical Chemistry, Uppsala University, Uppsala, Sweden
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Benjamin Davies
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Marcel den Hoed
- Beijer Laboratory and Department of Immunology, Genetics and Pathology, Uppsala University and SciLifeLab, Uppsala, Sweden
| | - Anna L Gloyn
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK.
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Division of Endocrinology, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
- Oxford NIHR Biomedical Research Centre, Churchill Hospital, Oxford, UK.
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60
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Verwilligen RAF, Mulder L, Araújo PM, Carneiro M, Bussmann J, Hoekstra M, Van Eck M. Zebrafish as outgroup model to study evolution of scavenger receptor class B type I functions. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159308. [PMID: 36931457 DOI: 10.1016/j.bbalip.2023.159308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/26/2023] [Accepted: 02/25/2023] [Indexed: 03/17/2023]
Abstract
BACKGROUND AND AIMS Scavenger receptor class B1 (SCARB1) - also known as the high-density lipoprotein (HDL) receptor - is a multi-ligand scavenger receptor that is primarily expressed in liver and steroidogenic organs. This receptor is known for its function in reverse cholesterol transport (RCT) in mammals and hence disruption leads to a massive increase in HDL cholesterol in these species. The extracellular domain of SCARB1 - which is important for cholesterol handling - is highly conserved across multiple vertebrates, except in zebrafish. METHODS To examine the functional conservation of SCARB1 among vertebrates, two stable scarb1 knockout zebrafish lines, scarb1 715delA (scarb1 -1 nt) and scarb1 715_716insGG (scarb1 +2 nt), were created using CRISPR-Cas9 technology. RESULTS We demonstrate that, in zebrafish, SCARB1 deficiency leads to disruption of carotenoid-based pigmentation, reduced fertility, and a decreased larvae survival rate, whereas steroidogenesis was unaltered. The observed reduced fertility is driven by defects in female fertility (-50 %, p < 0.001). Importantly, these alterations were independent of changes in free (wild-type 2.4 ± 0.2 μg/μl versus scarb1-/- 2.0 ± 0.1 μg/μl) as well as total (wild-type 4.2 ± 0.4 μg/μl versus scarb1-/- 4.0 ± 0.3 μg/μl) plasma cholesterol levels. Uptake of HDL in the liver of scarb1-/- zebrafish larvae was reduced (-86.7 %, p < 0.001), but this coincided with reduced perfusion of the liver. No effect was observed on lipoprotein uptake in the caudal vein. SCARB1 deficient canaries, which also lack carotenoids in their plumage, similarly as scarb1-/- zebrafish, failed to show an increase in plasma free- and total cholesterol levels. CONCLUSION Our findings suggest that the specific function of SCARB1 in maintaining plasma cholesterol could be an evolutionary novelty that became prominent in mammals, while other known functions were already present earlier during vertebrate evolution.
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Affiliation(s)
- Robin A F Verwilligen
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands.
| | - Lindsay Mulder
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Pedro M Araújo
- University of Coimbra, MARE - Marine and Environmental Sciences Centre, Department Life Sciences, Coimbra, Portugal; CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Miguel Carneiro
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Vairão, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Vairão, Portugal
| | - Jeroen Bussmann
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands
| | - Menno Hoekstra
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Pharmacy Leiden, Leiden, the Netherlands
| | - Miranda Van Eck
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Division of Systems Pharmacology and Pharmacy, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, the Netherlands; Pharmacy Leiden, Leiden, the Netherlands
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61
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Goldblatt D, Huang S, Greaney MR, Hamling KR, Voleti V, Perez-Campos C, Patel KB, Li W, Hillman EMC, Bagnall MW, Schoppik D. Neuronal birthdate reveals topography in a vestibular brainstem circuit for gaze stabilization. Curr Biol 2023; 33:1265-1281.e7. [PMID: 36924768 PMCID: PMC10089979 DOI: 10.1016/j.cub.2023.02.048] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/03/2023] [Accepted: 02/15/2023] [Indexed: 03/17/2023]
Abstract
Across the nervous system, neurons with similar attributes are topographically organized. This topography reflects developmental pressures. Oddly, vestibular (balance) nuclei are thought to be disorganized. By measuring activity in birthdated neurons, we revealed a functional map within the central vestibular projection nucleus that stabilizes gaze in the larval zebrafish. We first discovered that both somatic position and stimulus selectivity follow projection neuron birthdate. Next, with electron microscopy and loss-of-function assays, we found that patterns of peripheral innervation to projection neurons were similarly organized by birthdate. Finally, birthdate revealed spatial patterns of axonal arborization and synapse formation to projection neuron outputs. Collectively, we find that development reveals previously hidden organization to the input, processing, and output layers of a highly conserved vertebrate sensorimotor circuit. The spatial and temporal attributes we uncover constrain the developmental mechanisms that may specify the fate, function, and organization of vestibulo-ocular reflex neurons. More broadly, our data suggest that, like invertebrates, temporal mechanisms may assemble vertebrate sensorimotor architecture.
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Affiliation(s)
- Dena Goldblatt
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10004, USA
| | - Stephanie Huang
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; Center for Neural Science, New York University, New York, NY 10004, USA
| | - Marie R Greaney
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA; University of Chicago, Chicago, IL 60637, USA
| | - Kyla R Hamling
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Venkatakaushik Voleti
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Citlali Perez-Campos
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kripa B Patel
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Wenze Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Elizabeth M C Hillman
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Martha W Bagnall
- Department of Neuroscience, Washington University, St. Louis, MO 63130, USA
| | - David Schoppik
- Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA.
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62
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Rovira M, Miserocchi M, Montanari A, Hammou L, Chomette L, Pozo J, Imbault V, Bisteau X, Wittamer V. Zebrafish Galectin 3 binding protein is the target antigen of the microglial 4C4 monoclonal antibody. Dev Dyn 2023; 252:400-414. [PMID: 36285351 DOI: 10.1002/dvdy.549] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 09/15/2022] [Accepted: 10/16/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Two decades ago, the fish-specific monoclonal antibody 4C4 was found to be highly reactive to zebrafish microglia, the macrophages of the central nervous system. This has resulted in 4C4 being widely used, in combination with available fluorescent transgenic reporters to identify and isolate microglia. However, the target protein of 4C4 remains unidentified, which represents a major caveat. In addition, whether the 4C4 expression pattern is strictly restricted to microglial cells in zebrafish has never been investigated. RESULTS Having demonstrated that 4C4 is able to capture its native antigen from adult brain lysates, we used immunoprecipitation/mass-spectrometry, coupled to recombinant expression analyses, to identify its target. The cognate antigen was found to be a paralog of Galectin 3 binding protein (Lgals3bpb), known as MAC2-binding protein in mammals. Notably, 4C4 did not recognize other paralogs, demonstrating specificity. Moreover, our data show that Lgals3bpb expression, while ubiquitous in microglia, also identifies leukocytes in the periphery, including populations of gut and liver macrophages. CONCLUSIONS The 4C4 monoclonal antibody recognizes Lgals3bpb, a predicted highly glycosylated protein whose function in the microglial lineage is currently unknown. Identification of Lgals3bpb as a new pan-microglia marker will be fundamental in forthcoming studies using the zebrafish model.
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Affiliation(s)
- Mireia Rovira
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Magali Miserocchi
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Alice Montanari
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Latifa Hammou
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Laura Chomette
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Jennifer Pozo
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Virginie Imbault
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Xavier Bisteau
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Valérie Wittamer
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
- ULB Neuroscience Institute (UNI), Université Libre de Bruxelles (ULB), Bruxelles, Belgium
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63
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Elworthy S, Rutherford HA, Prajsnar TK, Hamilton NM, Vogt K, Renshaw SA, Condliffe AM. Activated PI3K delta syndrome 1 mutations cause neutrophilia in zebrafish larvae. Dis Model Mech 2023; 16:dmm049841. [PMID: 36805642 PMCID: PMC10655814 DOI: 10.1242/dmm.049841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
People with activated PI3 kinase delta syndrome 1 (APDS1) suffer from immune deficiency and severe bronchiectasis. APDS1 is caused by dominant activating mutations of the PIK3CD gene that encodes the PI3 kinase delta (PI3Kδ) catalytic subunit. Despite the importance of innate immunity defects in bronchiectasis, there has been limited investigation of neutrophils or macrophages in APDS1 patients or mouse models. Zebrafish embryos provide an ideal system to study neutrophils and macrophages. We used CRISPR-Cas9 and CRISPR-Cpf1, with oligonucleotide-directed homologous repair, to engineer zebrafish equivalents of the two most prevalent human APDS1 disease mutations. These zebrafish pik3cd alleles dominantly caused excessive neutrophilic inflammation in a tail-fin injury model. They also resulted in total body neutrophilia in the absence of any inflammatory stimulus but normal numbers of macrophages. Exposure of zebrafish to the PI3Kδ inhibitor CAL-101 reversed the total body neutrophilia. There was no apparent defect in neutrophil maturation or migration, and tail-fin regeneration was unimpaired. Overall, the finding is of enhanced granulopoeisis, in the absence of notable phenotypic change in neutrophils and macrophages.
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Affiliation(s)
- Stone Elworthy
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
| | - Holly A. Rutherford
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
| | - Tomasz K. Prajsnar
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
- Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research, Jagiellonian University, Gronostajowa 9, 30-387 Krakow, Poland
| | - Noémie M. Hamilton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
| | - Katja Vogt
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
| | - Stephen A. Renshaw
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
| | - Alison M. Condliffe
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield S10 2TN, UK
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64
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Massaquoi MS, Kong GL, Chilin-Fuentes D, Ngo JS, Horve PF, Melancon E, Hamilton MK, Eisen JS, Guillemin K. Cell-type-specific responses to the microbiota across all tissues of the larval zebrafish. Cell Rep 2023; 42:112095. [PMID: 36787219 PMCID: PMC10423310 DOI: 10.1016/j.celrep.2023.112095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/22/2022] [Accepted: 01/25/2023] [Indexed: 02/15/2023] Open
Abstract
Animal development proceeds in the presence of intimate microbial associations, but the extent to which different host cells across the body respond to resident microbes remains to be fully explored. Using the vertebrate model organism, the larval zebrafish, we assessed transcriptional responses to the microbiota across the entire body at single-cell resolution. We find that cell types across the body, not limited to tissues at host-microbe interfaces, respond to the microbiota. Responses are cell-type-specific, but across many tissues the microbiota enhances cell proliferation, increases metabolism, and stimulates a diversity of cellular activities, revealing roles for the microbiota in promoting developmental plasticity. This work provides a resource for exploring transcriptional responses to the microbiota across all cell types of the vertebrate body and generating new hypotheses about the interactions between vertebrate hosts and their microbiota.
