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Kaiser M, Zikmund T, Vora S, Metscher B, Adameyko I, Richman JM, Kaiser J. 3D atlas of the human fetal chondrocranium in the middle trimester. Sci Data 2024; 11:626. [PMID: 38871782 PMCID: PMC11176318 DOI: 10.1038/s41597-024-03455-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 05/31/2024] [Indexed: 06/15/2024] Open
Abstract
The chondrocranium provides the key initial support for the fetal brain, jaws and cranial sensory organs in all vertebrates. The patterns of shaping and growth of the chondrocranium set up species-specific development of the entire craniofacial complex. The 3D development of chondrocranium have been studied primarily in animal model organisms, such as mice or zebrafish. In comparison, very little is known about the full 3D human chondrocranium, except from drawings made by anatomists many decades ago. The knowledge of human-specific aspects of chondrocranial development are essential for understanding congenital craniofacial defects and human evolution. Here advanced microCT scanning was used that includes contrast enhancement to generate the first 3D atlas of the human fetal chondrocranium during the middle trimester (13 to 19 weeks). In addition, since cartilage and bone are both visible with the techniques used, the endochondral ossification of cranial base was mapped since this region is so critical for brain and jaw growth. The human 3D models are published as a scientific resource for human development.
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Affiliation(s)
- Markéta Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomáš Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Siddharth Vora
- The Life Sciences Institute, The University of British Columbia, Vancouver, Canada
| | - Brian Metscher
- Department of Evolutionary Biology, University of Vienna, Vienna, Austria
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University of Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Joy M Richman
- The Life Sciences Institute, The University of British Columbia, Vancouver, Canada.
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic.
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2
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Hopwood N. Species Choice and Model Use: Reviving Research on Human Development. JOURNAL OF THE HISTORY OF BIOLOGY 2024; 57:231-279. [PMID: 39075321 PMCID: PMC11341657 DOI: 10.1007/s10739-024-09775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/13/2024] [Indexed: 07/31/2024]
Abstract
While model organisms have had many historians, this article places studies of humans, and particularly our development, in the politics of species choice. Human embryos, investigated directly rather than via animal surrogates, have gone through cycles of attention and neglect. In the past 60 years they moved from the sidelines to center stage. Research was resuscitated in anatomy, launched in reproductive biomedicine, molecular genetics, and stem-cell science, and made attractive in developmental biology. I explain this surge of interest in terms of rivalry with models and reliance on them. The greater involvement of medicine in human reproduction, especially through in vitro fertilization, gave access to fresh sources of material that fed critiques of extrapolation from mice and met demands for clinical relevance or "translation." Yet much of the revival depended on models. Supply infrastructures and digital standards, including biobanks and virtual atlases, emulated community resources for model organisms. Novel culture, imaging, molecular, and postgenomic methods were perfected on less precious samples. Toing and froing from the mouse affirmed the necessity of the exemplary mammal and its insufficiency justified inquiries into humans. Another kind of model-organoids and embryo-like structures derived from stem cells-enabled experiments that encouraged the organization of a new field, human developmental biology. Research on humans has competed with and counted on models.
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Affiliation(s)
- Nick Hopwood
- Department of History and Philosophy of Science, University of Cambridge, Free School Lane, Cambridge, CB2 3RH, UK.
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3
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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] [MESH Headings] [Grants] [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
- Division 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
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Shahida Din
- Edinburgh IBD Unit Western General Hospital, NHS Lothian, Edinburgh, UK
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, Cambridge, UK
| | - Michael Glinka
- Division 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
- Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Derek Houghton
- Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Mehran Sharghi
- Department of Computer Science, School of Mathematical and Computer Sciences, Heriot-Watt University, Edinburgh, UK
| | - Michael Wicks
- Division 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
- Division 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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Abstract
The segmented body plan of vertebrates is established during somitogenesis, a well-studied process in model organisms; however, the details of this process in humans remain largely unknown owing to ethical and technical limitations. Despite recent advances with pluripotent stem cell-based approaches1-5, models that robustly recapitulate human somitogenesis in both space and time remain scarce. Here we introduce a pluripotent stem cell-derived mesoderm-based 3D model of human segmentation and somitogenesis-which we termed 'axioloid'-that captures accurately the oscillatory dynamics of the segmentation clock and the morphological and molecular characteristics of sequential somite formation in vitro. Axioloids show proper rostrocaudal patterning of forming segments and robust anterior-posterior FGF-WNT signalling gradients and retinoic acid signalling components. We identify an unexpected critical role of retinoic acid signalling in the stabilization of forming segments, indicating distinct, but also synergistic effects of retinoic acid and extracellular matrix on the formation and epithelialization of somites. Comparative analysis demonstrates marked similarities of axioloids to the human embryo, further validated by the presence of a Hox code in axioloids. Finally, we demonstrate the utility of axioloids for studying the pathogenesis of human congenital spine diseases using induced pluripotent stem cells with mutations in HES7 and MESP2. Our results indicate that axioloids represent a promising platform for the study of axial development and disease in humans.
