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Burger A, Baldock RA, Adams DJ, Din S, Papatheodorou I, Glinka M, Hill B, Houghton D, Sharghi M, Wicks M, Arends MJ. Towards a clinically-based common coordinate framework for the human gut cell atlas: the gut models. BMC Med Inform Decis Mak 2023; 23:36. [PMID: 36793076 PMCID: PMC9933383 DOI: 10.1186/s12911-023-02111-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/13/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND The Human Cell Atlas resource will deliver single cell transcriptome data spatially organised in terms of gross anatomy, tissue location and with images of cellular histology. This will enable the application of bioinformatics analysis, machine learning and data mining revealing an atlas of cell types, sub-types, varying states and ultimately cellular changes related to disease conditions. To further develop the understanding of specific pathological and histopathological phenotypes with their spatial relationships and dependencies, a more sophisticated spatial descriptive framework is required to enable integration and analysis in spatial terms. METHODS We describe a conceptual coordinate model for the Gut Cell Atlas (small and large intestines). Here, we focus on a Gut Linear Model (1-dimensional representation based on the centreline of the gut) that represents the location semantics as typically used by clinicians and pathologists when describing location in the gut. This knowledge representation is based on a set of standardised gut anatomy ontology terms describing regions in situ, such as ileum or transverse colon, and landmarks, such as ileo-caecal valve or hepatic flexure, together with relative or absolute distance measures. We show how locations in the 1D model can be mapped to and from points and regions in both a 2D model and 3D models, such as a patient's CT scan where the gut has been segmented. RESULTS The outputs of this work include 1D, 2D and 3D models of the human gut, delivered through publicly accessible Json and image files. We also illustrate the mappings between models using a demonstrator tool that allows the user to explore the anatomical space of the gut. All data and software is fully open-source and available online. CONCLUSIONS Small and large intestines have a natural "gut coordinate" system best represented as a 1D centreline through the gut tube, reflecting functional differences. Such a 1D centreline model with landmarks, visualised using viewer software allows interoperable translation to both a 2D anatomogram model and multiple 3D models of the intestines. This permits users to accurately locate samples for data comparison.
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Affiliation(s)
- Albert Burger
- Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK.
| | - Richard A. Baldock
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
| | - David J. Adams
- grid.10306.340000 0004 0606 5382Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Shahida Din
- grid.39489.3f0000 0001 0388 0742Edinburgh IBD Unit Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Irene Papatheodorou
- grid.225360.00000 0000 9709 7726European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge, UK
| | - Michael Glinka
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
| | - Bill Hill
- grid.9531.e0000000106567444Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Derek Houghton
- grid.9531.e0000000106567444Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Mehran Sharghi
- grid.9531.e0000000106567444Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Michael Wicks
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
| | - Mark J. Arends
- grid.4305.20000 0004 1936 7988Division of Pathology, Centre for Comparative Pathology, Edinburgh Cancer Research Centre, Institute of Cancer and Genetics, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU UK
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Gómez-Gaviro MV, Balaban E, Bocancea D, Lorrio MT, Pompeiano M, Desco M, Ripoll J, Vaquero JJ. Optimized CUBIC protocol for three-dimensional imaging of chicken embryos at single-cell resolution. Development 2017; 144:2092-2097. [PMID: 28432219 DOI: 10.1242/dev.145805] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/07/2017] [Indexed: 01/17/2023]
Abstract
The CUBIC tissue-clearing protocol has been optimized to produce translucent immunostained whole chicken embryos and embryo brains. When combined with multispectral light-sheet microscopy, the validated protocol presented here provides a rapid, inexpensive and reliable method for acquiring accurate histological images that preserve three-dimensional structural relationships with single-cell resolution in whole early-stage chicken embryos and in the whole brains of late-stage embryos.
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Affiliation(s)
- María Victoria Gómez-Gaviro
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, 28911, Spain .,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28007, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, 28029, Spain
| | - Evan Balaban
- Department of Psychology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Diana Bocancea
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, 28911, Spain
| | - María Teresa Lorrio
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, 28911, Spain
| | - Maria Pompeiano
- Department of Psychology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Manuel Desco
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, 28911, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28007, Spain.,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, 28029, Spain
| | - Jorge Ripoll
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, 28911, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28007, Spain
| | - Juan José Vaquero
- Departamento de Bioingeniería e Ingeniería Aeroespacial, Universidad Carlos III de Madrid, Leganés, 28911, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, 28007, Spain
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Anderson C, Khan MAF, Wong F, Solovieva T, Oliveira NMM, Baldock RA, Tickle C, Burt DW, Stern CD. A strategy to discover new organizers identifies a putative heart organizer. Nat Commun 2016; 7:12656. [PMID: 27557800 DOI: 10.1038/ncomms12656] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/19/2016] [Indexed: 11/09/2022] Open
Abstract
Organizers are regions of the embryo that can both induce new fates and impart pattern on other regions. So far, surprisingly few organizers have been discovered, considering the number of patterned tissue types generated during development. This may be because their discovery has relied on transplantation and ablation experiments. Here we describe a new approach, using chick embryos, to discover organizers based on a common gene expression signature, and use it to uncover the anterior intestinal portal (AIP) endoderm as a putative heart organizer. We show that the AIP can induce cardiac identity from non-cardiac mesoderm and that it can pattern this by specifying ventricular and suppressing atrial regional identity. We also uncover some of the signals responsible. The method holds promise as a tool to discover other novel organizers acting during development.
