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Mok GF, Turner S, Smith EL, Mincarelli L, Lister A, Lipscombe J, Uzun V, Haerty W, Macaulay IC, Münsterberg AE. Single cell RNA-sequencing and RNA-tomography of the avian embryo extending body axis. Front Cell Dev Biol 2024; 12:1382960. [PMID: 38863942 PMCID: PMC11165230 DOI: 10.3389/fcell.2024.1382960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 04/29/2024] [Indexed: 06/13/2024] Open
Abstract
Introduction: Vertebrate body axis formation initiates during gastrulation and continues within the tail bud at the posterior end of the embryo. Major structures in the trunk are paired somites, which generate the musculoskeletal system, the spinal cord-forming part of the central nervous system, and the notochord, with important patterning functions. The specification of these different cell lineages by key signalling pathways and transcription factors is essential, however, a global map of cell types and expressed genes in the avian trunk is missing. Methods: Here we use high-throughput sequencing approaches to generate a molecular map of the emerging trunk and tailbud in the chick embryo. Results and Discussion: Single cell RNA-sequencing (scRNA-seq) identifies discrete cell lineages including somites, neural tube, neural crest, lateral plate mesoderm, ectoderm, endothelial and blood progenitors. In addition, RNA-seq of sequential tissue sections (RNA-tomography) provides a spatially resolved, genome-wide expression dataset for the avian tailbud and emerging body, comparable to other model systems. Combining the single cell and RNA-tomography datasets, we identify spatially restricted genes, focusing on somites and early myoblasts. Thus, this high-resolution transcriptome map incorporating cell types in the embryonic trunk can expose molecular pathways involved in body axis development.
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Affiliation(s)
- G. F. Mok
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - S. Turner
- Earlham Institute, Norwich, United Kingdom
| | - E. L. Smith
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | | | - A. Lister
- Earlham Institute, Norwich, United Kingdom
| | | | - V. Uzun
- Earlham Institute, Norwich, United Kingdom
| | - W. Haerty
- Earlham Institute, Norwich, United Kingdom
| | | | - A. E. Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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2
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Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024; 15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [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: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Tissue-specific gene expression is fundamental in development and evolution, and is mediated by transcription factors and by the cis-regulatory regions (enhancers) that they control. Transcription factors and their respective tissue-specific enhancers are essential components of gene regulatory networks responsible for the development of tissues and organs. Although numerous transcription factors have been characterized from different organisms, the knowledge of the enhancers responsible for their tissue-specific expression remains fragmentary. Here we use Ciona to study the enhancers associated with ten transcription factors expressed in the notochord, an evolutionary hallmark of the chordate phylum. Our results illustrate how two evolutionarily conserved transcription factors, Brachyury and Foxa2, coordinate the deployment of other notochord transcription factors. The results of these detailed cis-regulatory analyses delineate a high-resolution view of the essential notochord gene regulatory network of Ciona, and provide a reference for studies of transcription factors, enhancers, and their roles in development, disease, and evolution.
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Affiliation(s)
- Lenny J Negrón-Piñeiro
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Yushi Wu
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA
| | - Sydney Popsuj
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Diana S José-Edwards
- Post-Baccalaureate Premedical Program, Washington University, St. Louis, MO, 63130, USA
| | - Alberto Stolfi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Anna Di Gregorio
- Department of Molecular Pathobiology, New York University College of Dentistry, New York, NY, 10010, USA.
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3
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Piacentino ML, Fasse AJ, Camacho-Avila A, Grabylnikov I, Bronner ME. SMPD3 expression is spatially regulated in the developing embryo by SOXE factors. Dev Biol 2024; 506:31-41. [PMID: 38052296 PMCID: PMC10872304 DOI: 10.1016/j.ydbio.2023.11.011] [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: 08/10/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
During epithelial-to-mesenchymal transition (EMT), significant rearrangements occur in plasma membrane protein and lipid content that are important for membrane function and acquisition of cell motility. To gain insight into how neural crest cells regulate their lipid content at the transcriptional level during EMT, here we identify critical enhancer sequences that regulate the expression of SMPD3, a gene responsible for sphingomyelin hydrolysis to produce ceramide and necessary for neural crest EMT. We uncovered three enhancer regions within the first intron of the SMPD3 locus that drive reporter expression in distinct spatial and temporal domains, together collectively recapitulating the expression domains of endogenous SMPD3 within the ectodermal lineages. We further dissected one enhancer that is specifically active in the migrating neural crest. By mutating putative transcriptional input sites or knocking down upstream regulators, we find that the SOXE-family transcription factors SOX9 and SOX10 regulate the expression of SMPD3 in migrating neural crest cells. Further, ChIP-seq and nascent transcription analysis reveal that SOX10 directly regulates expression of an SMPD3 enhancer specific to migratory neural crest cells. Together these results shed light on how core components of developmental gene regulatory networks interact with metabolic effector genes to control changes in membrane lipid content.