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Keenan ID, Green E, Haagensen E, Hancock R, Scotcher KS, Swainson H, Swamy M, Walker S, Woodhouse L. Pandemic-Era Digital Education: Insights from an Undergraduate Medical Programme. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1397:1-19. [DOI: 10.1007/978-3-031-17135-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Burger A, Baldock R, 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.. [DOI: 10.1101/2022.12.08.519665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2024]
Abstract
AbstractBackgroundThe 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.MethodsWe 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 regionsin 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.ResultsThe 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.ConclusionsSmall 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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Abdel Meguid EM, Holland JC, Keenan ID, Mishall P. Exploring Visualisation for Embryology Education: A Twenty-First-Century Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1356:173-193. [PMID: 35146622 DOI: 10.1007/978-3-030-87779-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Embryology and congenital malformations play a key role in multiple medical specialties including obstetrics and paediatrics. The process of learning clinical embryology involves two basic principles; firstly, understanding time-sensitive morphological changes that happen in the developing embryo and, secondly, appreciating the clinical implications of congenital conditions when development varies from the norm. Visualising the sequence of dynamic events in embryonic development is likely to be challenging for students, as these processes occur not only in three dimensions but also in the fourth dimensions of time. Consequently, features identified at any one timepoint can subsequently undergo morphological transitions into distinct structures or may degenerate and disappear. When studying embryology, learners face significant challenges in understanding complex, multiple and simultaneous events which are likely to increase student cognitive load. Moreover, the embryology content is very nonlinear. This nonlinear content presentation makes embryology teaching challenging for educators. Embryology is typically taught in large groups, via didactic lecture presentations that incorporate two-dimensional diagrams or foetal ultrasound images. This approach is limited by incomplete or insufficient visualisation and lack of interactivity.It is recommended that the focus of embryology teaching should instill an understanding of embryological processes and emphasise conceptualising the potential congenital conditions that can occur, linking pre-clinical and clinical disciplines together. A variety of teaching methods within case-based and problem-based curricula are commonly used to teach embryology. Additional and supplementary resources including animations and videos are also typically utilised to demonstrate complex embryological processes such as septation, rotation and folding.We propose that there is a need for embryology teaching in the twenty-first century to evolve. This is particularly required in terms of appropriate visualisation resources and teaching methodologies which can ensure embryology learning is relevant to real-world scenarios. Here we explore embryology teaching resources and methodologies and review existing evidence-based studies on their implementation and impact on student learning. In doing so, we aim to inform and support the practice of embryology educators and the learning of their students.
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8
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Azkue JJ. External surface anatomy of the postfolding human embryo: Computer-aided, three-dimensional reconstruction of printable digital specimens. J Anat 2021; 239:1438-1451. [PMID: 34275144 PMCID: PMC8602026 DOI: 10.1111/joa.13514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 01/20/2023] Open
Abstract
Opportunities for clinicians, researchers, and medical students to become acquainted with the three‐dimensional (3D) anatomy of the human embryo have historically been limited. This work was aimed at creating a collection of digital, printable 3D surface models demonstrating major morphogenetic changes in the embryo's external anatomy, including typical features used for external staging. Twelve models were digitally reconstructed based on optical projection tomography, high‐resolution episcopic microscopy and magnetic resonance imaging datasets of formalin‐fixed specimens of embryos of developmental stages 12 through 23, that is, stages following longitudinal and transverse embryo folding. The reconstructed replica reproduced the external anatomy of the actual specimens in great detail, and the progress of development over stages was recognizable in a variety of external anatomical features and bodily structures, including the general layout and curvature of the body, the pharyngeal arches and cervical sinus, the physiological gut herniation, and external genitalia. In addition, surface anatomy features commonly used for embryo staging, such as distinct steps in the morphogenesis of facial primordia and limb buds, were also apparent. These digital replica, which are all provided for 3D visualization and printing, can serve as a novel resource for teaching and learning embryology and may contribute to a better appreciation of the human embryonic development.
