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Shah AN, Leesch F, Lorenzo-Orts L, Grundmann L, Novatchkova M, Haselbach D, Calo E, Pauli A. A dual ribosomal system in the zebrafish soma and germline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610041. [PMID: 39257781 PMCID: PMC11383705 DOI: 10.1101/2024.08.29.610041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Protein synthesis during vertebrate embryogenesis is driven by ribosomes of two distinct origins: maternal ribosomes synthesized during oogenesis and stored in the egg, and somatic ribosomes, produced by the developing embryo after zygotic genome activation (ZGA). In zebrafish, these two ribosome types are expressed from different genomic loci and also differ in their ribosomal RNA (rRNA) sequence. To characterize this dual ribosome system further, we examined the expression patterns of maternal and somatic rRNAs during embryogenesis and in adult tissues. We found that maternal rRNAs are not only expressed during oogenesis but are continuously produced in the zebrafish germline. Proteomic analyses of maternal and somatic ribosomes unveiled differences in core ribosomal protein composition. Most nucleotide differences between maternal and somatic rRNAs are located in the flexible, structurally not resolved expansion segments. Our in vivo data demonstrated that both maternal and somatic ribosomes can be translationally active in the embryo. Using transgenically tagged maternal or somatic ribosome subunits, we experimentally confirm the presence of hybrid 80S ribosomes composed of 40S and 60S subunits from both origins and demonstrate the preferential in vivo association of maternal ribosomes with germline-specific transcripts. Our study identifies a distinct type of ribosomes in the zebrafish germline and thus presents a foundation for future explorations into possible regulatory mechanisms and functional roles of heterogeneous ribosomes.
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Affiliation(s)
- Arish N. Shah
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Friederike Leesch
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Laura Lorenzo-Orts
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Lorenz Grundmann
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - David Haselbach
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States
| | - Andrea Pauli
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
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2
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Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Here we present the Multisite Assembly of Gateway Induced Clones (MAGIC) system, which harnesses site-specific recombination-based cloning via Gateway technology for rapid, modular assembly of between 1 and 3 "Entry" vector components, all into a fourth, standard high copy "Destination" plasmid backbone. The MAGIC toolkit spans a range of in vitro and in vivo uses, from directing tunable gene expression, to driving simultaneous expression of microRNAs and fluorescent reporters, to enabling site-specific recombinase-dependent gene expression. All MAGIC system components are directly compatible with existing multisite gateway Tol2 systems currently used in zebrafish, as well as existing eukaryotic cell culture expression Destination plasmids, and available mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. Moreover, herein we describe novel vectors with flanking piggyBac transposon elements for stable genomic integration in vitro or in vivo when used with piggyBac transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, electroporated mouse and chick embryos, as well as in injected zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
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3
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Weinberger M, Simões FC, Gungoosingh T, Sauka-Spengler T, Riley PR. Distinct epicardial gene regulatory programs drive development and regeneration of the zebrafish heart. Dev Cell 2024; 59:351-367.e6. [PMID: 38237592 DOI: 10.1016/j.devcel.2023.12.012] [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: 08/05/2022] [Revised: 08/12/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
Unlike the adult mammalian heart, which has limited regenerative capacity, the zebrafish heart fully regenerates following injury. Reactivation of cardiac developmental programs is considered key to successfully regenerating the heart, yet the regulation underlying the response to injury remains elusive. Here, we compared the transcriptome and epigenome of the developing and regenerating zebrafish epicardia. We identified epicardial enhancer elements with specific activity during development or during adult heart regeneration. By generating gene regulatory networks associated with epicardial development and regeneration, we inferred genetic programs driving each of these processes, which were largely distinct. Loss of Hif1ab, Nrf1, Tbx2b, and Zbtb7a, central regulators of the regenerating epicardial network, in injured hearts resulted in elevated epicardial cell numbers infiltrating the wound and excess fibrosis after cryoinjury. Our work identifies differences between the regulatory blueprint deployed during epicardial development and regeneration, underlining that heart regeneration goes beyond the reactivation of developmental programs.
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Affiliation(s)
- Michael Weinberger
- Department of Physiology, Anatomy and Genetics, Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford OX3 7TY, Oxfordshire, UK; Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, Oxfordshire, UK
| | - Filipa C Simões
- Department of Physiology, Anatomy and Genetics, Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford OX3 7TY, Oxfordshire, UK
| | - Trishalee Gungoosingh
- Department of Physiology, Anatomy and Genetics, Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford OX3 7TY, Oxfordshire, UK
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, Oxfordshire, UK; Stowers Institute for Medical Research, Kansas City, MO, USA.
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford OX3 7TY, Oxfordshire, UK.
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4
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Chong-Morrison V, Mayes S, Simões FC, Senanayake U, Carroll DS, Riley PR, Wilson SW, Sauka-Spengler T. Ac/Ds transposition for CRISPR/dCas9-SID4x epigenome modulation in zebrafish. Biol Open 2023; 12:bio059995. [PMID: 37367831 PMCID: PMC10320716 DOI: 10.1242/bio.059995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
Due to its genetic amenability coupled with advances in genome editing, zebrafish is an excellent model to examine the function of (epi)genomic elements. Here, we repurposed the Ac/Ds maize transposition system to efficiently characterise zebrafish cis-regulated elements, also known as enhancers, in F0-microinjected embryos. We further used the system to stably express guide RNAs enabling CRISPR/dCas9-interference (CRISPRi) perturbation of enhancers without disrupting the underlying genetic sequence. In addition, we probed the phenomenon of antisense transcription at two neural crest gene loci. Our study highlights the utility of Ac/Ds transposition as a new tool for transient epigenome modulation in zebrafish.
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Affiliation(s)
- Vanessa Chong-Morrison
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Sarah Mayes
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Filipa C. Simões
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
- University of Oxford, Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, Oxford OX3 7DQ, UK
| | - Upeka Senanayake
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Dervla S. Carroll
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Paul R. Riley
- University of Oxford, Institute of Developmental and Regenerative Medicine, Department of Physiology, Anatomy and Genetics, Oxford OX3 7DQ, UK
| | - Stephen W. Wilson
- University College London, Department of Cell & Developmental Biology, London WC1E 6BT, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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5
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Tornini VA, Miao L, Lee HJ, Gerson T, Dube SE, Schmidt V, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar CE, Bazzini AA, Krishnaswamy S, Rihel J, Giraldez AJ. linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. eLife 2023; 12:e82249. [PMID: 37191016 PMCID: PMC10188112 DOI: 10.7554/elife.82249] [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: 07/28/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
Thousands of long intergenic non-coding RNAs (lincRNAs) are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open-reading frames and are speculated to encode micropeptides. However, systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here, we show that two putative lincRNAs (linc-mipep, also called lnc-rps25, and linc-wrb) encode micropeptides with homology to the vertebrate-specific chromatin architectural protein, Hmgn1, and demonstrate that they are required for development of vertebrate-specific brain cell types. Specifically, we show that NMDA receptor-mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes - evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions, with implications for neurodevelopmental disorders and disease.