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Affiliation(s)
- Claire Anderson
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Mohsin A F Khan
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Frances Wong
- Department of Genomics and Genetics, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Tatiana Solovieva
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Nidia M M Oliveira
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Richard A Baldock
- Biomedical Systems Analysis Section, MRC Human Genetics Unit, IGMM, University of Edinburgh, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Cheryll Tickle
- Department of Biology &Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Dave W Burt
- Department of Genomics and Genetics, The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Claudio D Stern
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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Abstract
Mouse anatomy ontologies provide standard nomenclature for describing normal and mutant mouse anatomy, and are essential for the description and integration of data directly related to anatomy such as gene expression patterns. Building on our previous work on anatomical ontologies for the embryonic and adult mouse, we have recently developed a new and substantially revised anatomical ontology covering all life stages of the mouse. Anatomical terms are organized in complex hierarchies enabling multiple relationships between terms. Tissue classification as well as partonomic, developmental, and other types of relationships can be represented. Hierarchies for specific developmental stages can also be derived. The ontology forms the core of the eMouse Atlas Project (EMAP) and is used extensively for annotating and integrating gene expression patterns and other data by the Gene Expression Database (GXD), the eMouse Atlas of Gene Expression (EMAGE) and other database resources. Here we illustrate the evolution of the developmental and adult mouse anatomical ontologies toward one combined system. We report on recent ontology enhancements, describe the current status, and discuss future plans for mouse anatomy ontology development and application in integrating data resources.
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Correlations Between the Morphology of Sonic Hedgehog Expression Domains and Embryonic Craniofacial Shape. Evol Biol 2015; 42:379-386. [PMID: 26321772 DOI: 10.1007/s11692-015-9321-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Quantitative analysis of gene expression domains and investigation of relationships between gene expression and developmental and phenotypic outcomes are central to advancing our understanding of the genotype-phenotype map. Gene expression domains typically have smooth but irregular shapes lacking homologous landmarks, making it difficult to analyze shape variation with the tools of landmark-based geometric morphometrics. In addition, 3D image acquisition and processing introduce many artifacts that further exacerbate the problem. To overcome these difficulties, this paper presents a method that combines optical projection tomography scanning, a shape regularization technique and a landmark-free approach to quantify variation in the morphology of Sonic hedgehog expression domains in the frontonasal ectodermal zone (FEZ) of avians and investigate relationships with embryonic craniofacial shape. The model reveals axes in FEZ and embryonic-head morphospaces along which variation exhibits a sharp linear relationship at high statistical significance. The technique should be applicable to analyses of other 3D biological structures that can be modeled as smooth surfaces and have ill-defined shape.
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Johnson EJ, Neely DM, Dunn IC, Davey MG. Direct functional consequences of ZRS enhancer mutation combine with secondary long range SHH signalling effects to cause preaxial polydactyly. Dev Biol 2014; 392:209-20. [PMID: 24907417 PMCID: PMC4111902 DOI: 10.1016/j.ydbio.2014.05.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 05/22/2014] [Accepted: 05/28/2014] [Indexed: 12/20/2022]
Abstract
Sonic hedgehog (SHH) plays a central role in patterning numerous embryonic tissues including, classically, the developing limb bud where it controls digit number and identity. This study utilises the polydactylous Silkie (Slk) chicken breed, which carries a mutation in the long range limb-specific regulatory element of SHH, the ZRS. Using allele specific SHH expression analysis combined with quantitative protein analysis, we measure allele specific changes in SHH mRNA and concentration of SHH protein over time. This confirms that the Slk ZRS enhancer mutation causes increased SHH expression in the posterior leg mesenchyme. Secondary consequences of this increased SHH signalling include increased FGF pathway signalling and growth as predicted by the SHH/GREM1/FGF feedback loop and the Growth/Morphogen models. Manipulation of Hedgehog, FGF signalling and growth demonstrate that anterior-ectopic expression of SHH and induction of preaxial polydactyly is induced secondary to increased SHH signalling and Hedgehog-dependent growth directed from the posterior limb. We predict that increased long range SHH signalling acts in combination with changes in activation of SHH transcription from the Slk ZRS allele. Through analysis of the temporal dynamics of anterior SHH induction we predict a gene regulatory network which may contribute to activation of anterior SHH expression from the Slk ZRS. Overexpression of posterior SHH in the limb bud can cause preaxial polydactyly. Increased activation of SHH/GREM/FGF feedback and growth induces Slk preaxial polydactyly. Autoregulated expression of SHH can occur within 1.5–2 h in the limb bud.