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Affiliation(s)
- Michelle S Massaquoi
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Thermo Fisher Scientific, 29851 Willow Creek Road, Eugene, OR 97402, USA; Thermo Fisher Scientific, 22025 20th Avenue SE, Bothell, WA 98021, USA
| | - Garth L Kong
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Daisy Chilin-Fuentes
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Julia S Ngo
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Patrick F Horve
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA
| | - Ellie Melancon
- Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - M Kristina Hamilton
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA; Thermo Fisher Scientific, 29851 Willow Creek Road, Eugene, OR 97402, USA
| | - Judith S Eisen
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Institute of Neuroscience, University of Oregon, 1254 University of Oregon, Eugene, OR 97403, USA
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, 1318 Franklin Boulevard, Eugene, OR 97403, USA; Humans and the Microbiome Program, CIFAR, Toronto, ON M5G 1M1, Canada.
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65
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Quint WH, Tadema KCD, Kokke NCCJ, Meester-Smoor MA, Miller AC, Willemsen R, Klaver CCW, Iglesias AI. Post-GWAS screening of candidate genes for refractive error in mutant zebrafish models. Sci Rep 2023; 13:2017. [PMID: 36737489 PMCID: PMC9898536 DOI: 10.1038/s41598-023-28944-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Genome-wide association studies (GWAS) have dissected numerous genetic factors underlying refractive errors (RE) such as myopia. Despite significant insights into understanding the genetic architecture of RE, few studies have validated and explored the functional role of candidate genes within these loci. To functionally follow-up on GWAS and characterize the potential role of candidate genes on the development of RE, we prioritized nine genes (TJP2, PDE11A, SHISA6, LAMA2, LRRC4C, KCNQ5, GNB3, RBFOX1, and GRIA4) based on biological and statistical evidence; and used CRISPR/cas9 to generate knock-out zebrafish mutants. These mutant fish were screened for abnormalities in axial length by spectral-domain optical coherence tomography and refractive status by eccentric photorefraction at the juvenile (2 months) and adult (4 months) developmental stage. We found a significantly increased axial length and myopic shift in refractive status in three of our studied mutants, indicating a potential involvement of the human orthologs (LAMA2, LRRC4C, and KCNQ5) in myopia development. Further, in-situ hybridization studies showed that all three genes are expressed throughout the zebrafish retina. Our zebrafish models provide evidence of a functional role of these three genes in refractive error development and offer opportunities to elucidate pathways driving the retina-to-sclera signaling cascade that leads to myopia.
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Affiliation(s)
- Wim H Quint
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Kirke C D Tadema
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nina C C J Kokke
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Magda A Meester-Smoor
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adam C Miller
- Institute of Neuroscience, University of Oregon, Eugene, USA
| | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Adriana I Iglesias
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands.
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66
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Bomkamp C, Musgrove L, Marques DMC, Fernando GF, Ferreira FC, Specht EA. Differentiation and Maturation of Muscle and Fat Cells in Cultivated Seafood: Lessons from Developmental Biology. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:1-29. [PMID: 36374393 PMCID: PMC9931865 DOI: 10.1007/s10126-022-10174-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Cultivated meat, also known as cultured or cell-based meat, is meat produced directly from cultured animal cells rather than from a whole animal. Cultivated meat and seafood have been proposed as a means of mitigating the substantial harms associated with current production methods, including damage to the environment, antibiotic resistance, food security challenges, poor animal welfare, and-in the case of seafood-overfishing and ecological damage associated with fishing and aquaculture. Because biomedical tissue engineering research, from which cultivated meat draws a great deal of inspiration, has thus far been conducted almost exclusively in mammals, cultivated seafood suffers from a lack of established protocols for producing complex tissues in vitro. At the same time, fish such as the zebrafish Danio rerio have been widely used as model organisms in developmental biology. Therefore, many of the mechanisms and signaling pathways involved in the formation of muscle, fat, and other relevant tissue are relatively well understood for this species. The same processes are understood to a lesser degree in aquatic invertebrates. This review discusses the differentiation and maturation of meat-relevant cell types in aquatic species and makes recommendations for future research aimed at recapitulating these processes to produce cultivated fish and shellfish.
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Affiliation(s)
- Claire Bomkamp
- Department of Science & Technology, The Good Food Institute, Washington, DC USA
| | - Lisa Musgrove
- University of the Sunshine Coast, Sippy Downs, Queensland Australia
| | - Diana M. C. Marques
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Gonçalo F. Fernando
- Department of Science & Technology, The Good Food Institute, Washington, DC USA
| | - Frederico C. Ferreira
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Elizabeth A. Specht
- Department of Science & Technology, The Good Food Institute, Washington, DC USA
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67
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Ma Y, Hui KL, Gelashvili Z, Niethammer P. Oxoeicosanoid signaling mediates early antimicrobial defense in zebrafish. Cell Rep 2023; 42:111974. [PMID: 36640321 PMCID: PMC9973399 DOI: 10.1016/j.celrep.2022.111974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 10/19/2022] [Accepted: 12/23/2022] [Indexed: 01/11/2023] Open
Abstract
5-oxoETE is a bioactive lipid derived from arachidonic acid generated when phospholipase A2 activation coincides with oxidative stress. Through its G protein-coupled receptor OXER1, pure 5-oxoETE is a potent leukocyte chemoattractant. Yet, its physiological function has remained elusive owing to the unusual OXER1 conservation pattern. OXER1 is conserved from fish to primates but not in rodents, precluding genetic loss-of-function studies in mouse. To determine its physiological role, we combine transcriptomic, lipidomic, and intravital imaging assays with genetic perturbations of the OXER1 ortholog hcar1-4 in zebrafish. Pseudomonas aeruginosa infection induces the synthesis of 5-oxoETE and its receptor, along with other inflammatory pathways. Hcar1-4 deletion attenuates neutrophil recruitment and decreases post-infection survival, which could be rescued by ectopic expression of hcar1-4 or human OXER1. By revealing 5-oxoETE as dominant lipid regulator of the early antimicrobial response in a non-rodent vertebrate, our work expands the current, rodent-centric view of early inflammation.
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Affiliation(s)
- Yanan Ma
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - King Lam Hui
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Zaza Gelashvili
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA,Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Philipp Niethammer
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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68
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Stress resilience is established during development and is regulated by complement factors. Cell Rep 2023; 42:111973. [PMID: 36640352 DOI: 10.1016/j.celrep.2022.111973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 11/21/2022] [Accepted: 12/23/2022] [Indexed: 01/13/2023] Open
Abstract
Individuals in a population respond differently to stressful situations. While resilient individuals recover efficiently, others are susceptible to the same stressors. However, it remains challenging to determine if resilience is established as a trait during development or acquired later in life. Using a behavioral paradigm in zebrafish larvae, we show that resilience is a stable and heritable trait, which is determined and exhibited early in life. Resilient larvae show unique stress-induced transcriptional response, and larvae with mutations in resilience-associated genes, such as neuropeptide Y and miR218, are less resilient. Transcriptome analysis shows that resilient larvae downregulate multiple factors of the innate immune complement cascade in response to stress. Perturbation of critical complement factors leads to an increase in resilience. We conclude that resilience is established as a stable trait early during development and that neuropeptides and the complement pathway play positive and negative roles in determining resilience, respectively.
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69
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Kim YI, O’Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525932. [PMID: 36747868 PMCID: PMC9900950 DOI: 10.1101/2023.01.27.525932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual mature rhombomeres requires resolution of mixed transcription and chromatin states.
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Affiliation(s)
| | | | - Charles G. Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO 80045
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70
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Wang R, Zhang P, Wang J, Ma L, E W, Suo S, Jiang M, Li J, Chen H, Sun H, Fei L, Zhou Z, Zhou Y, Chen Y, Zhang W, Wang X, Mei Y, Sun Z, Yu C, Shao J, Fu Y, Xiao Y, Ye F, Fang X, Wu H, Guo Q, Fang X, Li X, Gao X, Wang D, Xu PF, Zeng R, Xu G, Zhu L, Wang L, Qu J, Zhang D, Ouyang H, Huang H, Chen M, NG SC, Liu GH, Yuan GC, Guo G, Han X. Construction of a cross-species cell landscape at single-cell level. Nucleic Acids Res 2023; 51:501-516. [PMID: 35929025 PMCID: PMC9881150 DOI: 10.1093/nar/gkac633] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 02/06/2023] Open
Abstract
Individual cells are basic units of life. Despite extensive efforts to characterize the cellular heterogeneity of different organisms, cross-species comparisons of landscape dynamics have not been achieved. Here, we applied single-cell RNA sequencing (scRNA-seq) to map organism-level cell landscapes at multiple life stages for mice, zebrafish and Drosophila. By integrating the comprehensive dataset of > 2.6 million single cells, we constructed a cross-species cell landscape and identified signatures and common pathways that changed throughout the life span. We identified structural inflammation and mitochondrial dysfunction as the most common hallmarks of organism aging, and found that pharmacological activation of mitochondrial metabolism alleviated aging phenotypes in mice. The cross-species cell landscape with other published datasets were stored in an integrated online portal-Cell Landscape. Our work provides a valuable resource for studying lineage development, maturation and aging.
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Affiliation(s)
- Renying Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Peijing Zhang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Jingjing Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Lifeng Ma
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Weigao E
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | | | - Mengmeng Jiang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Jiaqi Li
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Haide Chen
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Huiyu Sun
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Lijiang Fei
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ziming Zhou
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yincong Zhou
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yao Chen
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing 100101, China
| | - Xinru Wang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yuqing Mei
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Zhongyi Sun
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Chengxuan Yu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Jikai Shao
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yuting Fu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Yanyu Xiao
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Fang Ye
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xing Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Hanyu Wu
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Qile Guo
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
| | - Xiunan Fang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xia Li
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Xianzhi Gao
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Dan Wang
- Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Peng-Fei Xu
- Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Rui Zeng
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Gang Xu
- Division of Nephrology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Lijun Zhu
- Zhejiang Provincial Key Laboratory for Diagnosis and Treatment of Aging and Physic-chemical Injury Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Lie Wang
- Institute of Immunology and Bone Marrow Transplantation Center, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jing Qu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, PR China
| | - Hongwei Ouyang
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - He Huang
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shyh-Chang NG
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guang-Hui Liu
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, NY, NY 10029, USA
| | - Guoji Guo
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 314400, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoping Han
- Center for Stem Cell and Regenerative Medicine, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310000, China
- Zhejiang Provincial Key Lab for Tissue Engineering and Regenerative Medicine, Dr. Li Dak Sum & Yip Yio Chin Center for Stem Cell and Regenerative Medicine, Hangzhou, Zhejiang 310058, China
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71
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Haws W, England S, Grieb G, Susana G, Hernandez S, Mirer H, Lewis K. Analyses of binding partners and functional domains for the developmentally essential protein Hmx3a/HMX3. Sci Rep 2023; 13:1151. [PMID: 36670152 PMCID: PMC9859826 DOI: 10.1038/s41598-023-27878-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/09/2023] [Indexed: 01/22/2023] Open
Abstract
HMX3 is a homeodomain protein with essential roles in CNS and ear development. Homeodomains are DNA-binding domains and hence homeodomain-containing proteins are usually assumed to be transcription factors. However, intriguingly, our recent data suggest that zebrafish Hmx3a may not require its homeodomain to function, raising the important question of what molecular interactions mediate its effects. To investigate this, we performed a yeast two-hybrid screen and identified 539 potential binding partners of mouse HMX3. Using co-immunoprecipitation, we tested whether a prioritized subset of these interactions are conserved in zebrafish and found that Tle3b, Azin1b, Prmt2, Hmgb1a, and Hmgn3 bind Hmx3a. Next, we tested whether these proteins bind the products of four distinct hmx3a mutant alleles that all lack the homeodomain. Embryos homozygous for two of these alleles develop abnormally and die, whereas zebrafish homozygous for the other two alleles are viable. We found that all four mutations abrogate binding to Prmt2 and Tle3b, whereas Azin1b binding was preserved in all cases. Interestingly, Hmgb1a and Hmgn3 had more affinity for products of the viable mutant alleles. These data shed light on how HMX3/Hmx3a might function at a molecular level and identify new targets for future study in these vital developmental processes.