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Affiliation(s)
| | - Liyun Miao
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Ho-Joon Lee
- Department of Genetics, Yale UniversityNew HavenUnited States
- Yale Center for Genome Analysis, Yale UniversityNew HavenUnited States
| | - Timothy Gerson
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Sarah E Dube
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Valeria Schmidt
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - François Kroll
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Yin Tang
- Department of Genetics, Yale UniversityNew HavenUnited States
| | - Katherine Du
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | - Manik Kuchroo
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | | | - Ariel Alejandro Bazzini
- Stowers Institute for Medical ResearchKansas CityUnited States
- Department of Molecular & Integrative Physiology, University of Kansas School of MedicineKansas CityUnited States
| | - Smita Krishnaswamy
- Department of Genetics, Yale UniversityNew HavenUnited States
- Department of Computer Science, Yale UniversityNew HavenUnited States
| | - Jason Rihel
- Department of Cell and Developmental Biology, University College LondonLondonUnited Kingdom
| | - Antonio J Giraldez
- Department of Genetics, Yale UniversityNew HavenUnited States
- Yale Stem Cell Center, Yale University School of MedicineNew HavenUnited States
- Yale Cancer Center, Yale University School of MedicineNew HavenUnited States
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6
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Wang P, Kitano M, Keomanee-Dizon K, Truong TV, Fraser SE, Cutrale F. A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy. CELL REPORTS METHODS 2023; 3:100441. [PMID: 37159674 PMCID: PMC10162951 DOI: 10.1016/j.crmeth.2023.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 05/11/2023]
Abstract
Hyperspectral fluorescence imaging improves multiplexed observations of biological samples by utilizing multiple color channels across the spectral range to compensate for spectral overlap between labels. Typically, spectral resolution comes at a cost of decreased detection efficiency, which both hampers imaging speed and increases photo-toxicity to the samples. Here, we present a high-speed, high-efficiency snapshot spectral acquisition method, based on optical compression of the fluorescence spectra via Fourier transform, that overcomes the challenges of discrete spectral sampling: single-shot hyperspectral phasor camera (SHy-Cam). SHy-Cam captures fluorescence spatial and spectral information in a single exposure with a standard scientific CMOS camera, with photon efficiency of over 80%, easily and with acquisition rates exceeding 30 datasets per second, making it a powerful tool for multi-color in vivo imaging. Its simple design, using readily available optical components, and its easy integration provide a low-cost solution for multi-color fluorescence imaging with increased efficiency and speed.
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Affiliation(s)
- Pu Wang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Kevin Keomanee-Dizon
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Thai V. Truong
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
- Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
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7
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Chen HJ, Barske L, Talbot JC, Dinwoodie OM, Roberts RR, Farmer DT, Jimenez C, Merrill AE, Tucker AS, Crump JG. Nuclear receptor Nr5a2 promotes diverse connective tissue fates in the jaw. Dev Cell 2023; 58:461-473.e7. [PMID: 36905926 PMCID: PMC10050118 DOI: 10.1016/j.devcel.2023.02.011] [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: 09/15/2022] [Revised: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023]
Abstract
Organ development involves the sustained production of diverse cell types with spatiotemporal precision. In the vertebrate jaw, neural-crest-derived progenitors produce not only skeletal tissues but also later-forming tendons and salivary glands. Here we identify the pluripotency factor Nr5a2 as essential for cell-fate decisions in the jaw. In zebrafish and mice, we observe transient expression of Nr5a2 in a subset of mandibular postmigratory neural-crest-derived cells. In zebrafish nr5a2 mutants, nr5a2-expressing cells that would normally form tendons generate excess jaw cartilage. In mice, neural-crest-specific Nr5a2 loss results in analogous skeletal and tendon defects in the jaw and middle ear, as well as salivary gland loss. Single-cell profiling shows that Nr5a2, distinct from its roles in pluripotency, promotes jaw-specific chromatin accessibility and gene expression that is essential for tendon and gland fates. Thus, repurposing of Nr5a2 promotes connective tissue fates to generate the full repertoire of derivatives required for jaw and middle ear function.
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Affiliation(s)
- Hung-Jhen Chen
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lindsey Barske
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Jared C Talbot
- School of Biology and Ecology, University of Maine, Orono, ME 04469, USA
| | - Olivia M Dinwoodie
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - Ryan R Roberts
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Department of Biomedical Sciences, Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - D'Juan T Farmer
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA; Molecular, Cell and Developmental Biology Department and Orthopaedic Surgery, University of California, Los Angeles, CA 90095, USA
| | - Christian Jimenez
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Amy E Merrill
- Department of Biomedical Sciences, Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA 90033, USA; Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Abigail S Tucker
- Centre for Craniofacial and Regenerative Biology, King's College London, London, SE1 9RT, UK
| | - J Gage Crump
- Eli and Edythe Broad Center for Regenerative Medicine, Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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8
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Collective cell migration during optic cup formation features changing cell-matrix interactions linked to matrix topology. Curr Biol 2022; 32:4817-4831.e9. [PMID: 36208624 DOI: 10.1016/j.cub.2022.09.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/28/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
Cell migration is crucial for organismal development and shapes organisms in health and disease. Although a lot of research has revealed the role of intracellular components and extracellular signaling in driving single and collective cell migration, the influence of physical properties of the tissue and the environment on migration phenomena in vivo remains less explored. In particular, the role of the extracellular matrix (ECM), which many cells move upon, is currently unclear. To overcome this gap, we use zebrafish optic cup formation, and by combining novel transgenic lines and image analysis pipelines, we study how ECM properties influence cell migration in vivo. We show that collectively migrating rim cells actively move over an immobile extracellular matrix. These cell movements require cryptic lamellipodia that are extended in the direction of migration. Quantitative analysis of matrix properties revealed that the topology of the matrix changes along the migration path. These changes in matrix topologies are accompanied by changes in the dynamics of cell-matrix interactions. Experiments and theoretical modeling suggest that matrix porosity could be linked to efficient migration. Indeed, interfering with matrix topology by increasing its porosity results in a loss of cryptic lamellipodia, less-directed cell-matrix interactions, and overall inefficient migration. Thus, matrix topology is linked to the dynamics of cell-matrix interactions and the efficiency of directed collective rim cell migration during vertebrate optic cup morphogenesis.
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9
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Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022; 5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/17/2022] [Indexed: 01/31/2023] Open
Abstract
CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.