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Affiliation(s)
- Edward J Johnson
- Division of Developmental Biology, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - David M Neely
- Division of Developmental Biology, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Ian C Dunn
- Division of Genetics and Genomics, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Megan G Davey
- Division of Developmental Biology, The Roslin Institute and R(D)SVS, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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Kain KH, Miller JWI, Jones-Paris CR, Thomason RT, Lewis JD, Bader DM, Barnett JV, Zijlstra A. The chick embryo as an expanding experimental model for cancer and cardiovascular research. Dev Dyn 2013; 243:216-28. [PMID: 24357262 DOI: 10.1002/dvdy.24093] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 10/28/2013] [Accepted: 10/28/2013] [Indexed: 12/17/2022] Open
Abstract
A long and productive history in biomedical research defines the chick as a model for human biology. Fundamental discoveries, including the description of directional circulation propelled by the heart and the link between oncogenes and the formation of cancer, indicate its utility in cardiac biology and cancer. Despite the more recent arrival of several vertebrate and invertebrate animal models during the last century, the chick embryo remains a commonly used model for vertebrate biology and provides a tractable biological template. With new molecular and genetic tools applied to the avian genome, the chick embryo is accelerating the discovery of normal development and elusive disease processes. Moreover, progress in imaging and chick culture technologies is advancing real-time visualization of dynamic biological events, such as tissue morphogenesis, angiogenesis, and cancer metastasis. A rich background of information, coupled with new technologies and relative ease of maintenance, suggest an expanding utility for the chick embryo in cardiac biology and cancer research.
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Sheng G. Day-1 chick development. Dev Dyn 2013; 243:357-67. [DOI: 10.1002/dvdy.24087] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/22/2013] [Accepted: 10/22/2013] [Indexed: 02/04/2023] Open
Affiliation(s)
- Guojun Sheng
- Laboratory for Early Embryogenesis; RIKEN Center for Developmental Biology; Kobe Hyogo Japan
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Antin PB, Yatskievych TA, Davey S, Darnell DK. GEISHA: an evolving gene expression resource for the chicken embryo. Nucleic Acids Res 2013; 42:D933-7. [PMID: 24150938 PMCID: PMC3964962 DOI: 10.1093/nar/gkt962] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
GEISHA (Gallus Expression In Situ Hybridization Analysis; http://geisha.arizona.edu) is an in situ hybridization gene expression and genomic resource for the chicken embryo. This update describes modifications that enhance its utility to users. During the past 5 years, GEISHA has undertaken a significant restructuring to more closely conform to the data organization and formatting of Model Organism Databases in other species. This has involved migrating from an entry-centric format to one that is gene-centered. Database restructuring has enabled the inclusion of data pertaining to chicken genes and proteins and their orthologs in other species. This new information is presented through an updated user interface. In situ hybridization data in mouse, frog, zebrafish and fruitfly are integrated with chicken genomic and expression information. A resource has also been developed that integrates the GEISHA interface information with the Online Mendelian Inheritance in Man human disease gene database. Finally, the Chicken Gene Nomenclature Committee database and the GEISHA database have been integrated so that they draw from the same data resources.
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Affiliation(s)
- Parker B Antin
- Molecular Cardiovascular Research Program, Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
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LifeMap Discovery™: the embryonic development, stem cells, and regenerative medicine research portal. PLoS One 2013; 8:e66629. [PMID: 23874394 PMCID: PMC3714290 DOI: 10.1371/journal.pone.0066629] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 04/29/2013] [Indexed: 11/19/2022] Open
Abstract
LifeMap Discovery™ provides investigators with an integrated database of embryonic development, stem cell biology and regenerative medicine. The hand-curated reconstruction of cell ontology with stem cell biology; including molecular, cellular, anatomical and disease-related information, provides efficient and easy-to-use, searchable research tools. The database collates in vivo and in vitro gene expression and guides translation from in vitro data to the clinical utility, and thus can be utilized as a powerful tool for research and discovery in stem cell biology, developmental biology, disease mechanisms and therapeutic discovery. LifeMap Discovery is freely available to academic nonprofit institutions at http://discovery.lifemapsc.com.
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