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Affiliation(s)
- William Haws
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Samantha England
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Ginny Grieb
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Gabriela Susana
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Sophie Hernandez
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Hunter Mirer
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA
| | - Katharine Lewis
- Department of Biology, Syracuse University, 107 College Place, Syracuse, NY, 13244, USA.
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72
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Luderman LN, Michaels MT, Levic DS, Knapik EW. Zebrafish Erc1b mediates motor innervation and organization of craniofacial muscles in control of jaw movement. Dev Dyn 2023; 252:104-123. [PMID: 35708710 DOI: 10.1002/dvdy.511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Movement of the lower jaw, a common behavior observed among vertebrates, is required for eating and processing food. This movement is controlled by signals sent from the trigeminal motor nerve through neuromuscular junctions (NMJs) to the masticatory muscles. Dysfunctional jaw movements contribute to craniomandibular disorders, yet the pathophysiology of these disorders is not well understood, as limited studies have been conducted on the molecular mechanisms of jaw movement. RESULTS Using erc1b/kimm533 genetic loss of function mutant, we evaluated lower jaw muscle organization and innervation by the cranial motor nerves in developing zebrafish. Using time-lapse confocal imaging of the erc1b mutant in a transgenic fluorescent reporter line, we found delayed trigeminal nerve growth and disrupted nerve branching architecture during muscle innervation. By automated 3D image analysis of NMJ distribution, we identified an increased number of small, disorganized NMJ clusters in erc1b mutant larvae compared to WT siblings. Using genetic replacement experiments, we determined the Rab GTPase binding domain of Erc1b is required for cranial motor nerve branching, but not NMJ organization or muscle attachment. CONCLUSIONS We identified Erc1b/ERC1 as a novel component of a genetic pathway contributing to muscle organization, trigeminal nerve outgrowth, and NMJ spatial distribution during development that is required for jaw movement.
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Affiliation(s)
- Lauryn N Luderman
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
| | - Mackenzie T Michaels
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel S Levic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
- Neuroscience Graduate Program, Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee, USA
| | - Ela W Knapik
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
- Department of Cell Biology, Duke University Medical Center, Durham, North Carolina, USA
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73
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Lagman D, Haines HJ, Abalo XM, Larhammar D. Ancient multiplicity in cyclic nucleotide-gated (CNG) cation channel repertoire was reduced in the ancestor of Olfactores before re-expansion by whole genome duplications in vertebrates. PLoS One 2022; 17:e0279548. [PMID: 36584110 PMCID: PMC9803222 DOI: 10.1371/journal.pone.0279548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/09/2022] [Indexed: 12/31/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) cation channels are important heterotetrameric proteins in the retina, with different subunit composition in cone and rod photoreceptor cells: three CNGA3 and one CNGB3 in cones and three CNGA1 and one CNGB1 in rods. CNGA and CNGB subunits form separate subfamilies. We have analyzed the evolution of the CNG gene family in metazoans, with special focus on vertebrates by using sequence-based phylogeny and conservation of chromosomal synteny to deduce paralogons resulting from the early vertebrate whole genome duplications (WGDs). Our analyses show, unexpectedly, that the CNGA subfamily had four sister subfamilies in the ancestor of bilaterians and cnidarians that we named CNGC, CNGD, CNGE and CNGF. Of these, CNGC, CNGE and CNGF were lost in the ancestor of Olfactores while CNGD was lost in the vertebrate ancestor. The remaining CNGA and CNGB genes were expanded by a local duplication of CNGA and the subsequent chromosome duplications in the basal vertebrate WGD events. Upon some losses, this resulted in the gnathostome ancestor having three members in the visual CNGA subfamily (CNGA1-3), a single CNGA4 gene, and two members in the CNGB subfamily (CNGB1 and CNGB3). The nature of chromosomal rearrangements in the vertebrate CNGA paralogon was resolved by including the genomes of a non-teleost actinopterygian and an elasmobranch. After the teleost-specific WGD, additional duplicates were generated and retained for CNGA1, CNGA2, CNGA3 and CNGB1. Furthermore, teleosts retain a local duplicate of CNGB3. The retention of duplicated CNG genes is explained by their subfunctionalisation and photoreceptor-specific expression. In conclusion, this study provides evidence for four previously unknown CNG subfamilies in metazoans and further evidence that the early vertebrate WGD events were instrumental in the evolution of the vertebrate visual and central nervous systems.
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Affiliation(s)
- David Lagman
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
- * E-mail:
| | - Helen J. Haines
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Xesús M. Abalo
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Dan Larhammar
- Science for Life Laboratory, Department of Medical Cell Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
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74
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Bearce EA, Irons ZH, O'Hara-Smith JR, Kuhns CJ, Fisher SI, Crow WE, Grimes DT. Urotensin II-related peptides, Urp1 and Urp2, control zebrafish spine morphology. eLife 2022; 11:e83883. [PMID: 36453722 PMCID: PMC9836392 DOI: 10.7554/elife.83883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
The spine provides structure and support to the body, yet how it develops its characteristic morphology as the organism grows is little understood. This is underscored by the commonality of conditions in which the spine curves abnormally such as scoliosis, kyphosis, and lordosis. Understanding the origin of these spinal curves has been challenging in part due to the lack of appropriate animal models. Recently, zebrafish have emerged as promising tools with which to understand the origin of spinal curves. Using zebrafish, we demonstrate that the urotensin II-related peptides (URPs), Urp1 and Urp2, are essential for maintaining spine morphology. Urp1 and Urp2 are 10-amino acid cyclic peptides expressed by neurons lining the central canal of the spinal cord. Upon combined genetic loss of Urp1 and Urp2, adolescent-onset planar curves manifested in the caudal region of the spine. Highly similar curves were caused by mutation of Uts2r3, an URP receptor. Quantitative comparisons revealed that urotensin-associated curves were distinct from other zebrafish spinal curve mutants in curve position and direction. Last, we found that the Reissner fiber, a proteinaceous thread that sits in the central canal and has been implicated in the control of spine morphology, breaks down prior to curve formation in mutants with perturbed cilia motility but was unaffected by loss of Uts2r3. This suggests a Reissner fiber-independent mechanism of curvature in urotensin-deficient mutants. Overall, our results show that Urp1 and Urp2 control zebrafish spine morphology and establish new animal models of spine deformity.
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Affiliation(s)
- Elizabeth A Bearce
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - Zoe H Irons
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | | | - Colin J Kuhns
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - Sophie I Fisher
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - William E Crow
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
| | - Daniel T Grimes
- Institute of Molecular Biology, Department of Biology, University of OregonEugeneUnited States
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75
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Zhao M, Lin XH, Zeng YH, Su HZ, Wang C, Yang K, Chen YK, Lin BW, Yao XP, Chen WJ. Knockdown of myorg leads to brain calcification in zebrafish. Mol Brain 2022; 15:65. [PMID: 35870928 PMCID: PMC9308368 DOI: 10.1186/s13041-022-00953-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 07/09/2022] [Indexed: 11/17/2022] Open
Abstract
Primary familial brain calcification (PFBC) is a neurogenetic disorder characterized by bilateral calcified deposits in the brain. We previously identified that MYORG as the first pathogenic gene for autosomal recessive PFBC, and established a Myorg-KO mouse model. However, Myorg-KO mice developed brain calcifications until nine months of age, which limits their utility as a facile PFBC model system. Hence, whether there is another typical animal model for mimicking PFBC phenotypes in an early stage still remained unknown. In this study, we profiled the mRNA expression pattern of myorg in zebrafish, and used a morpholino-mediated blocking strategy to knockdown myorg mRNA at splicing and translation initiation levels. We observed multiple calcifications throughout the brain by calcein staining at 2–4 days post-fertilization in myorg-deficient zebrafish, and rescued the calcification phenotype by replenishing myorg cDNA. Overall, we built a novel model for PFBC via knockdown of myorg by antisense oligonucleotides in zebrafish, which could shorten the observation period and replenish the Myorg-KO mouse model phenotype in mechanistic and therapeutic studies.
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76
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The CXCR4-CXCL12 axis promotes T cell reconstitution via efficient hematopoietic immigration. J Genet Genomics 2022; 49:1138-1150. [PMID: 35483564 DOI: 10.1016/j.jgg.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/07/2022] [Accepted: 04/13/2022] [Indexed: 01/20/2023]
Abstract
T cells play a critical role in immunity to protect against pathogens and malignant cells. T cell immunodeficiency is detrimental, especially when T cell perturbation occurs during severe infection, irradiation, chemotherapy, and age-related thymic atrophy. Therefore, strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here, we report the construction of a T cell ablation model in Tg(coro1a:DenNTR) zebrafish via metronidazole administration. The nascent T cells are mainly derived from the hematopoietic cells migrated from the kidney, the functional homolog of bone marrow and the complete recovery time is 6.5 days post-treatment. The cxcr4b gene is upregulated in the responsive hematopoietic cells. Functional interference of CXCR4 via both genetic and chemical manipulations does not greatly affect T lymphopoiesis, but delays T cell regeneration by disrupting hematopoietic migration. In contrast, cxcr4b accelerates the replenishment of hematopoietic cells in the thymus. Consistently, Cxcl12b, a ligand of Cxcr4, is increased in the thymic epithelial cells of the injured animals. Decreased or increased expression of Cxcl12b results in compromised or accelerated T cell recovery, respectively, similar to those observed with Cxcr4b. Taken together, our study reveals a role of CXCR4-CXCL12 signaling in promoting T cell recovery and provides a promising target for the treatment of immunodeficiency due to T cell injury.