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Affiliation(s)
- Oana Pelea
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tudor A. Fulga
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; and Kansas City, Missouri, USA
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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10
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Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022; 138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is an emblematic population of embryonic stem-like cells with remarkable migratory ability. These distinctive attributes have inspired the curiosity of developmental biologists for over 150 years, however only recently the regulatory mechanisms controlling the complex features of the NC have started to become elucidated at genomic scales. Regulatory control of NC development is achieved through combinatorial transcription factor binding and recruitment of associated transcriptional complexes to distal cis-regulatory elements. Together, they regulate when, where and to what extent transcriptional programmes are actively deployed, ultimately shaping ontogenetic processes. Here, we discuss how transcriptional networks control NC ontogeny, with a special emphasis on the molecular mechanisms underlying specification of the cephalic NC. We also cover emerging properties of transcriptional regulation revealed in diverse developmental systems, such as the role of three-dimensional conformation of chromatin, and how they are involved in the regulation of NC ontogeny. Finally, we highlight how advances in deciphering the NC transcriptional network have afforded new insights into the molecular basis of human diseases.
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Affiliation(s)
- Ivan L Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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11
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Stream A, Madigan CA. Zebrafish: an underutilized tool for discovery in host-microbe interactions. Trends Immunol 2022; 43:426-437. [PMID: 35527182 PMCID: PMC11302990 DOI: 10.1016/j.it.2022.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 12/31/2022]
Abstract
Zebrafish are relatively new to the field of host-pathogen interactions, although they have been a valuable vertebrate model for decades in developmental biology and neuroscience. Transparent zebrafish larvae have most components of the human innate immune system, and adult zebrafish also produce cells of the adaptive immune system. Recent discoveries using zebrafish infection models include mechanisms of pathogen survival and host cell sensing of microbes. These discoveries were enabled by zebrafish technology, which is constantly evolving and providing new opportunities for immunobiology research. Recent tools include CRISPR/Cas9 mutagenesis, in vivo biotinylation, and genetically encoded biosensors. We argue that the zebrafish model - which remains underutilized in immunology - provides fertile ground for a new understanding of host-microbe interactions in a transparent host.
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Affiliation(s)
- Alexandra Stream
- Department of Biological Sciences, University of California San Diego (UCSD), San Diego, CA, USA
| | - Cressida A Madigan
- Department of Biological Sciences, University of California San Diego (UCSD), San Diego, CA, USA.
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12
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Cunningham RL, Kramer ET, DeGeorgia SK, Godoy PM, Zarov AP, Seneviratne S, Grigura V, Kaufman CK. Functional in vivo characterization of sox10 enhancers in neural crest and melanoma development. Commun Biol 2021; 4:695. [PMID: 34099848 PMCID: PMC8184803 DOI: 10.1038/s42003-021-02211-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023] Open
Abstract
The role of a neural crest developmental transcriptional program, which critically involves Sox10 upregulation, is a key conserved aspect of melanoma initiation in both humans and zebrafish, yet transcriptional regulation of sox10 expression is incompletely understood. Here we used ATAC-Seq analysis of multiple zebrafish melanoma tumors to identify recurrently open chromatin domains as putative melanoma-specific sox10 enhancers. Screening in vivo with EGFP reporter constructs revealed 9 of 11 putative sox10 enhancers with embryonic activity in zebrafish. Focusing on the most active enhancer region in melanoma, we identified a region 23 kilobases upstream of sox10, termed peak5, that drives EGFP reporter expression in a subset of neural crest cells, Kolmer-Agduhr neurons, and early melanoma patches and tumors with high specificity. A ~200 base pair region, conserved in Cyprinidae, within peak5 is required for transgenic reporter activity in neural crest and melanoma. This region contains dimeric SoxE/Sox10 dimeric binding sites essential for peak5 neural crest and melanoma activity. We show that deletion of the endogenous peak5 conserved genomic locus decreases embryonic sox10 expression and disrupts adult stripe patterning in our melanoma model background. Our work demonstrates the power of linking developmental and cancer models to better understand neural crest identity in melanoma.
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Affiliation(s)
- Rebecca L Cunningham
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Eva T Kramer
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Sophia K DeGeorgia
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Paula M Godoy
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Anna P Zarov
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Shayana Seneviratne
- School of Arts and Sciences, Washington University in Saint Louis, St. Louis, MO, USA
| | - Vadim Grigura
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA
| | - Charles K Kaufman
- Division of Medical Oncology, Department of Medicine and Department of Developmental Biology, Washington University in Saint Louis, St. Louis, MO, USA.
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13
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Artinger KB, Monsoro-Burq AH. Neural crest multipotency and specification: power and limits of single cell transcriptomic approaches. Fac Rev 2021; 10:38. [PMID: 34046642 PMCID: PMC8130411 DOI: 10.12703/r/10-38] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The neural crest is a unique population of multipotent cells forming in vertebrate embryos. Their vast cell fate potential enables the generation of a diverse array of differentiated cell types in vivo. These include, among others, connective tissue, cartilage and bone of the face and skull, neurons and glia of the peripheral nervous system (including enteric nervous system), and melanocytes. Following migration, these derivatives extensively populate multiple germ layers. Within the competent neural border ectoderm, an area located at the junction between the neural and non-neural ectoderm during embryonic development, neural crest cells form in response to a series of inductive secreted cues including BMP, Wnt, and FGF signals. As cells become progressively specified, they express transcriptional modules conducive with their stage of fate determination or cell state. Those sequential states include the neural border state, the premigratory neural crest state, the epithelium-to-mesenchyme transitional state, and the migratory state to end with post-migratory and differentiation states. However, despite the extensive knowledge accumulated over 150 years of neural crest biology, many key questions remain open, in particular the timing of neural crest lineage determination, the control of potency during early developmental stages, and the lineage relationships between different subpopulations of neural crest cells. In this review, we discuss the recent advances in understanding early neural crest formation using cutting-edge high-throughput single cell sequencing approaches. We will discuss how this new transcriptomic data, from 2017 to 2021, has advanced our knowledge of the steps in neural crest cell lineage commitment and specification, the mechanisms driving multipotency, and diversification. We will then discuss the questions that remain to be resolved and how these approaches may continue to unveil the biology of these fascinating cells.
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Affiliation(s)
- Kristin B Artinger
- Department of Craniofacial Biology, University of Colorado School of Dental Medicine, Aurora, CO, USA
| | - Anne H Monsoro-Burq
- Université Paris-Saclay, Faculté des Sciences d'Orsay, France
- Institut Curie, INSERM U1021, CNRS UMR3347, Orsay, France
- Institut Universitaire de France, Paris, France
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14
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Figiel DM, Elsayed R, Nelson AC. Investigating the molecular guts of endoderm formation using zebrafish. Brief Funct Genomics 2021:elab013. [PMID: 33754635 DOI: 10.1093/bfgp/elab013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
The vertebrate endoderm makes major contributions to the respiratory and gastrointestinal tracts and all associated organs. Zebrafish and humans share a high degree of genetic homology and strikingly similar endodermal organ systems. Combined with a multitude of experimental advantages, zebrafish are an attractive model organism to study endoderm development and disease. Recent functional genomics studies have shed considerable light on the gene regulatory programs governing early zebrafish endoderm development, while advances in biological and technological approaches stand to further revolutionize our ability to investigate endoderm formation, function and disease. Here, we discuss the present understanding of endoderm specification in zebrafish compared to other vertebrates, how current and emerging methods will allow refined and enhanced analysis of endoderm formation, and how integration with human data will allow modeling of the link between non-coding sequence variants and human disease.