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Affiliation(s)
- Michael L Piacentino
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA; Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
| | - Aria J Fasse
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Alexis Camacho-Avila
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Ilya Grabylnikov
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Marianne E Bronner
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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4
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Hartley M, Kleywegt GJ, Patwardhan A, Sarkans U, Swedlow JR, Brazma A. The BioImage Archive - Building a Home for Life-Sciences Microscopy Data. J Mol Biol 2022; 434:167505. [PMID: 35189131 DOI: 10.1016/j.jmb.2022.167505] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/04/2022] [Accepted: 02/15/2022] [Indexed: 01/15/2023]
Abstract
Despite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/.
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Affiliation(s)
- Matthew Hartley
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
| | - Gerard J Kleywegt
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ardan Patwardhan
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ugis Sarkans
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Jason R Swedlow
- Division of Computational Biology, Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
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5
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Mantri M, Scuderi GJ, Abedini-Nassab R, Wang MFZ, McKellar D, Shi H, Grodner B, Butcher JT, De Vlaminck I. Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. Nat Commun 2021; 12:1771. [PMID: 33741943 PMCID: PMC7979764 DOI: 10.1038/s41467-021-21892-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 02/17/2021] [Indexed: 01/01/2023] Open
Abstract
Single-cell RNA sequencing is a powerful tool to study developmental biology but does not preserve spatial information about tissue morphology and cellular interactions. Here, we combine single-cell and spatial transcriptomics with algorithms for data integration to study the development of the chicken heart from the early to late four-chambered heart stage. We create a census of the diverse cellular lineages in developing hearts, their spatial organization, and their interactions during development. Spatial mapping of differentiation transitions in cardiac lineages defines transcriptional differences between epithelial and mesenchymal cells within the epicardial lineage. Using spatially resolved expression analysis, we identify anatomically restricted expression programs, including expression of genes implicated in congenital heart disease. Last, we discover a persistent enrichment of the small, secreted peptide, thymosin beta-4, throughout coronary vascular development. Overall, our study identifies an intricate interplay between cellular differentiation and morphogenesis.
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Affiliation(s)
- Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Computational Biology Ph.D. Program, Cornell University, Ithaca, NY, USA
| | - Gaetano J Scuderi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Roozbeh Abedini-Nassab
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Department of Engineering, University of Neyshabur, Neyshabur, Iran
| | - Michael F Z Wang
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
- Computational Biology Ph.D. Program, Cornell University, Ithaca, NY, USA
| | - David McKellar
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Hao Shi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Benjamin Grodner
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Jonathan T Butcher
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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Vijayan A, Tofanelli R, Strauss S, Cerrone L, Wolny A, Strohmeier J, Kreshuk A, Hamprecht FA, Smith RS, Schneitz K. A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule. eLife 2021; 10:e63262. [PMID: 33404501 PMCID: PMC7787667 DOI: 10.7554/elife.63262] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 12/19/2020] [Indexed: 12/23/2022] Open
Abstract
A fundamental question in biology is how morphogenesis integrates the multitude of processes that act at different scales, ranging from the molecular control of gene expression to cellular coordination in a tissue. Using machine-learning-based digital image analysis, we generated a three-dimensional atlas of ovule development in Arabidopsis thaliana, enabling the quantitative spatio-temporal analysis of cellular and gene expression patterns with cell and tissue resolution. We discovered novel morphological manifestations of ovule polarity, a new mode of cell layer formation, and previously unrecognized subepidermal cell populations that initiate ovule curvature. The data suggest an irregular cellular build-up of WUSCHEL expression in the primordium and new functions for INNER NO OUTER in restricting nucellar cell proliferation and the organization of the interior chalaza. Our work demonstrates the analytical power of a three-dimensional digital representation when studying the morphogenesis of an organ of complex architecture that eventually consists of 1900 cells.