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77
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Genetic duplication of tissue factor reveals subfunctionalization in venous and arterial hemostasis. PLoS Genet 2022; 18:e1010534. [PMID: 36449521 PMCID: PMC9744294 DOI: 10.1371/journal.pgen.1010534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
Tissue factor (TF) is an evolutionarily conserved protein necessary for initiation of hemostasis. Zebrafish have two copies of the tissue factor gene (f3a and f3b) as the result of an ancestral teleost fish duplication event (so called ohnologs). In vivo physiologic studies of TF function have been difficult given early lethality of TF knockout in the mouse. We used genome editing to produce knockouts of both f3a and f3b in zebrafish. Since ohnologs arose through sub- or neofunctionalization, they can unmask unknown functions of non-teleost genes and could reveal whether mammalian TF has developmental functions distinct from coagulation. Here we show that a single copy of either f3a or f3b is necessary and sufficient for normal lifespan. Complete loss of TF results in lethal hemorrhage by 2-4 months despite normal embryonic and vascular development. Larval vascular endothelial injury reveals predominant roles for TFa in venous circulation and TFb in arterial circulation. Finally, we demonstrate that loss of TF predisposes to a stress-induced cardiac tamponade independent of its role in fibrin formation. Overall, our data suggest partial subfunctionalization of TFa and TFb. This multigenic zebrafish model has the potential to facilitate study of the role of TF in different vascular beds.
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78
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Watson CJ, Tang WJ, Rojas MF, Fiedler IAK, Morfin Montes de Oca E, Cronrath AR, Callies LK, Swearer AA, Ahmed AR, Sethuraman V, Addish S, Farr GH, Gómez AE, Rai J, Monstad-Rios AT, Gardiner EM, Karasik D, Maves L, Busse B, Hsu YH, Kwon RY. wnt16 regulates spine and muscle morphogenesis through parallel signals from notochord and dermomyotome. PLoS Genet 2022; 18:e1010496. [PMID: 36346812 PMCID: PMC9674140 DOI: 10.1371/journal.pgen.1010496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/18/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022] Open
Abstract
Bone and muscle are coupled through developmental, mechanical, paracrine, and autocrine signals. Genetic variants at the CPED1-WNT16 locus are dually associated with bone- and muscle-related traits. While Wnt16 is necessary for bone mass and strength, this fails to explain pleiotropy at this locus. Here, we show wnt16 is required for spine and muscle morphogenesis in zebrafish. In embryos, wnt16 is expressed in dermomyotome and developing notochord, and contributes to larval myotome morphology and notochord elongation. Later, wnt16 is expressed at the ventral midline of the notochord sheath, and contributes to spine mineralization and osteoblast recruitment. Morphological changes in wnt16 mutant larvae are mirrored in adults, indicating that wnt16 impacts bone and muscle morphology throughout the lifespan. Finally, we show that wnt16 is a gene of major effect on lean mass at the CPED1-WNT16 locus. Our findings indicate that Wnt16 is secreted in structures adjacent to developing bone (notochord) and muscle (dermomyotome) where it affects the morphogenesis of each tissue, thereby rendering wnt16 expression into dual effects on bone and muscle morphology. This work expands our understanding of wnt16 in musculoskeletal development and supports the potential for variants to act through WNT16 to influence bone and muscle via parallel morphogenetic processes. In humans, genetic variants (DNA sequences that vary amongst individuals) have been identified that appear to influence two tissues, bone and skeletal muscle. However, how single genes and genetic variants exert dual influence on both tissues is not well understood. In this study, we found that the wnt16 gene is necessary for specifying the size and shape of both muscle and bone during development in zebrafish. We also disentangled how wnt16 affects both tissues: distinct cellular populations adjacent to muscle and bone secrete Wnt16, where it acts as a signal guiding the size and shape of each tissue. This is important because in humans, genetic variants near the WNT16 gene have effects on both bone- and muscle-related traits. This study expands our understanding of the role of WNT16 in bone and muscle development, and helps to explain how genetic variants near WNT16 affect traits for both tissues. Moreover, WNT16 is actively being explored as a target for osteoporosis therapies, thus our study could have implications with regard to the potential of targeting WNT16 to treat bone and muscle simultaneously.
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Affiliation(s)
- Claire J. Watson
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - W. Joyce Tang
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Maria F. Rojas
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Imke A. K. Fiedler
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ernesto Morfin Montes de Oca
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Andrea R. Cronrath
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Lulu K. Callies
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Avery Angell Swearer
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Ali R. Ahmed
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Visali Sethuraman
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Sumaya Addish
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Gist H. Farr
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Arianna Ericka Gómez
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Jyoti Rai
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Adrian T. Monstad-Rios
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - Edith M. Gardiner
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
| | - David Karasik
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, United States of America
| | - Lisa Maves
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, Division of Cardiology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Bjorn Busse
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yi-Hsiang Hsu
- Institute for Aging Research, Hebrew SeniorLife, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and Massachusetts Institute of Technology, Boston, Massachusetts, United States of America
| | - Ronald Young Kwon
- Department of Orthopaedics and Sports Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
- Insitute for Stem Cell and Regenerative Medicines, University of Washington, Seattle Washington, United States of America
- * E-mail:
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79
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Li YF, Cheng T, Zhang YJ, Fu XX, Mo J, Zhao GQ, Xue MG, Zhuo DH, Xing YY, Huang Y, Sun XZ, Wang D, Liu X, Dong Y, Zhu XS, He F, Ma J, Chen D, Jin X, Xu PF. Mycn regulates intestinal development through ribosomal biogenesis in a zebrafish model of Feingold syndrome 1. PLoS Biol 2022; 20:e3001856. [PMID: 36318514 PMCID: PMC9624419 DOI: 10.1371/journal.pbio.3001856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Feingold syndrome type 1, caused by loss-of-function of MYCN, is characterized by varied phenotypes including esophageal and duodenal atresia. However, no adequate model exists for studying the syndrome's pathological or molecular mechanisms, nor is there a treatment strategy. Here, we developed a zebrafish Feingold syndrome type 1 model with nonfunctional mycn, which had severe intestinal atresia. Single-cell RNA-seq identified a subcluster of intestinal cells that were highly sensitive to Mycn, and impaired cell proliferation decreased the overall number of intestinal cells in the mycn mutant fish. Bulk RNA-seq and metabolomic analysis showed that expression of ribosomal genes was down-regulated and that amino acid metabolism was abnormal. Northern blot and ribosomal profiling analysis showed abnormal rRNA processing and decreases in free 40S, 60S, and 80S ribosome particles, which led to impaired translation in the mutant. Besides, both Ribo-seq and western blot analysis showed that mTOR pathway was impaired in mycn mutant, and blocking mTOR pathway by rapamycin treatment can mimic the intestinal defect, and both L-leucine and Rheb, which can elevate translation via activating TOR pathway, could rescue the intestinal phenotype of mycn mutant. In summary, by this zebrafish Feingold syndrome type 1 model, we found that disturbance of ribosomal biogenesis and blockage of protein synthesis during development are primary causes of the intestinal defect in Feingold syndrome type 1. Importantly, our work suggests that leucine supplementation may be a feasible and easy treatment option for this disease.
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Affiliation(s)
- Yun-Fei Li
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Cheng
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying-Jie Zhang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xin-Xin Fu
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Jing Mo
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Guo-Qin Zhao
- Department of Immunology, Guizhou Medical University, Guiyang, China
| | - Mao-Guang Xue
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Ding-Hao Zhuo
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan-Yi Xing
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Huang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Zhi Sun
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Dan Wang
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiang Liu
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Dong
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiao-Sheng Zhu
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
| | - Feng He
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Ma
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dong Chen
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Jin
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- * E-mail: (XJ); (P-FX)
| | - Peng-Fei Xu
- Institute of Genetics and Department of Human Genetics, Zhejiang University School of Medicine, Hangzhou, China
- Women’s Hospital, Zhejiang University School of Medicine, Hangzhou, China
- * E-mail: (XJ); (P-FX)
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80
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Jones EF, Butler MG, Trendafilova D, Mendez MS, Jernigan LA, Gahtan E, Steele J. In vivo tracking of KCC2b expression during early brain development. J Comp Neurol 2022; 531:48-57. [PMID: 36217249 DOI: 10.1002/cne.25411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/03/2022] [Accepted: 08/27/2022] [Indexed: 11/07/2022]
Abstract
The neuronal chloride (Cl-) exporter, KCC2, regulates neuron excitability and development and undergoes a stereotypical pattern of delayed upregulation as neurons mature. KCC2 upregulation favors neural inhibition by establishing a negative Cl- gradient, ensuring GABA-induced Cl- currents are inward and inhibitory. We developed a zebrafish fluorescent reporter line, KCC2b:mCitrine, to track KCC2 expression in vivo during early brain development. KCC2b:mCitrine was first detected at 16 h postfertilization and by day 6 labeled most central and peripheral neurons and processes. At 20 h, expression was greatest in the soma-dense basal neuroepithelium but largely absent in apical and mantle zones where differentiation and migration primarily occur, and time lapse imaging at this stage supports a postmigration upregulation of KCC2b. Central dopamine neurons showed low KCC2b expression as observed in other species. KCC2b:mCitrine fluorescence was stable over minutes in most neurons, but brightness transients observed in single cells fit our expectation for real-time tracking of KCC2b upregulation in new neurons. To further assess whether fluorescence brightness tracks KCC2b expression, zebrafish embryos were exposed to bisphenol-A (BPA), which is known to suppress KCC2 expression. Fluorescence decreased after 6 days of BPA exposure but not after 2 or 4 days, suggesting that it is an accurate but delayed indicator of KCC2b expression. KCC2b:mCitrine zebrafish present a new method for visualizing KCC2b's complex dynamics during brain development, and potentially screening compounds aimed at modulating KCC2 expression.
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Affiliation(s)
- Emma F Jones
- Department of Psychology, Cal Poly Humboldt, Arcata, California, USA.,Department of Biology, Cal Poly Humboldt, Arcata, California, USA
| | | | | | - Mayra S Mendez
- Department of Psychology, Cal Poly Humboldt, Arcata, California, USA
| | - Luke A Jernigan
- Department of Chemistry, Cal Poly Humboldt, Arcata, California, USA
| | - Ethan Gahtan
- Department of Psychology, Cal Poly Humboldt, Arcata, California, USA.,Department of Biology, Cal Poly Humboldt, Arcata, California, USA
| | - John Steele
- Department of Biology, Cal Poly Humboldt, Arcata, California, USA
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81
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Ncube D, Tallafuss A, Serafin J, Bruckner J, Farnsworth DR, Miller AC, Eisen JS, Washbourne P. A conserved transcriptional fingerprint of multi-neurotransmitter neurons necessary for social behavior. BMC Genomics 2022; 23:675. [PMID: 36175871 PMCID: PMC9523972 DOI: 10.1186/s12864-022-08879-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 09/02/2022] [Indexed: 11/11/2022] Open
Abstract
Background An essential determinant of a neuron’s functionality is its neurotransmitter phenotype. We previously identified a defined subpopulation of cholinergic neurons required for social orienting behavior in zebrafish. Results We transcriptionally profiled these neurons and discovered that they are capable of synthesizing both acetylcholine and GABA. We also established a constellation of transcription factors and neurotransmitter markers that can be used as a “transcriptomic fingerprint” to recognize a homologous neuronal population in another vertebrate. Conclusion Our results suggest that this transcriptomic fingerprint and the cholinergic-GABAergic neuronal subtype that it defines are evolutionarily conserved. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08879-w.