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Affiliation(s)
- Daniela M Figiel
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
| | - Randa Elsayed
- Medical Research Council Doctoral Training Partnership in Interdisciplinary Biomedical Research at Warwick Medical School
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15
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Chong-Morrison V, Sauka-Spengler T. The Cranial Neural Crest in a Multiomics Era. Front Physiol 2021; 12:634440. [PMID: 33732166 PMCID: PMC7956944 DOI: 10.3389/fphys.2021.634440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Neural crest ontogeny plays a prominent role in craniofacial development. In this Perspective article, we discuss recent advances to the understanding of mechanisms underlying the cranial neural crest gene regulatory network (cNC-GRN) stemming from omics-based studies. We briefly summarize how parallel considerations of transcriptome, interactome, and epigenome data significantly elaborated the roles of key players derived from pre-omics era studies. Furthermore, the growing cohort of cNC multiomics data revealed contribution of the non-coding genomic landscape. As technological improvements are constantly being developed, we reflect on key questions we are poised to address by taking advantage of the unique perspective a multiomics approach has to offer.
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16
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Lukoseviciute M, Ling ITC, Senanayake U, Candido-Ferreira I, Taylor G, Williams RM, Sauka-Spengler T. Tissue-Specific In Vivo Biotin Chromatin Immunoprecipitation with Sequencing in Zebrafish and Chicken. STAR Protoc 2020; 1:100066. [PMID: 33111104 PMCID: PMC7580215 DOI: 10.1016/j.xpro.2020.100066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Chromatin immunoprecipitation with sequencing (ChIP-seq) has been instrumental in understanding transcription factor (TF) binding during gene regulation. ChIP-seq requires specific antibodies against desired TFs, which are not available for numerous species. Here, we describe a tissue-specific biotin ChIP-seq protocol for zebrafish and chicken embryos which utilizes AVI tagging of TFs, permitting their biotinylation by a co-expressed nuclear biotin ligase. Subsequently, biotinylated factors can be precipitated with streptavidin beads, enabling the user to construct TF genome-wide binding landscapes like conventional ChIP-seq methods. For complete details on the use and execution of this protocol, please see Lukoseviciute et al. (2018) and Ling and Sauka-Spengler (2019). Tissue-specific in vivo ChIP for biotinylated DNA-binding proteins of interest Protocol generates genome-wide binding maps in chicken or zebrafish ChIP-seq can be performed without antibody usage and cell sorting Protocol requires a relatively low number of cells as input (100,000–150,000)
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Affiliation(s)
- Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
| | - Irving T C Ling
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
| | - Ivan Candido-Ferreira
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
| | - Gunes Taylor
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
| | - Ruth M Williams
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute for Molecular Medicine, John Radcliffe, Oxford OX3 9DS, UK
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17
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Weinberger M, Simões FC, Patient R, Sauka-Spengler T, Riley PR. Functional Heterogeneity within the Developing Zebrafish Epicardium. Dev Cell 2020; 52:574-590.e6. [PMID: 32084358 PMCID: PMC7063573 DOI: 10.1016/j.devcel.2020.01.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/07/2019] [Accepted: 01/22/2020] [Indexed: 12/31/2022]
Abstract
The epicardium is essential during cardiac development, homeostasis, and repair, and yet fundamental insights into its underlying cell biology, notably epicardium formation, lineage heterogeneity, and functional cross-talk with other cell types in the heart, are currently lacking. In this study, we investigated epicardial heterogeneity and the functional diversity of discrete epicardial subpopulations in the developing zebrafish heart. Single-cell RNA sequencing uncovered three epicardial subpopulations with specific genetic programs and distinctive spatial distribution. Perturbation of unique gene signatures uncovered specific functions associated with each subpopulation and established epicardial roles in cell adhesion, migration, and chemotaxis as a mechanism for recruitment of leukocytes into the heart. Understanding which mechanisms epicardial cells employ to establish a functional epicardium and how they communicate with other cardiovascular cell types during development will bring us closer to repairing cellular relationships that are disrupted during cardiovascular disease. scRNA-seq uncovered 3 developmental epicardial subpopulations (Epi1-3) in the zebrafish Epi1-specific gene, tgm2b, regulates the cell numbers in the main epicardial sheet Epi2-specific gene, sema3fb, restricts the number of tbx18+ cells in the cardiac outflow tract Epi3-specific gene, cxcl12a, guides ptprc/CD45+ myeloid cells to the developing heart
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Affiliation(s)
- Michael Weinberger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, Oxfordshire OX1 3PT, UK; MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | - Filipa C Simões
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, Oxfordshire OX1 3PT, UK; MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | - Roger Patient
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, Oxfordshire OX3 9DS, UK.
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, Oxfordshire OX1 3PT, UK.
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18
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Simões FC, Cahill TJ, Kenyon A, Gavriouchkina D, Vieira JM, Sun X, Pezzolla D, Ravaud C, Masmanian E, Weinberger M, Mayes S, Lemieux ME, Barnette DN, Gunadasa-Rohling M, Williams RM, Greaves DR, Trinh LA, Fraser SE, Dallas SL, Choudhury RP, Sauka-Spengler T, Riley PR. Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nat Commun 2020; 11:600. [PMID: 32001677 PMCID: PMC6992796 DOI: 10.1038/s41467-019-14263-2] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/27/2019] [Indexed: 12/14/2022] Open
Abstract
Canonical roles for macrophages in mediating the fibrotic response after a heart attack include extracellular matrix turnover and activation of cardiac fibroblasts to initiate collagen deposition. Here we reveal that macrophages directly contribute collagen to the forming post-injury scar. Unbiased transcriptomics shows an upregulation of collagens in both zebrafish and mouse macrophages following heart injury. Adoptive transfer of macrophages, from either collagen-tagged zebrafish or adult mouse GFPtpz-collagen donors, enhances scar formation via cell autonomous production of collagen. In zebrafish, the majority of tagged collagen localises proximal to the injury, within the overlying epicardial region, suggesting a possible distinction between macrophage-deposited collagen and that predominantly laid-down by myofibroblasts. Macrophage-specific targeting of col4a3bpa and cognate col4a1 in zebrafish significantly reduces scarring in cryoinjured hosts. Our findings contrast with the current model of scarring, whereby collagen deposition is exclusively attributed to myofibroblasts, and implicate macrophages as direct contributors to fibrosis during heart repair. Macrophages mediate the fibrotic response after a heart attack by extracellular matrix turnover and cardiac fibroblasts activation. Here the authors identify an evolutionarily-conserved function of macrophages that contributes directly to the forming post-injury scar through cell-autonomous deposition of collagen.