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Affiliation(s)
- Athul Vijayan
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
| | - Rachele Tofanelli
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Lorenzo Cerrone
- Heidelberg Collaboratory for Image Processing, Dept. of Physics and Astronomy, Heidelberg UniversityHeidelbergGermany
| | - Adrian Wolny
- Heidelberg Collaboratory for Image Processing, Dept. of Physics and Astronomy, Heidelberg UniversityHeidelbergGermany
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Joanna Strohmeier
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
| | - Anna Kreshuk
- European Molecular Biology LaboratoryHeidelbergGermany
| | - Fred A Hamprecht
- Heidelberg Collaboratory for Image Processing, Dept. of Physics and Astronomy, Heidelberg UniversityHeidelbergGermany
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding ResearchCologneGermany
| | - Kay Schneitz
- Plant Developmental Biology, School of Life Sciences, Technical University of MunichFreisingGermany
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7
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Marr N, Hopkinson M, Hibbert AP, Pitsillides AA, Thorpe CT. Bimodal Whole-Mount Imaging of Tendon Using Confocal Microscopy and X-ray Micro-Computed Tomography. Biol Proced Online 2020; 22:13. [PMID: 32624710 PMCID: PMC7329428 DOI: 10.1186/s12575-020-00126-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/21/2020] [Indexed: 12/25/2022] Open
Abstract
Background Three-dimensional imaging modalities for optically dense connective tissues such as tendons are limited and typically have a single imaging methodological endpoint. Here, we have developed a bimodal procedure utilising fluorescence-based confocal microscopy and x-ray micro-computed tomography for the imaging of adult tendons to visualise and analyse extracellular sub-structure and cellular composition in small and large animal species. Results Using fluorescent immunolabelling and optical clearing, we visualised the expression of the novel cross-species marker of tendon basement membrane, laminin-α4 in 3D throughout whole rat Achilles tendons and equine superficial digital flexor tendon 5 mm segments. This revealed a complex network of laminin-α4 within the tendon core that predominantly localises to the interfascicular matrix compartment. Furthermore, we implemented a chemical drying process capable of creating contrast densities enabling visualisation and quantification of both fascicular and interfascicular matrix volume and thickness by x-ray micro-computed tomography. We also demonstrated that both modalities can be combined using reverse clarification of fluorescently labelled tissues prior to chemical drying to enable bimodal imaging of a single sample. Conclusions Whole-mount imaging of tendon allowed us to identify the presence of an extensive network of laminin-α4 within tendon, the complexity of which cannot be appreciated using traditional 2D imaging techniques. Creating contrast for x-ray micro-computed tomography imaging of tendon using chemical drying is not only simple and rapid, but also markedly improves on previously published methods. Combining these methods provides the ability to gain spatio-temporal information and quantify tendon substructures to elucidate the relationship between morphology and function.
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Affiliation(s)
- Neil Marr
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, UK
| | - Mark Hopkinson
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, UK
| | - Andrew P Hibbert
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, UK
| | - Andrew A Pitsillides
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, UK
| | - Chavaunne T Thorpe
- Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, UK
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Optical Projection Tomography Using a Commercial Microfluidic System. MICROMACHINES 2020; 11:mi11030293. [PMID: 32168806 PMCID: PMC7142877 DOI: 10.3390/mi11030293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/17/2023]
Abstract
Optical projection tomography (OPT) is the direct optical equivalent of X-ray computed tomography (CT). To obtain a larger depth of field, traditional OPT usually decreases the numerical aperture (NA) of the objective lens to decrease the resolution of the image. So, there is a trade-off between sample size and resolution. Commercial microfluidic systems can observe a sample in flow mode. In this paper, an OPT instrument is constructed to observe samples. The OPT instrument is combined with commercial microfluidic systems to obtain a three-dimensional and time (3D + T)/four-dimensional (4D) video of the sample. “Focal plane scanning” is also used to increase the images’ depth of field. A series of two-dimensional (2D) images in different focal planes was observed and compared with images simulated using our program. Our work dynamically monitors 3D OPT images. Commercial microfluidic systems simulate blood flow, which has potential application in blood monitoring and intelligent drug delivery platforms. We design an OPT adaptor to perform OPT on a commercial wide-field inverted microscope (Olympusix81). Images in different focal planes are observed and analyzed. Using a commercial microfluidic system, a video is also acquired to record motion pictures of samples at different flow rates. To our knowledge, this is the first time an OPT setup has been combined with a microfluidic system.
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