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Affiliation(s)
- Denver Ncube
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Alexandra Tallafuss
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Jen Serafin
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Joseph Bruckner
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Dylan R Farnsworth
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Adam C Miller
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Judith S Eisen
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA
| | - Philip Washbourne
- Institute of Neuroscience, 1254 University of Oregon, Eugene, OR, 97403, USA.
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82
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Transcriptional profiling from whole embryos to single neuroblast lineages in Drosophila. Dev Biol 2022; 489:21-33. [PMID: 35660371 PMCID: PMC9805786 DOI: 10.1016/j.ydbio.2022.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/06/2022] [Accepted: 05/25/2022] [Indexed: 01/03/2023]
Abstract
Embryonic development results in the production of distinct tissue types, and different cell types within each tissue. A major goal of developmental biology is to uncover the "parts list" of cell types that comprise each organ. Here we perform single cell RNA sequencing (scRNA-seq) of the Drosophila embryo to identify the genes that characterize different cell and tissue types during development. We assay three different timepoints, revealing a coordinated change in gene expression within each tissue. Interestingly, we find that the elav and Mhc genes, whose protein products are widely used as markers for neurons and muscles, respectively, show broad pan-embryonic expression, indicating the importance of post-transcriptional regulation. We next focus on the central nervous system (CNS), where we identify genes whose expression is enriched at each stage of neuronal differentiation: from neural progenitors, called neuroblasts, to their immediate progeny ganglion mother cells (GMCs), followed by new-born neurons, young neurons, and the most mature neurons. Finally, we ask whether the clonal progeny of a single neuroblast (NB7-1) share a similar transcriptional identity. Surprisingly, we find that clonal identity does not lead to transcriptional clustering, showing that neurons within a lineage are diverse, and that neurons with a similar transcriptional profile (e.g. motor neurons, glia) are distributed among multiple neuroblast lineages. Although each lineage consists of diverse progeny, we were able to identify a previously uncharacterized gene, Fer3, as an excellent marker for the NB7-1 lineage. Within the NB7-1 lineage, neurons which share a temporal identity (e.g. Hunchback, Kruppel, Pdm, and Castor temporal transcription factors in the NB7-1 lineage) have shared transcriptional features, allowing for the identification of candidate novel temporal factors or targets of the temporal transcription factors. In conclusion, we have characterized the embryonic transcriptome for all major tissue types and for three stages of development, as well as the first transcriptomic analysis of a single, identified neuroblast lineage, finding a lineage-enriched transcription factor.
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83
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Dillon N, Cocanougher B, Sood C, Yuan X, Kohn AB, Moroz LL, Siegrist SE, Zlatic M, Doe CQ. Single cell RNA-seq analysis reveals temporally-regulated and quiescence-regulated gene expression in Drosophila larval neuroblasts. Neural Dev 2022; 17:7. [PMID: 36002894 PMCID: PMC9404614 DOI: 10.1186/s13064-022-00163-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/19/2022] [Indexed: 12/12/2022] Open
Abstract
The mechanisms that generate neural diversity during development remains largely unknown. Here, we use scRNA-seq methodology to discover new features of the Drosophila larval CNS across several key developmental timepoints. We identify multiple progenitor subtypes - both stem cell-like neuroblasts and intermediate progenitors - that change gene expression across larval development, and report on new candidate markers for each class of progenitors. We identify a pool of quiescent neuroblasts in newly hatched larvae and show that they are transcriptionally primed to respond to the insulin signaling pathway to exit from quiescence, including relevant pathway components in the adjacent glial signaling cell type. We identify candidate "temporal transcription factors" (TTFs) that are expressed at different times in progenitor lineages. Our work identifies many cell type specific genes that are candidates for functional roles, and generates new insight into the differentiation trajectory of larval neurons.
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Affiliation(s)
- Noah Dillon
- Institute of Neuroscience, Howard Hughes Medical Institute, University of Oregon, OR, 97403, Eugene, USA
| | - Ben Cocanougher
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Chhavi Sood
- Department of Biology, University of Virginia, VA, 22904, Charlottesville, USA
| | - Xin Yuan
- Department of Biology, University of Virginia, VA, 22904, Charlottesville, USA
| | - Andrea B Kohn
- Whitney Laboratory for Marine Biosciences, University of Florida, FL, 32080, St. Augustine, USA
| | - Leonid L Moroz
- Whitney Laboratory for Marine Biosciences, University of Florida, FL, 32080, St. Augustine, USA
| | - Sarah E Siegrist
- Department of Biology, University of Virginia, VA, 22904, Charlottesville, USA
| | - Marta Zlatic
- MRC Laboratory of Molecular Biology, Dept of Zoology, University of Cambridge, Cambridge, UK.,Janelia Research Campus, VA, Ashburn, USA
| | - Chris Q Doe
- Institute of Neuroscience, Howard Hughes Medical Institute, University of Oregon, OR, 97403, Eugene, USA.
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84
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Wu L, Xue R, Chen J, Xu J. dock8 deficiency attenuates microglia colonization in early zebrafish larvae. Cell Death Dis 2022; 8:366. [PMID: 35977943 PMCID: PMC9386030 DOI: 10.1038/s41420-022-01155-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/09/2022]
Abstract
Microglia are tissue-resident macrophages that carry out immune functions in the brain. The deficiency or dysfunction of microglia has been implicated in many neurodegenerative disorders. DOCK8, a member of the DOCK family, functions as a guanine nucleotide exchange factor and plays key roles in immune regulation and neurological diseases. The functions of DOCK8 in microglia development are not fully understood. Here, we generated zebrafish dock8 mutants by CRISPR/Cas9 genome editing and showed that dock8 mutations attenuate microglia colonization in the zebrafish midbrain at early larvae stages. In vivo time-lapse imaging revealed that the motility of macrophages was reduced in the dock8 mutant. We further found that cdc42/cdc42l, which encode the small GTPase activated by Dock8, also regulate microglia colonization in zebrafish. Collectively, our study suggests that the Dock8-Cdc42 pathway is required for microglia colonization in zebrafish larvae.
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Affiliation(s)
- Linxiu Wu
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China
| | - Rongtao Xue
- Department of Hematology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, 510515, China
| | - Jiahao Chen
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
| | - Jin Xu
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, 510006, China.
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85
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Annona G, Sato I, Pascual-Anaya J, Osca D, Braasch I, Voss R, Stundl J, Soukup V, Ferrara A, Fontenot Q, Kuratani S, Postlethwait JH, D'Aniello S. Evolution of the nitric oxide synthase family in vertebrates and novel insights in gill development. Proc Biol Sci 2022; 289:20220667. [PMID: 35946155 PMCID: PMC9363997 DOI: 10.1098/rspb.2022.0667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/19/2022] [Indexed: 12/20/2022] Open
Abstract
Nitric oxide (NO) is an ancestral key signalling molecule essential for life and has enormous versatility in biological systems, including cardiovascular homeostasis, neurotransmission and immunity. Although our knowledge of NO synthases (Nos), the enzymes that synthesize NO in vivo, is substantial, the origin of a large and diversified repertoire of nos gene orthologues in fishes with respect to tetrapods remains a puzzle. The recent identification of nos3 in the ray-finned fish spotted gar, which was considered lost in this lineage, changed this perspective. This finding prompted us to explore nos gene evolution, surveying vertebrate species representing key evolutionary nodes. This study provides noteworthy findings: first, nos2 experienced several lineage-specific gene duplications and losses. Second, nos3 was found to be lost independently in two different teleost lineages, Elopomorpha and Clupeocephala. Third, the expression of at least one nos paralogue in the gills of developing shark, bichir, sturgeon, and gar, but not in lamprey, suggests that nos expression in this organ may have arisen in the last common ancestor of gnathostomes. These results provide a framework for continuing research on nos genes' roles, highlighting subfunctionalization and reciprocal loss of function that occurred in different lineages during vertebrate genome duplications.
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Affiliation(s)
- Giovanni Annona
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
| | - Iori Sato
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
| | - Juan Pascual-Anaya
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Department of Animal Biology, Faculty of Sciences, University of Málaga, Spain
- Andalusian Centre for Nanomedicine and Biotechnology (BIONAND), Málaga, Spain
| | - David Osca
- Faculty of Marine Sciences, University Institute of Environmental Studies and Natural Resources (IUNAT), University of Las Palmas de Gran Canaria, Canary Islands, Spain
| | - Ingo Braasch
- Department of Integrative Biology and Program in Ecology, Evolution and Behavior (EEB), Michigan State University, East Lansing, MI 48824, USA
| | - Randal Voss
- Department of Neuroscience, Spinal Cord and Brain Injury Research Center, and Ambystoma Genetic Stock Center, University of Kentucky, Lexington, KY, USA
| | - Jan Stundl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in Ceske Budejovice, Vodnany, Czech Republic
| | - Vladimir Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Allyse Ferrara
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70301, USA
| | - Quenton Fontenot
- Department of Biological Sciences, Nicholls State University, Thibodaux, LA 70301, USA
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research (BDR), Kobe 650-0047, Japan
- Evolutionary Morphology Laboratory, RIKEN Cluster for Pioneering Research (CPR), Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | | | - Salvatore D'Aniello
- Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli 80121, Italy
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86
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Gurung S, Restrepo NK, Chestnut B, Klimkaite L, Sumanas S. Single-cell transcriptomic analysis of vascular endothelial cells in zebrafish embryos. Sci Rep 2022; 12:13065. [PMID: 35906287 PMCID: PMC9338088 DOI: 10.1038/s41598-022-17127-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Vascular endothelial cells exhibit substantial phenotypic and transcriptional heterogeneity which is established during early embryogenesis. However, the molecular mechanisms involved in establishing endothelial cell diversity are still not well understood. Zebrafish has emerged as an advantageous model to study vascular development. Despite its importance, the single-cell transcriptomic profile of vascular endothelial cells during zebrafish development is still missing. To address this, we applied single-cell RNA-sequencing (scRNA-seq) of vascular endothelial cells isolated from zebrafish embryos at the 24 hpf stage. Six distinct clusters or subclusters related to vascular endothelial cells were identified which include arterial, two venous, cranial, endocardial and endothelial progenitor cell subtypes. Furthermore, we validated our findings by characterizing novel markers for arterial, venous, and endocardial cells. We experimentally confirmed the presence of two transcriptionally different venous cell subtypes, demonstrating heterogeneity among venous endothelial cells at this early developmental stage. This dataset will be a valuable resource for future functional characterization of vascular endothelial cells and interrogation of molecular mechanisms involved in the establishment of their heterogeneity and cell-fate decisions.
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Affiliation(s)
- Suman Gurung
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.,Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, 560 Channelside Dr, Tampa, FL, 33602, USA
| | - Nicole K Restrepo
- Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, 560 Channelside Dr, Tampa, FL, 33602, USA
| | - Brendan Chestnut
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Laurita Klimkaite
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Saulius Sumanas
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA. .,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA. .,Department of Pathology and Cell Biology, USF Health Heart Institute, University of South Florida, 560 Channelside Dr, Tampa, FL, 33602, USA.