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Affiliation(s)
- Filipa C Simões
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,BHF Oxbridge Centre of Regenerative Medicine, University of Oxford, Oxford, UK
| | - Thomas J Cahill
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,BHF Oxbridge Centre of Regenerative Medicine, University of Oxford, Oxford, UK.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Amy Kenyon
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.,Molecular Genetics Unit, Okinawa Institute of Science & Technology, 1919-1 Tancha, Onna, 904-0495, Japan
| | - Joaquim M Vieira
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,BHF Oxbridge Centre of Regenerative Medicine, University of Oxford, Oxford, UK
| | - Xin Sun
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,BHF Oxbridge Centre of Regenerative Medicine, University of Oxford, Oxford, UK
| | - Daniela Pezzolla
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Christophe Ravaud
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,BHF Oxbridge Centre of Regenerative Medicine, University of Oxford, Oxford, UK
| | - Eva Masmanian
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Michael Weinberger
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Sarah Mayes
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK.,Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | | | - Damien N Barnette
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Mala Gunadasa-Rohling
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - David R Greaves
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Le A Trinh
- Translational Imaging Centre, University of Southern California, Los Angeles, CA, USA
| | - Scott E Fraser
- Translational Imaging Centre, University of Southern California, Los Angeles, CA, USA
| | - Sarah L Dallas
- School of Dentistry, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Robin P Choudhury
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Paul R Riley
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK. .,BHF Oxbridge Centre of Regenerative Medicine, University of Oxford, Oxford, UK.
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19
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Hockman D, Chong-Morrison V, Green SA, Gavriouchkina D, Candido-Ferreira I, Ling ITC, Williams RM, Amemiya CT, Smith JJ, Bronner ME, Sauka-Spengler T. A genome-wide assessment of the ancestral neural crest gene regulatory network. Nat Commun 2019; 10:4689. [PMID: 31619682 PMCID: PMC6795873 DOI: 10.1038/s41467-019-12687-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/23/2019] [Indexed: 12/17/2022] Open
Abstract
The neural crest (NC) is an embryonic cell population that contributes to key vertebrate-specific features including the craniofacial skeleton and peripheral nervous system. Here we examine the transcriptional and epigenomic profiles of NC cells in the sea lamprey, in order to gain insight into the ancestral state of the NC gene regulatory network (GRN). Transcriptome analyses identify clusters of co-regulated genes during NC specification and migration that show high conservation across vertebrates but also identify transcription factors (TFs) and cell-adhesion molecules not previously implicated in NC migration. ATAC-seq analysis uncovers an ensemble of cis-regulatory elements, including enhancers of Tfap2B, SoxE1 and Hox-α2 validated in the embryo. Cross-species deployment of lamprey elements identifies the deep conservation of lamprey SoxE1 enhancer activity, mediating homologous expression in jawed vertebrates. Our data provide insight into the core GRN elements conserved to the base of the vertebrates and expose others that are unique to lampreys.
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Affiliation(s)
- Dorit Hockman
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Division of Cell Biology, Department of Human Biology, Neuroscience Institute, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Division of Biosciences, Faculty of Life Sciences, University College London, London, UK
| | - Stephen A Green
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Okinawa Institute of Science and Technology, Molecular Genetics Unit, Onna, Japan
| | - Ivan Candido-Ferreira
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Irving T C Ling
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Chris T Amemiya
- Molecular Cell Biology, School of Natural Sciences, University of California, Merced, CA, USA
| | - Jeramiah J Smith
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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20
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Shin M, Nozaki T, Idrizi F, Isogai S, Ogasawara K, Ishida K, Yuge S, Roscoe B, Wolfe SA, Fukuhara S, Mochizuki N, Deguchi T, Lawson ND. Valves Are a Conserved Feature of the Zebrafish Lymphatic System. Dev Cell 2019; 51:374-386.e5. [PMID: 31564611 DOI: 10.1016/j.devcel.2019.08.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/19/2019] [Accepted: 08/28/2019] [Indexed: 12/19/2022]
Abstract
The lymphatic system comprises blind-ended tubes that collect interstitial fluid and return it to the circulatory system. In mammals, unidirectional lymphatic flow is driven by muscle contraction working in conjunction with valves. Accordingly, defective lymphatic valve morphogenesis results in backflow leading to edema. In fish species, studies dating to the 18th century failed to identify lymphatic valves, a precedent that currently persists, raising the question of whether the zebrafish could be used to study the development of these structures. Here, we provide functional and morphological evidence of valves in the zebrafish lymphatic system. Electron microscopy revealed valve ultrastructure similar to mammals, while live imaging using transgenic lines identified the developmental origins of lymphatic valve progenitors. Zebrafish embryos bearing mutations in genes required for mammalian valve morphogenesis show defective lymphatic valve formation and edema. Together, our observations provide a foundation from which to further investigate lymphatic valve formation in zebrafish.
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Affiliation(s)
- Masahiro Shin
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Takayuki Nozaki
- Technical Support Center for Life Science Research, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Feston Idrizi
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Sumio Isogai
- Department of Medical Education, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Katsutoshi Ogasawara
- Technical Support Center for Life Science Research, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Kinji Ishida
- Technical Support Center for Life Science Research, Iwate Medical University, Shiwa, Iwate 028-3694, Japan
| | - Shinya Yuge
- Department of Molecular Pathophysiology, Institute of Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugi-machi, Nakahara-ku, Kawasaki, Kanagawa 211-8533, Japan
| | - Benjamin Roscoe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Scot A Wolfe
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute of Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugi-machi, Nakahara-ku, Kawasaki, Kanagawa 211-8533, Japan
| | - Naoki Mochizuki
- Department of Cell Biology and AMED-CREST, National Cerebral and Cardiovascular Center, Research Institute, Suita, Osaka 565-8565, Japan
| | - Tomonori Deguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563-8577, Japan
| | - Nathan D Lawson
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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21
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Dooley CM, Wali N, Sealy IM, White RJ, Stemple DL, Collins JE, Busch-Nentwich EM. The gene regulatory basis of genetic compensation during neural crest induction. PLoS Genet 2019; 15:e1008213. [PMID: 31199790 PMCID: PMC6594659 DOI: 10.1371/journal.pgen.1008213] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/26/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022] Open
Abstract
The neural crest (NC) is a vertebrate-specific cell type that contributes to a wide range of different tissues across all three germ layers. The gene regulatory network (GRN) responsible for the formation of neural crest is conserved across vertebrates. Central to the induction of the NC GRN are AP-2 and SoxE transcription factors. NC induction robustness is ensured through the ability of some of these transcription factors to compensate loss of function of gene family members. However the gene regulatory events underlying compensation are poorly understood. We have used gene knockout and RNA sequencing strategies to dissect NC induction and compensation in zebrafish. We genetically ablate the NC using double mutants of tfap2a;tfap2c or remove specific subsets of the NC with sox10 and mitfa knockouts and characterise genome-wide gene expression levels across multiple time points. We find that compensation through a single wild-type allele of tfap2c is capable of maintaining early NC induction and differentiation in the absence of tfap2a function, but many target genes have abnormal expression levels and therefore show sensitivity to the reduced tfap2 dosage. This separation of morphological and molecular phenotypes identifies a core set of genes required for early NC development. We also identify the 15 somites stage as the peak of the molecular phenotype which strongly diminishes at 24 hpf even as the morphological phenotype becomes more apparent. Using gene knockouts, we associate previously uncharacterised genes with pigment cell development and establish a role for maternal Hippo signalling in melanocyte differentiation. This work extends and refines the NC GRN while also uncovering the transcriptional basis of genetic compensation via paralogues. Embryonic development is an intricate process that requires genes to be active at the right time and place. Organisms have evolved mechanisms that ensure faithful execution of developmental programmes even if genes fail to function. For example, in a process called genetic compensation, one or more genes become activated in response to loss of function of another. In this work we use the zebrafish model to investigate how two related genes, tfap2a and tfap2c, interact to ensure establishment of the neural crest, a vertebrate-specific cell type that contributes to many different tissues. Losing tfap2a activity causes mild morphological defects and losing tfap2c has no visible effect. Yet when both are inactive, embryos are severely abnormal due to lack of neural crest-derived tissues. Here we show that loss of tfap2a triggers upregulation of tfap2c which prevents the loss of neural crest tissue. However, the genes normally regulated by tfap2a respond differently to tfap2c allowing us to identify the first tier of the Ap2 network and new players in neural crest biology. Our work demonstrates that the expression signature of partial, but morphologically sufficient, genetic compensation provides an opportunity to dissect gene regulatory networks.
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Affiliation(s)
| | - Neha Wali
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Ian M. Sealy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Richard J. White
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - John E. Collins
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elisabeth M. Busch-Nentwich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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22
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Lukoseviciute M, Gavriouchkina D, Williams RM, Hochgreb-Hagele T, Senanayake U, Chong-Morrison V, Thongjuea S, Repapi E, Mead A, Sauka-Spengler T. From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo. Dev Cell 2019; 47:608-628.e6. [PMID: 30513303 PMCID: PMC6286384 DOI: 10.1016/j.devcel.2018.11.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/15/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
Abstract
The neural crest (NC) is a transient embryonic stem cell-like population characterized by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that, during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses differential partners for each role. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from “permissive” to “repressive” nucleosome and chromatin organization to maintain multipotency and define cell fates. FoxD3 primes neural crest specification by modulating distal enhancers FoxD3 represses a number of neural crest migration and differentiation genes In neural crest, FoxD3 acts to switch chromatin from “permissive” to “repressive” Distinctive gene regulatory mechanisms underlie the bimodal action of FoxD3
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Affiliation(s)
- Martyna Lukoseviciute
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hagele
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Supat Thongjuea
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam Mead
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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23
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Prasad MS, Charney RM, García-Castro MI. Specification and formation of the neural crest: Perspectives on lineage segregation. Genesis 2019; 57:e23276. [PMID: 30576078 PMCID: PMC6570420 DOI: 10.1002/dvg.23276] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022]
Abstract
The neural crest is a fascinating embryonic population unique to vertebrates that is endowed with remarkable differentiation capacity. Thought to originate from ectodermal tissue, neural crest cells generate neurons and glia of the peripheral nervous system, and melanocytes throughout the body. However, the neural crest also generates many ectomesenchymal derivatives in the cranial region, including cell types considered to be of mesodermal origin such as cartilage, bone, and adipose tissue. These ectomesenchymal derivatives play a critical role in the formation of the vertebrate head, and are thought to be a key attribute at the center of vertebrate evolution and diversity. Further, aberrant neural crest cell development and differentiation is the root cause of many human pathologies, including cancers, rare syndromes, and birth malformations. In this review, we discuss the current findings of neural crest cell ontogeny, and consider tissue, cell, and molecular contributions toward neural crest formation. We further provide current perspectives into the molecular network involved during the segregation of the neural crest lineage.
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Affiliation(s)
- Maneeshi S Prasad
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
| | - Rebekah M Charney
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
| | - Martín I García-Castro
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, California
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24
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Trinh LA, Chong-Morrison V, Sauka-Spengler T. Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods 2018; 150:24-31. [DOI: 10.1016/j.ymeth.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022] Open
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25
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Rogers CD, Nie S. Specifying neural crest cells: From chromatin to morphogens and factors in between. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018; 7:e322. [PMID: 29722151 PMCID: PMC6215528 DOI: 10.1002/wdev.322] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 12/16/2022]
Abstract
Neural crest (NC) cells are a stem-like multipotent population of progenitor cells that are present in vertebrate embryos, traveling to various regions in the developing organism. Known as the "fourth germ layer," these cells originate in the ectoderm between the neural plate (NP), which will become the brain and spinal cord, and nonneural tissues that will become the skin and the sensory organs. NC cells can differentiate into more than 30 different derivatives in response to the appropriate signals including, but not limited to, craniofacial bone and cartilage, sensory nerves and ganglia, pigment cells, and connective tissue. The molecular and cellular mechanisms that control the induction and specification of NC cells include epigenetic control, multiple interactive and redundant transcriptional pathways, secreted signaling molecules, and adhesion molecules. NC cells are important not only because they transform into a wide variety of tissue types, but also because their ability to detach from their epithelial neighbors and migrate throughout developing embryos utilizes mechanisms similar to those used by metastatic cancer cells. In this review, we discuss the mechanisms required for the induction and specification of NC cells in various vertebrate species, focusing on the roles of early morphogenesis, cell adhesion, signaling from adjacent tissues, and the massive transcriptional network that controls the formation of these amazing cells. This article is categorized under: Nervous System Development > Vertebrates: General Principles Gene Expression and Transcriptional Hierarchies > Regulatory Mechanisms Gene Expression and Transcriptional Hierarchies > Gene Networks and Genomics Signaling Pathways > Cell Fate Signaling.