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87
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van den Bosch QCC, Nguyen JQN, Brands T, van den Bosch TPP, Verdijk RM, Paridaens D, Naus NC, de Klein A, Kiliç E, Brosens E. FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14153668. [PMID: 35954332 PMCID: PMC9367502 DOI: 10.3390/cancers14153668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Despite successful treatment of primary uveal melanoma (UM), metastases still occur in approximately 50% of the patients. Unfortunately, little is known about the mechanism behind metastasized UM. By reanalyzing publicly available single-cell RNA sequencing data of embryonic zebrafish larvae and validating the results with UM data, we have identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. The most significant finding is FOXD1, which is nearly exclusively expressed in high-risk UM and is associated with poor survival. FOXD1 is a novel gene which could be involved in the metastatic capability of UM. Elucidating its function and role in metastatic UM could help to understand and develop treatment for UM. Abstract Uveal melanoma (UM) is a deadly ocular malignancy, originating from uveal melanocytes. Although much is known regarding prognostication in UM, the exact mechanism of metastasis is mostly unknown. Metastatic tumor cells are known to express a more stem-like RNA profile which is seen often in cell-specific embryonic development to induce tumor progression. Here, we identified novel transcription regulators by reanalyzing publicly available single cell RNA sequencing experiments. We identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. Our most significant finding is FOXD1, as this gene is nearly exclusively expressed in high-risk UM and its expression is associated with a poor prognosis. Even within the BAP1-mutated UM, the expression of FOXD1 is correlated with poor survival. FOXD1 is a novel factor which could potentially be involved in the metastatic capacity of high-risk UM. Elucidating the function of FOXD1 in UM could provide insight into the malignant transformation of uveal melanocytes, especially in high-risk UM.
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Affiliation(s)
- Quincy C. C. van den Bosch
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Thierry P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dion Paridaens
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
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Petersen AM, Small CM, Yan Y, Wilson C, Batzel P, Bremiller RA, Buck CL, von Hippel FA, Cresko WA, Postlethwait JH. Evolution and developmental expression of the sodium-iodide symporter ( NIS, slc5a5) gene family: Implications for perchlorate toxicology. Evol Appl 2022; 15:1079-1098. [PMID: 35899258 PMCID: PMC9309457 DOI: 10.1111/eva.13424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 05/02/2022] [Accepted: 05/03/2022] [Indexed: 11/27/2022] Open
Abstract
The vertebrate sodium-iodide symporter (NIS or SLC5A5) transports iodide into the thyroid follicular cells that synthesize thyroid hormone. The SLC5A protein family includes transporters of vitamins, minerals, and nutrients. Disruption of SLC5A5 function by perchlorate, a pervasive environmental contaminant, leads to human pathologies, especially hypothyroidism. Perchlorate also disrupts the sexual development of model animals, including threespine stickleback (Gasterosteus aculeatus) and zebrafish (Danio rerio), but the mechanism of action is unknown. To test the hypothesis that SLC5A5 paralogs are expressed in tissues necessary for the development of reproductive organs, and therefore are plausible candidates to mediate the effects of perchlorate on sexual development, we first investigated the evolutionary history of Slc5a paralogs to better understand potential functional trajectories of the gene family. We identified two clades of slc5a paralogs with respect to an outgroup of sodium/choline cotransporters (slc5a7); these clades are the NIS clade of sodium/iodide and lactate cotransporters (slc5a5, slc5a6, slc5a8, slc5a8, and slc5a12) and the SGLT clade of sodium/glucose cotransporters (slc5a1, slc5a2, slc5a3, slc5a4, slc5a10, and slc5a11). We also characterized expression patterns of slc5a genes during development. Stickleback embryos and early larvae expressed NIS clade genes in connective tissue, cartilage, teeth, and thyroid. Stickleback males and females expressed slc5a5 and its paralogs in gonads. Single-cell transcriptomics (scRNA-seq) on zebrafish sex-genotyped gonads revealed that NIS clade-expressing cells included germ cells (slc5a5, slc5a6a, and slc5a6b) and gonadal soma cells (slc5a8l). These results are consistent with the hypothesis that perchlorate exerts its effects on sexual development by interacting with slc5a5 or its paralogs in reproductive tissues. These findings show novel expression domains of slc5 genes in stickleback and zebrafish, which suggest similar functions across vertebrates including humans, and provide candidates to mediate the effects of perchlorate on sexual development.
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Affiliation(s)
- Ann M. Petersen
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregonUSA
- J.J. Howard Marine Lab, Northeast Fisheries Science CenterNational Oceanographic and Atmospheric AdministrationSandy HookNew JerseyUSA
| | - Clayton M. Small
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregonUSA
| | - Yi‐Lin Yan
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - Catherine Wilson
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - Peter Batzel
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - Ruth A. Bremiller
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
| | - C. Loren Buck
- Department of Biological SciencesNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Frank A. von Hippel
- Department of Community, Environment & Policy, Mel & Enid Zuckerman College of Public HealthUniversity of ArizonaTucsonArizonaUSA
| | - William A. Cresko
- Department of Biology, Institute of Ecology and EvolutionUniversity of OregonEugeneOregonUSA
| | - John H. Postlethwait
- Department of Biology, Institute of NeuroscienceUniversity of OregonEugeneOregonUSA
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89
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Baranasic D, Hörtenhuber M, Balwierz PJ, Zehnder T, Mukarram AK, Nepal C, Várnai C, Hadzhiev Y, Jimenez-Gonzalez A, Li N, Wragg J, D'Orazio FM, Relic D, Pachkov M, Díaz N, Hernández-Rodríguez B, Chen Z, Stoiber M, Dong M, Stevens I, Ross SE, Eagle A, Martin R, Obasaju O, Rastegar S, McGarvey AC, Kopp W, Chambers E, Wang D, Kim HR, Acemel RD, Naranjo S, Łapiński M, Chong V, Mathavan S, Peers B, Sauka-Spengler T, Vingron M, Carninci P, Ohler U, Lacadie SA, Burgess SM, Winata C, van Eeden F, Vaquerizas JM, Gómez-Skarmeta JL, Onichtchouk D, Brown BJ, Bogdanovic O, van Nimwegen E, Westerfield M, Wardle FC, Daub CO, Lenhard B, Müller F. Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements. Nat Genet 2022; 54:1037-1050. [PMID: 35789323 PMCID: PMC9279159 DOI: 10.1038/s41588-022-01089-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 05/03/2022] [Indexed: 12/12/2022]
Abstract
Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center ( https://danio-code.zfin.org ) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.
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Affiliation(s)
- Damir Baranasic
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Matthias Hörtenhuber
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Piotr J Balwierz
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Tobias Zehnder
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Abdul Kadir Mukarram
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Csilla Várnai
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Ada Jimenez-Gonzalez
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nan Li
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joseph Wragg
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Fabio M D'Orazio
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Dorde Relic
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Mikhail Pachkov
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Institute of Marine Sciences, Barcelona, Spain
| | | | - Zelin Chen
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Marcus Stoiber
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michaël Dong
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Irene Stevens
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden
| | - Samuel E Ross
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Anne Eagle
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Ryan Martin
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Oluwapelumi Obasaju
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems - Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Alison C McGarvey
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Wolfgang Kopp
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Emily Chambers
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Dennis Wang
- Sheffield Bioinformatics Core, Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK
- Singapore Institute for Clinical Sciences, Singapore, Singapore
| | - Hyejeong R Kim
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Rafael D Acemel
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- Epigenetics and Sex Development Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Maciej Łapiński
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Vanessa Chong
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Bernard Peers
- Laboratory of Zebrafish Development and Disease Models (ZDDM), GIGA-R, SART TILMAN, University of Liège, Liège, Belgium
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Martin Vingron
- Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Berlin, Germany
| | - Piero Carninci
- Laboratory for Transcriptome Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Fondazione Human Technopole, Milano, Italy
| | - Uwe Ohler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biology, Humboldt University, Berlin, Germany
| | - Scott Allen Lacadie
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Shawn M Burgess
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Cecilia Winata
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Freek van Eeden
- Bateson Centre/Biomedical Science, University of Sheffield, Sheffield, UK
| | - Juan M Vaquerizas
- MRC London Institute of Medical Sciences, London, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
| | - Daria Onichtchouk
- Department of Developmental Biology, Signalling Research Centers BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Ben James Brown
- Environmental Genomics & Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Erik van Nimwegen
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
| | | | - Fiona C Wardle
- Randall Centre for Cell & Molecular Biophysics, Guy's Campus, King's College London, London, UK
| | - Carsten O Daub
- Department of Biosciences and Nutrition, Karolinska Institutet, NEO, Huddinge, Sweden.
- Science for Life Laboratory, Solna, Sweden.
| | - Boris Lenhard
- MRC London Institute of Medical Sciences, London, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, Birmingham Centre for Genome Biology, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK.
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90
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Gao Y, Hu B, Flores R, Xie H, Lin F. Fibronectin and Integrin α5 play overlapping and independent roles in regulating the development of pharyngeal endoderm and cartilage. Dev Biol 2022; 489:122-133. [PMID: 35732225 DOI: 10.1016/j.ydbio.2022.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/12/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022]
Abstract
Craniofacial skeletal elements are derived from cranial neural crest cells (CNCCs), which migrate along discrete paths and populate distinct pharyngeal arches, structures that are separated by the neighboring endodermal pouches (EPs). Interactions between the CNCCs and the endoderm are critical for proper craniofacial development. In zebrafish, integrin α5 (Itga5) functions in the endoderm to regulate formation of specifically the first EP (EP1) and the development of the hyoid cartilage. Here we show that fibronectin (Fn), a major component of the extracellular matrix (ECM), is also required for these developmental processes, and that the penetrance of defects in mutants is temperature-dependent. fn1a-/- embryos exhibited defects that are similar to, but much more severe than, those of itga5-/- embryos, and a loss of integrin av (itgav) function enhanced both endoderm and cartilage defects in itga5-/- embryos, suggesting that Itga5 and Itgav cooperate to transmit signals from Fn to regulate the development of endoderm and cartilage. Whereas the endodermal defects in itga5; itga5v-/- double mutant embryos were comparable to those of fn1a-/- mutants, the cartilage defects were much milder. Furthermore, Fn assembly was detected in migrating CNCCs, and the epithelial organization and differentiation of CNCC-derived arches were impaired in fn1a-/- embryos, indicating that Fn1 exerts functions in arch development that are independent of Itga5 and Itgav. Additionally, reduction of itga5 function in fn1a-/- embryos led to profound defects in body axis elongation, as well as in endoderm and cartilage formation, suggesting that other ECM proteins signal through Itga5 to regulate development of the endoderm and cartilage. Thus, our studies reveal that Fn1a and Itga5 have both overlapping and independent functions in regulating development of the pharyngeal endoderm and cartilage.