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Affiliation(s)
- Crystal D. Rogers
- Department of Biology, College of Science and Mathematics, California State University Northridge, Northridge, California
| | - Shuyi Nie
- School of Biological Sciences and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia
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26
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Gurevich DB, Severn CE, Twomey C, Greenhough A, Cash J, Toye AM, Mellor H, Martin P. Live imaging of wound angiogenesis reveals macrophage orchestrated vessel sprouting and regression. EMBO J 2018; 37:embj.201797786. [PMID: 29866703 PMCID: PMC6028026 DOI: 10.15252/embj.201797786] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/21/2022] Open
Abstract
Wound angiogenesis is an integral part of tissue repair and is impaired in many pathologies of healing. Here, we investigate the cellular interactions between innate immune cells and endothelial cells at wounds that drive neoangiogenic sprouting in real time and in vivo. Our studies in mouse and zebrafish wounds indicate that macrophages are drawn to wound blood vessels soon after injury and are intimately associated throughout the repair process and that macrophage ablation results in impaired neoangiogenesis. Macrophages also positively influence wound angiogenesis by driving resolution of anti‐angiogenic wound neutrophils. Experimental manipulation of the wound environment to specifically alter macrophage activation state dramatically influences subsequent blood vessel sprouting, with premature dampening of tumour necrosis factor‐α expression leading to impaired neoangiogenesis. Complementary human tissue culture studies indicate that inflammatory macrophages associate with endothelial cells and are sufficient to drive vessel sprouting via vascular endothelial growth factor signalling. Subsequently, macrophages also play a role in blood vessel regression during the resolution phase of wound repair, and their absence, or shifted activation state, impairs appropriate vessel clearance.
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Affiliation(s)
| | - Charlotte E Severn
- School of Biochemistry, University of Bristol, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Unit in Red Blood Cell Products, University of Bristol, Bristol, UK
| | | | | | - Jenna Cash
- School of Biochemistry, University of Bristol, Bristol, UK.,MRC Centre for Inflammation Research, Edinburgh Medical School, The Queen's Medical Research Institute, Edinburgh, UK
| | - Ashley M Toye
- School of Biochemistry, University of Bristol, Bristol, UK.,National Institute for Health Research (NIHR) Blood and Transplant Unit in Red Blood Cell Products, University of Bristol, Bristol, UK.,Bristol Institute for Transfusion Sciences, NHS Blood and Transplant, Filton, Bristol, UK
| | - Harry Mellor
- School of Biochemistry, University of Bristol, Bristol, UK
| | - Paul Martin
- School of Biochemistry, University of Bristol, Bristol, UK .,School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, UK.,School of Medicine, University of Cardiff, Cardiff, UK
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27
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Schneider RA. Neural crest and the origin of species-specific pattern. Genesis 2018; 56:e23219. [PMID: 30134069 PMCID: PMC6108449 DOI: 10.1002/dvg.23219] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022]
Abstract
For well over half of the 150 years since the discovery of the neural crest, the special ability of these cells to function as a source of species-specific pattern has been clearly recognized. Initially, this observation arose in association with chimeric transplant experiments among differentially pigmented amphibians, where the neural crest origin for melanocytes had been duly noted. Shortly thereafter, the role of cranial neural crest cells in transmitting species-specific information on size and shape to the pharyngeal arch skeleton as well as in regulating the timing of its differentiation became readily apparent. Since then, what has emerged is a deeper understanding of how the neural crest accomplishes such a presumably difficult mission, and this includes a more complete picture of the molecular and cellular programs whereby neural crest shapes the face of each species. This review covers studies on a broad range of vertebrates and describes neural-crest-mediated mechanisms that endow the craniofacial complex with species-specific pattern. A major focus is on experiments in quail and duck embryos that reveal a hierarchy of cell-autonomous and non-autonomous signaling interactions through which neural crest generates species-specific pattern in the craniofacial integument, skeleton, and musculature. By controlling size and shape throughout the development of these systems, the neural crest underlies the structural and functional integration of the craniofacial complex during evolution.
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Affiliation(s)
- Richard A. Schneider
- Department of Orthopedic SurgeryUniversity of California at San Francisco, 513 Parnassus AvenueS‐1161San Francisco, California
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28
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Kenyon A, Gavriouchkina D, Zorman J, Chong-Morrison V, Napolitani G, Cerundolo V, Sauka-Spengler T. Generation of a double binary transgenic zebrafish model to study myeloid gene regulation in response to oncogene activation in melanocytes. Dis Model Mech 2018; 11:dmm030056. [PMID: 29666124 PMCID: PMC5963855 DOI: 10.1242/dmm.030056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022] Open
Abstract
A complex network of inflammatory genes is closely linked to somatic cell transformation and malignant disease. Immune cells and their associated molecules are responsible for detecting and eliminating cancer cells as they establish themselves as the precursors of a tumour. By the time a patient has a detectable solid tumour, cancer cells have escaped the initial immune response mechanisms. Here, we describe the development of a double binary zebrafish model that enables regulatory programming of the myeloid cells as they respond to oncogene-activated melanocytes to be explored, focussing on the initial phase when cells become the precursors of cancer. A hormone-inducible binary system allows for temporal control of expression of different Ras oncogenes (NRasQ61K, HRasG12V and KRasG12V) in melanocytes, leading to proliferation and changes in morphology of the melanocytes. This model was coupled to binary cell-specific biotagging models allowing in vivo biotinylation and subsequent isolation of macrophage or neutrophil nuclei for regulatory profiling of their active transcriptomes. Nuclear transcriptional profiling of neutrophils, performed as they respond to the earliest precursors of melanoma in vivo, revealed an intricate landscape of regulatory factors that may promote progression to melanoma, including Serpinb1l4, Fgf1, Fgf6, Cathepsin H, Galectin 1 and Galectin 3. The model presented here provides a powerful platform to study the myeloid response to the earliest precursors of melanoma.
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Affiliation(s)
- Amy Kenyon
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Daria Gavriouchkina
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Jernej Zorman
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Vanessa Chong-Morrison
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Giorgio Napolitani
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Vincenzo Cerundolo
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, United Kingdom
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29
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Quillien A, Abdalla M, Yu J, Ou J, Zhu LJ, Lawson ND. Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. Cell Rep 2018; 20:709-720. [PMID: 28723572 DOI: 10.1016/j.celrep.2017.06.070] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 02/08/2023] Open
Abstract
Identification of tissue-specific and developmentally active enhancers provides insights into mechanisms that control gene expression during embryogenesis. However, robust detection of these regulatory elements remains challenging, especially in vertebrate genomes. Here, we apply fluorescent-activated nuclei sorting (FANS) followed by Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) to identify developmentally active endothelial enhancers in the zebrafish genome. ATAC-seq of nuclei from Tg(fli1a:egfp)y1 transgenic embryos revealed expected patterns of nucleosomal positioning at transcriptional start sites throughout the genome and association with active histone modifications. Comparison of ATAC-seq from GFP-positive and -negative nuclei identified more than 5,000 open elements specific to endothelial cells. These elements flanked genes functionally important for vascular development and that displayed endothelial-specific gene expression. Importantly, a majority of tested elements drove endothelial gene expression in zebrafish embryos. Thus, FANS-assisted ATAC-seq using transgenic zebrafish embryos provides a robust approach for genome-wide identification of active tissue-specific enhancer elements.