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Affiliation(s)
- Yuanyuan Gao
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Bo Hu
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Rickcardo Flores
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Huaping Xie
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA
| | - Fang Lin
- Department of Anatomy and Cell Biology, Carver College of Medicine, The University of Iowa, Iowa City, IA, 52242, USA.
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91
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Bearce EA, Irons ZH, Craig SB, Kuhns CJ, Sabazali C, Farnsworth DR, Miller AC, Grimes DT. Daw1 regulates the timely onset of cilia motility during development. Development 2022; 149:275714. [PMID: 35708608 PMCID: PMC9270974 DOI: 10.1242/dev.200017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 05/05/2022] [Indexed: 12/15/2022]
Abstract
Motile cilia generate cell propulsion and extracellular fluid flows that are crucial for airway clearance, fertility and left-right patterning. Motility is powered by dynein arm complexes that are assembled in the cytoplasm then imported into the cilium. Studies in Chlamydomonas reinhardtii showed that ODA16 is a cofactor which promotes dynein arm import. Here, we demonstrate that the zebrafish homolog of ODA16, Daw1, facilitates the onset of robust cilia motility during development. Without Daw1, cilia showed markedly reduced motility during early development; however, motility subsequently increased to attain close to wild-type levels. Delayed motility onset led to differential effects on early and late cilia-dependent processes. Remarkably, abnormal body axis curves, which formed during the first day of development due to reduced cilia motility, self-corrected when motility later reached wild-type levels. Zebrafish larva therefore possess the ability to survey and correct body shape abnormalities. This work defines Daw1 as a factor which promotes the onset of timely cilia motility and can explain why human patients harboring DAW1 mutations exhibit significant laterality perturbations but mild airway and fertility complications. Summary: Daw1 promotes the onset of timely cilia motility for robust axial straightening during zebrafish development.
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Affiliation(s)
- Elizabeth A Bearce
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Zoe H Irons
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Samuel B Craig
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Colin J Kuhns
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Cynthia Sabazali
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Dylan R Farnsworth
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Adam C Miller
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Daniel T Grimes
- Institute of Molecular Biology, Department of Biology, University of Oregon, Eugene, OR 97403, USA
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92
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Ma X, Zhang X, Qiao Y, Zhong S, Xing Y, Chen X. Weighted gene co-expression network analysis of embryos and first instar larvae of the horseshoe crab Tachypleus tridentatus uncovers development gene networks. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100980. [PMID: 35303535 DOI: 10.1016/j.cbd.2022.100980] [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: 10/14/2021] [Revised: 02/03/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Horseshoe crabs are marine chelicerates that have existed on Earth for about 450 million years, and they are often used as an experimental model for studying marine invertebrate embryology. In this study, we performed transcriptome gene expression profiling of four continuous embryonic stages (Stages 18-21) and first instar larvae of Tachypleus tridentatus. A mean of 50,742,995 high-quality clean reads was obtained from each library. We then conducted weighted gene co-expression network analysis (WGCNA) for 13,698 genes with fragments per kilobase of exon per million mapped fragments values >5. We identified 17 modules, six of which likely play critical roles in development. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes was performed on the biologically significant modules. We found that several pathways, such as hedgehog signaling pathway, VEGF signaling pathway, dorso-ventral axis formation, may be involved in the embryonic development process of T. tridentatus. We also identified hub genes that were highly connected in the six critical modules. This is the first study to apply WGCNA to horseshoe crabs to identify hub genes that may play critical roles in development, and our results provide new insight into the mechanisms underlying early development in horseshoe crabs.
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Affiliation(s)
- Xiaowan Ma
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, People's Republic of China
| | - Xingzhi Zhang
- Guangxi Institute of Fisheries, Nanning 530000, People's Republic of China
| | - Ying Qiao
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, People's Republic of China.
| | - Shengping Zhong
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, People's Republic of China.
| | - Yongze Xing
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, People's Republic of China
| | - Xuyang Chen
- Key Laboratory of Tropical Marine Ecosystem and Bioresource, Fourth Institute of Oceanography, Ministry of Natural Resources, Beihai 536000, People's Republic of China
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93
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Annona G, Ferran JL, De Luca P, Conte I, Postlethwait JH, D’Aniello S. Expression Pattern of nos1 in the Developing Nervous System of Ray-Finned Fish. Genes (Basel) 2022; 13:918. [PMID: 35627303 PMCID: PMC9140475 DOI: 10.3390/genes13050918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/04/2022] [Accepted: 05/14/2022] [Indexed: 12/04/2022] Open
Abstract
Fish have colonized nearly all aquatic niches, making them an invaluable resource to understand vertebrate adaptation and gene family evolution, including the evolution of complex neural networks and modulatory neurotransmitter pathways. Among ancient regulatory molecules, the gaseous messenger nitric oxide (NO) is involved in a wide range of biological processes. Because of its short half-life, the modulatory capability of NO is strictly related to the local activity of nitric oxide synthases (Nos), enzymes that synthesize NO from L-arginine, making the localization of Nos mRNAs a reliable indirect proxy for the location of NO action domains, targets, and effectors. Within the diversified actinopterygian nos paralogs, nos1 (alias nnos) is ubiquitously present as a single copy gene across the gnathostome lineage, making it an ideal candidate for comparative studies. To investigate variations in the NO system across ray-finned fish phylogeny, we compared nos1 expression patterns during the development of two well-established experimental teleosts (zebrafish and medaka) with an early branching holostean (spotted gar), an important evolutionary bridge between teleosts and tetrapods. Data reported here highlight both conserved expression domains and species-specific nos1 territories, confirming the ancestry of this signaling system and expanding the number of biological processes implicated in NO activities.
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Affiliation(s)
- Giovanni Annona
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
- Research Infrastructure for Marine Biological Resources Department (RIMAR), Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy;
| | - José Luis Ferran
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, 30120 Murcia, Spain;
- Institute of Biomedical Research of Murcia—IMIB, Virgen de la Arrixaca University Hospital, 30120 Murcia, Spain
| | - Pasquale De Luca
- Research Infrastructure for Marine Biological Resources Department (RIMAR), Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy;
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine, 80078 Pozzuoli, Italy;
- Department of Biology, University of Napoli Federico II, 80126 Napoli, Italy
| | | | - Salvatore D’Aniello
- Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy
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94
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Brunsdon H, Brombin A, Peterson S, Postlethwait JH, Patton EE. Aldh2 is a lineage-specific metabolic gatekeeper in melanocyte stem cells. Development 2022; 149:275182. [PMID: 35485397 PMCID: PMC9188749 DOI: 10.1242/dev.200277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/20/2022] [Indexed: 12/31/2022]
Abstract
Melanocyte stem cells (McSCs) in zebrafish serve as an on-demand source of melanocytes during growth and regeneration, but metabolic programs associated with their activation and regenerative processes are not well known. Here, using live imaging coupled with scRNA-sequencing, we discovered that, during regeneration, quiescent McSCs activate a dormant embryonic neural crest transcriptional program followed by an aldehyde dehydrogenase (Aldh) 2 metabolic switch to generate progeny. Unexpectedly, although ALDH2 is well known for its aldehyde-clearing mechanisms, we find that, in regenerating McSCs, Aldh2 activity is required to generate formate – the one-carbon (1C) building block for nucleotide biosynthesis – through formaldehyde metabolism. Consequently, we find that disrupting the 1C cycle with low doses of methotrexate causes melanocyte regeneration defects. In the absence of Aldh2, we find that purines are the metabolic end product sufficient for activated McSCs to generate progeny. Together, our work reveals McSCs undergo a two-step cell state transition during regeneration, and that the reaction products of Aldh2 enzymes have tissue-specific stem cell functions that meet metabolic demands in regeneration. Summary: In zebrafish melanocyte regeneration, quiescent McSCs respond by re-expressing a neural crest identity, followed by an Aldh2-dependent metabolic switch to generate progeny.
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Affiliation(s)
- Hannah Brunsdon
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh EH4 2XU, UK.,Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh EH4 2XU, UK
| | - Alessandro Brombin
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh EH4 2XU, UK.,Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh EH4 2XU, UK
| | - Samuel Peterson
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | | | - E Elizabeth Patton
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh EH4 2XU, UK.,Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, The University of Edinburgh, Western General Hospital Campus, Crewe Road, Edinburgh EH4 2XU, UK
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95
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Bondhus L, Varma R, Hernandez Y, Arboleda VA. Balancing the transcriptome: leveraging sample similarity to improve measures of gene specificity. Brief Bioinform 2022; 23:6582882. [PMID: 35534150 PMCID: PMC9487600 DOI: 10.1093/bib/bbac158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 01/28/2023] Open
Abstract
The spatial and temporal domain of a gene's expression can range from ubiquitous to highly specific. Quantifying the degree to which this expression is unique to a specific tissue or developmental timepoint can provide insight into the etiology of genetic diseases. However, quantifying specificity remains challenging as measures of specificity are sensitive to similarity between samples in the sample set. For example, in the Gene-Tissue Expression project (GTEx), brain subregions are overrepresented at 13 of 54 (24%) unique tissues sampled. In this dataset, existing specificity measures have a decreased ability to identify genes specific to the brain relative to other organs. To solve this problem, we leverage sample similarity information to weight samples such that overrepresented tissues do not have an outsized effect on specificity estimates. We test this reweighting procedure on 4 measures of specificity, Z-score, Tau, Tsi and Gini, in the GTEx data and in single cell datasets for zebrafish and mouse. For all of these measures, incorporating sample similarity information to weight samples results in greater stability of sets of genes called as specific and decreases the overall variance in the change of specificity estimates as sample sets become more unbalanced. Furthermore, the genes with the largest improvement in their specificity estimate's stability are those with functions related to the overrepresented sample types. Our results demonstrate that incorporating similarity information improves specificity estimates' stability to the choice of the sample set used to define the transcriptome, providing more robust and reproducible measures of specificity for downstream analyses.
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Affiliation(s)
- Leroy Bondhus
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095
| | - Roshni Varma
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095
| | - Yenifer Hernandez
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Department of Computational Medicine, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095,Molecular Biology Institute, UCLA, Los Angeles, CA 90095,Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, 90095,Corresponding author. Valerie A. Arboleda, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA. Tel.: +1-310-983-3568; E-mail:
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96
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Lukowicz-Bedford RM, Farnsworth DR, Miller AC. Connexinplexity: the spatial and temporal expression of connexin genes during vertebrate organogenesis. G3 (BETHESDA, MD.) 2022; 12:jkac062. [PMID: 35325106 PMCID: PMC9073686 DOI: 10.1093/g3journal/jkac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/24/2022] [Indexed: 11/28/2022]
Abstract
Animal development requires coordinated communication between cells. The Connexin family of proteins is a major contributor to intercellular communication in vertebrates by forming gap junction channels that facilitate the movement of ions, small molecules, and metabolites between cells. Additionally, individual hemichannels can provide a conduit to the extracellular space for paracrine and autocrine signaling. Connexin-mediated communication is widely used in epithelial, neural, and vascular development and homeostasis, and most tissues likely use this form of communication. In fact, Connexin disruptions are of major clinical significance contributing to disorders developing from all major germ layers. Despite the fact that Connexins serve as an essential mode of cellular communication, the temporal and cell-type-specific expression patterns of connexin genes remain unknown in vertebrates. A major challenge is the large and complex connexin gene family. To overcome this barrier, we determined the expression of all connexins in zebrafish using single-cell RNA-sequencing of entire animals across several stages of organogenesis. Our analysis of expression patterns has revealed that few connexins are broadly expressed, but rather, most are expressed in tissue- or cell-type-specific patterns. Additionally, most tissues possess a unique combinatorial signature of connexin expression with dynamic temporal changes across the organism, tissue, and cell. Our analysis has identified new patterns for well-known connexins and assigned spatial and temporal expression to genes with no-existing information. We provide a field guide relating zebrafish and human connexin genes as a critical step toward understanding how Connexins contribute to cellular communication and development throughout vertebrate organogenesis.