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Affiliation(s)
- Aurelie Quillien
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Mary Abdalla
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jun Yu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Jianhong Ou
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA
| | - Lihua Julie Zhu
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA; Program in Bioinformatics and Integrative Biology, Department of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan D Lawson
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.
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30
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Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 2018; 10:474-485. [PMID: 29507920 DOI: 10.1039/c7mt00349h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Copper is essential for eukaryotic life, and animals must acquire this nutrient through the diet and distribute it to cells and organelles for proper function of biological targets. Indeed, mutations in the central copper exporter ATP7A contribute to a spectrum of diseases, including Menkes disease, with symptoms ranging from neurodegeneration to lax connective tissue. As such, a better understanding of the fundamental impacts of ATP7A mutations on in vivo copper distributions is of relevance to those affected by these diseases. Here we combine metal imaging and optical imaging techniques at a variety of spatial resolutions to identify tissues and structures with altered copper levels in the Calamitygw71 zebrafish model of Menkes disease. Rapid profiling of tissue slices with LA-ICP-MS identified reduced copper levels in the brain, neuroretina, and liver of Menkes fish compared to control specimens. High resolution nanoSIMS imaging of the neuroretina, combined with electron and confocal microscopies, identified the megamitochondria of photoreceptors as loci of copper accumulation in wildtype fish, with lower levels of megamitochondrial copper observed in Calamitygw71 zebrafish. Interestingly, this localized copper decrease does not result in impaired photoreceptor development or altered megamitochondrial morphology, suggesting the prioritization of copper at sufficient levels for maintaining essential mitochondrial functions. Together, these data establish the Calamitygw71 zebrafish as an optically transparent in vivo model for the study of neural copper misregulation, illuminate a role for the ATP7A copper exporter in trafficking copper to the neuroretina, and highlight the utility of combining multiple imaging techniques for studying metals in whole organism settings with spatial resolution.
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Affiliation(s)
- Cheri M Ackerman
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Peter K Weber
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
| | - Tong Xiao
- Department of Chemistry, University of California, Berkeley, California, USA. and Howard Hughes Medical Institute, University of California, Berkeley, California, USA
| | - Bao Thai
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Tiffani J Kuo
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Emily Zhang
- Department of Chemistry, University of California, Berkeley, California, USA.
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA.
| | - Christopher J Chang
- Department of Chemistry, University of California, Berkeley, California, USA. and Howard Hughes Medical Institute, University of California, Berkeley, California, USA and Department of Molecular and Cellular Biology, University of California, Berkeley, California, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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31
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White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017; 6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022] Open
Abstract
We have produced an mRNA expression time course of zebrafish development across 18 time points from 1 cell to 5 days post-fertilisation sampling individual and pools of embryos. Using poly(A) pulldown stranded RNA-seq and a 3′ end transcript counting method we characterise temporal expression profiles of 23,642 genes. We identify temporal and functional transcript co-variance that associates 5024 unnamed genes with distinct developmental time points. Specifically, a class of over 100 previously uncharacterised zinc finger domain containing genes, located on the long arm of chromosome 4, is expressed in a sharp peak during zygotic genome activation. In addition, the data reveal new genes and transcripts, differential use of exons and previously unidentified 3′ ends across development, new primary microRNAs and temporal divergence of gene paralogues generated in the teleost genome duplication. To make this dataset a useful baseline reference, the data can be browsed and downloaded at Expression Atlas and Ensembl.
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Affiliation(s)
| | - John E Collins
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Ian M Sealy
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Neha Wali
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Zsofia Digby
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Daniel N Murphy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anja Füllgrabe
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Matthew P Davis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Anton J Enright
- European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, United Kingdom
| | - Elisabeth M Busch-Nentwich
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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32
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Martik ML, Bronner ME. Regulatory Logic Underlying Diversification of the Neural Crest. Trends Genet 2017; 33:715-727. [PMID: 28851604 DOI: 10.1016/j.tig.2017.07.015] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 12/29/2022]
Abstract
The neural crest is a transient, multipotent population of cells that arises at the border of the developing nervous system. After closure of the neural tube, these cells undergo an epithelial-to-mesenchymal transition (EMT) to delaminate and migrate, often to distant locations in the embryo. Neural crest cells give rise to a diverse array of derivatives including neurons and glia of the peripheral nervous system, melanocytes, and bone and cartilage of the face. A gene regulatory network (GRN) controls the specification, delamination, migration, and differentiation of this fascinating cell type. With increasing technological advances, direct linkages within the neural crest GRN are being uncovered. The underlying circuitry is useful for understanding important topics such as reprogramming, evolution, and disease.
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Affiliation(s)
- Megan L Martik
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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33
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Kenyon A, Gavriouchkina D, Zorman J, Napolitani G, Cerundolo V, Sauka-Spengler T. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum. Sci Rep 2017; 7:6505. [PMID: 28747644 PMCID: PMC5529371 DOI: 10.1038/s41598-017-06099-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/07/2017] [Indexed: 12/17/2022] Open
Abstract
The mechanisms governing neutrophil response to Mycobacterium tuberculosis remain poorly understood. In this study we utilise biotagging, a novel genome-wide profiling approach based on cell type-specific in vivo biotinylation in zebrafish to analyse the initial response of neutrophils to Mycobacterium marinum, a close genetic relative of M. tuberculosis used to model tuberculosis. Differential expression analysis following nuclear RNA-seq of neutrophil active transcriptomes reveals a significant upregulation in both damage-sensing and effector components of the inflammasome, including caspase b, NLRC3 ortholog (wu: fb15h11) and il1β. Crispr/Cas9-mediated knockout of caspase b, which acts by proteolytic processing of il1β, results in increased bacterial burden and less infiltration of macrophages to sites of mycobacterial infection, thus impairing granuloma development. We also show that a number of immediate early response genes (IEGs) are responsible for orchestrating the initial neutrophil response to mycobacterial infection. Further perturbation of the IEGs exposes egr3 as a key transcriptional regulator controlling il1β transcription.
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Affiliation(s)
- Amy Kenyon
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom
| | - Daria Gavriouchkina
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom
| | - Jernej Zorman
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom
| | - Giorgio Napolitani
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom
| | - Vincenzo Cerundolo
- University of Oxford, Weatherall Institute of Molecular Medicine, MRC Human Immunology Unit, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom
| | - Tatjana Sauka-Spengler
- University of Oxford, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, OX3 9DS, United Kingdom.
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