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Affiliation(s)
| | - Dylan R Farnsworth
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
| | - Adam C Miller
- Institute of Neuroscience, Department of Biology, University of Oregon, Eugene, OR 97403, USA
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97
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Kenny C, Dilshat R, Seberg HE, Van Otterloo E, Bonde G, Helverson A, Franke CM, Steingrímsson E, Cornell RA. TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes. PLoS Genet 2022; 18:e1010207. [PMID: 35580127 PMCID: PMC9159589 DOI: 10.1371/journal.pgen.1010207] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/01/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
In developing melanocytes and in melanoma cells, multiple paralogs of the Activating-enhancer-binding Protein 2 family of transcription factors (TFAP2) contribute to expression of genes encoding pigmentation regulators, but their interaction with Microphthalmia transcription factor (MITF), a master regulator of these cells, is unclear. Supporting the model that TFAP2 facilitates MITF's ability to activate expression of pigmentation genes, single-cell seq analysis of zebrafish embryos revealed that pigmentation genes are only expressed in the subset of mitfa-expressing cells that also express tfap2 paralogs. To test this model in SK-MEL-28 melanoma cells we deleted the two TFAP2 paralogs with highest expression, TFAP2A and TFAP2C, creating TFAP2 knockout (TFAP2-KO) cells. We then assessed gene expression, chromatin accessibility, binding of TFAP2A and of MITF, and the chromatin marks H3K27Ac and H3K27Me3 which are characteristic of active enhancers and silenced chromatin, respectively. Integrated analyses of these datasets indicate TFAP2 paralogs directly activate enhancers near genes enriched for roles in pigmentation and proliferation, and directly repress enhancers near genes enriched for roles in cell adhesion. Consistently, compared to WT cells, TFAP2-KO cells proliferate less and adhere to one another more. TFAP2 paralogs and MITF co-operatively activate a subset of enhancers, with the former necessary for MITF binding and chromatin accessibility. By contrast, TFAP2 paralogs and MITF do not appear to co-operatively inhibit enhancers. These studies reveal a mechanism by which TFAP2 profoundly influences the set of genes activated by MITF, and thereby the phenotype of pigment cells and melanoma cells.
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Affiliation(s)
- Colin Kenny
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramile Dilshat
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Hannah E. Seberg
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eric Van Otterloo
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Gregory Bonde
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Annika Helverson
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Christopher M. Franke
- Department of Surgery, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, BioMedical Center, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Robert A. Cornell
- Department of Anatomy and Cell Biology, College of Medicine, University of Iowa, Iowa City, Iowa, United States of America
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98
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Yu F, Li JL, Feng WR, Tang YK, Su SY, Xu P, Zhong H. Heat Shock Procedure Affects Cell Division-Associated Genes in Gynogenetic Manipulation. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:354-365. [PMID: 35305189 DOI: 10.1007/s10126-022-10112-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Heat shock procedure is crucial for gynogenetic manipulation leading to diploidization of the maternal genomes; however, the underlying molecular mechanism especially the transcriptomic changes during this procedure has still not been unveiled yet. Here, the artificial gynogenesis of zebrafish (Danio rerio) using inactivated sperm from rare minnow (Gobiocypris rarus) was conducted. We found that artificial gynogenetic manipulation, including pseudo-fertilization and heat shock, decreased hatching rates, whereas heat shock treatment alone had medium hatching rates. The first cleavage changed the expression of genes associated with RNA transcription and protein synthesis. A co-expression network regulated by hub genes GIT1, Sepsecs, and FLNB was significantly correlated with heat shock procedure. The cyclin family and cyclin-dependent kinase-related genes were lowly expressed in embryos from gynogenetic zebrafish, and genes involved in controlling the cell cycle and genomic stability were significantly altered by the gynogenetic treatment. Our results show the effects of artificial gynogenesis on embryos and describe changes in gene expression that suggest drastic changes take place in cell division by heat shock procedure. These findings will contribute to an understanding of the molecular basis for germplasm improving, including the purifying effect and allogynogenetic biological effect by gynogenesis.
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Affiliation(s)
- Fan Yu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Jian-Lin Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Wen-Rong Feng
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Yong-Kai Tang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Sheng-Yan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, China.
| | - Huan Zhong
- Hunan Research Center of Engineering Technology for Utilization of Distinctive Aquatic Resource, Hunan Agricultural University, Changsha, 410128, China.
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99
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Abstract
In this manuscript, we address an essential question in developmental and evolutionary biology: How have changes in gene regulatory networks contributed to the invertebrate-to-vertebrate transition? To address this issue, we perturbed four signaling pathways critical for body plan formation in the cephalochordate amphioxus and in zebrafish and compared the effects of such perturbations on gene expression and gene regulation in both species. Our data reveal that many developmental genes have gained response to these signaling pathways in the vertebrate lineage. Moreover, we show that the interconnectivity between these pathways is much higher in zebrafish than in amphioxus. We conclude that this increased signaling pathway complexity likely contributed to vertebrate morphological novelties during evolution. Signaling pathways control a large number of gene regulatory networks (GRNs) during animal development, acting as major tools for body plan formation [A. Pires-daSilva, R. J. Sommer, Nat. Rev. Genet. 4, 39–49 (2003)], although only a few of these pathways operate during this period [J. J. Sanz-Ezquerro, A. E. Münsterberg, S. Stricker, Front. Cell Dev. Biol. 5, 76 (2017)]. Moreover, most of them have been largely conserved during metazoan evolution [L. S. Babonis, M. Q. Martindale, Philos. Trans. R. Soc. Lond. B Biol. Sci. 372, 20150477 (2017)]. How evolution has generated a vast diversity of animal morphologies with such a limited number of tools is still largely unknown. Here, we show that gain of interconnectivity between signaling pathways and the GRNs they control may have critically contributed to the origin of vertebrates. We perturbed the retinoic acid, Wnt, FGF, and Nodal signaling pathways during gastrulation in the invertebrate chordate amphioxus and zebrafish and compared the effects on gene expression and cis-regulatory elements (CREs). We found that multiple developmental genes gain response to these pathways through vertebrate-specific CREs. Moreover, in contrast to amphioxus, many of these CREs responded to multiple pathways in zebrafish, which reflects their high interconnectivity. Furthermore, we found that vertebrate-specific cell types are more enriched in highly interconnected genes than in tissues with more ancient origin. Thus, the increase of CREs in vertebrates integrating inputs from different signaling pathways probably contributed to gene expression complexity and to the formation of new cell types and morphological novelties in this lineage.
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Laghi V, Rezelj V, Boucontet L, Frétaud M, Da Costa B, Boudinot P, Salinas I, Lutfalla G, Vignuzzi M, Levraud JP. Exploring Zebrafish Larvae as a COVID-19 Model: Probable Abortive SARS-CoV-2 Replication in the Swim Bladder. Front Cell Infect Microbiol 2022; 12:790851. [PMID: 35360100 PMCID: PMC8963489 DOI: 10.3389/fcimb.2022.790851] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/04/2022] [Indexed: 12/16/2022] Open
Abstract
Animal models are essential to understanding COVID-19 pathophysiology and for preclinical assessment of drugs and other therapeutic or prophylactic interventions. We explored the small, cheap, and transparent zebrafish larva as a potential host for SARS-CoV-2. Bath exposure, as well as microinjection in the coelom, pericardium, brain ventricle, or bloodstream, resulted in a rapid decrease of SARS-CoV-2 RNA in wild-type larvae. However, when the virus was inoculated in the swim bladder, viral RNA stabilized after 24 h. By immunohistochemistry, epithelial cells containing SARS-CoV-2 nucleoprotein were observed in the swim bladder wall. Our data suggest an abortive infection of the swim bladder. In some animals, several variants of concern were also tested with no evidence of increased infectivity in our model. Low infectivity of SARS-CoV-2 in zebrafish larvae was not due to the host type I interferon response, as comparable viral loads were detected in type I interferon-deficient animals. A mosaic overexpression of human ACE2 was not sufficient to increase SARS-CoV-2 infectivity in zebrafish embryos or in fish cells in vitro. In conclusion, wild-type zebrafish larvae appear mostly non-permissive to SARS-CoV-2, except in the swim bladder, an aerial organ sharing similarities with the mammalian lung.
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Affiliation(s)
- Valerio Laghi
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité mixte de Recherche (UMR) 3637, Unité Macrophages et Développement de l’Immunité, Paris, France
| | - Veronica Rezelj
- Institut Pasteur, Unité Populations Virales et Pathogénèse, Institut Pasteur, Paris, France
| | - Laurent Boucontet
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité mixte de Recherche (UMR) 3637, Unité Macrophages et Développement de l’Immunité, Paris, France
| | - Maxence Frétaud
- Université Paris-Saclay, Institut National pour la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Versailles Saint-Quentin (UVSQ), Virologie et Immunologie Moléculaire (VIM), Jouy-en-Josas, France
| | - Bruno Da Costa
- Université Paris-Saclay, Institut National pour la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Versailles Saint-Quentin (UVSQ), Virologie et Immunologie Moléculaire (VIM), Jouy-en-Josas, France
| | - Pierre Boudinot
- Université Paris-Saclay, Institut National pour la Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Versailles Saint-Quentin (UVSQ), Virologie et Immunologie Moléculaire (VIM), Jouy-en-Josas, France
| | - Irene Salinas
- Department of Biology, University of New Mexico, Albuquerque, NM, United States
| | - Georges Lutfalla
- Laboratory of Pathogen-Host Interactions (LPHI), Centre National de la Recherche Scientifique (CNRS), Université de Montpellier, Montpellier, France
| | - Marco Vignuzzi
- Institut Pasteur, Unité Populations Virales et Pathogénèse, Institut Pasteur, Paris, France
| | - Jean-Pierre Levraud
- Institut Pasteur, Centre National de la Recherche Scientifique (CNRS) Unité mixte de Recherche (UMR) 3637, Unité Macrophages et Développement de l’Immunité, Paris, France
- Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), Institut Pasteur, Institut des Neurosciences Paris-Saclay, Gif-sur-Yvette, France
- *Correspondence: Jean-Pierre Levraud,
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