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Affiliation(s)
- Jon Jatsu Azkue
- Department of Neurosciences, School of Medicine and Nursery, Universty of the Basque Country, UPV/EHU, Leioa, Bizkaia, Spain
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9
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Rayon T, Stamataki D, Perez-Carrasco R, Garcia-Perez L, Barrington C, Melchionda M, Exelby K, Lazaro J, Tybulewicz VLJ, Fisher EMC, Briscoe J. Species-specific pace of development is associated with differences in protein stability. Science 2020; 369:eaba7667. [PMID: 32943498 PMCID: PMC7116327 DOI: 10.1126/science.aba7667] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 07/29/2020] [Indexed: 12/12/2022]
Abstract
Although many molecular mechanisms controlling developmental processes are evolutionarily conserved, the speed at which the embryo develops can vary substantially between species. For example, the same genetic program, comprising sequential changes in transcriptional states, governs the differentiation of motor neurons in mouse and human, but the tempo at which it operates differs between species. Using in vitro directed differentiation of embryonic stem cells to motor neurons, we show that the program runs more than twice as fast in mouse as in human. This is not due to differences in signaling, nor the genomic sequence of genes or their regulatory elements. Instead, there is an approximately two-fold increase in protein stability and cell cycle duration in human cells compared with mouse cells. This can account for the slower pace of human development and suggests that differences in protein turnover play a role in interspecies differences in developmental tempo.
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Affiliation(s)
- Teresa Rayon
- The Francis Crick Institute, London NW1 1AT, UK.
| | | | - Ruben Perez-Carrasco
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Mathematics, University College London, London WC1E 6BT, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | | | | | | | | | - Victor L J Tybulewicz
- The Francis Crick Institute, London NW1 1AT, UK
- Department of Immunology and Inflammation, Imperial College, London W12 0NN, UK
| | - Elizabeth M C Fisher
- UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
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10
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Cardoso-Moreira M, Halbert J, Valloton D, Velten B, Chen C, Shao Y, Liechti A, Ascenção K, Rummel C, Ovchinnikova S, Mazin PV, Xenarios I, Harshman K, Mort M, Cooper DN, Sandi C, Soares MJ, Ferreira PG, Afonso S, Carneiro M, Turner JMA, VandeBerg JL, Fallahshahroudi A, Jensen P, Behr R, Lisgo S, Lindsay S, Khaitovich P, Huber W, Baker J, Anders S, Zhang YE, Kaessmann H. Gene expression across mammalian organ development. Nature 2019; 571:505-509. [PMID: 31243369 PMCID: PMC6658352 DOI: 10.1038/s41586-019-1338-5] [Citation(s) in RCA: 396] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023]
Abstract
The evolution of gene expression in mammalian organ development remains largely uncharacterized. Here we report the transcriptomes of seven organs (cerebrum, cerebellum, heart, kidney, liver, ovary and testis) across developmental time points from early organogenesis to adulthood for human, rhesus macaque, mouse, rat, rabbit, opossum and chicken. Comparisons of gene expression patterns identified correspondences of developmental stages across species, and differences in the timing of key events during the development of the gonads. We found that the breadth of gene expression and the extent of purifying selection gradually decrease during development, whereas the amount of positive selection and expression of new genes increase. We identified differences in the temporal trajectories of expression of individual genes across species, with brain tissues showing the smallest percentage of trajectory changes, and the liver and testis showing the largest. Our work provides a resource of developmental transcriptomes of seven organs across seven species, and comparative analyses that characterize the development and evolution of mammalian organs.
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Affiliation(s)
- Margarida Cardoso-Moreira
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.
| | - Jean Halbert
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Delphine Valloton
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Britta Velten
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Chunyan Chen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Shao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Angélica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Kelly Ascenção
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Coralie Rummel
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Pavel V Mazin
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute) RAS, Moscow, Russia
- Faculty of Computer Science, HSE University, Moscow, Russia
| | - Ioannis Xenarios
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Keith Harshman
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Matthew Mort
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, UK
| | - Carmen Sandi
- Laboratory of Behavioral Genetics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Michael J Soares
- Institute for Reproduction and Perinatal Research, Departments of Pathology and Laboratory Medicine and Pediatrics, University of Kansas Medical Center, Kansas City, MO, USA
- Center for Perinatal Research, Children's Research Institute, Children's Mercy, Kansas City, MO, USA
| | - Paula G Ferreira
- Departamento de Anatomia, Universidade do Porto, Porto, Portugal
- ICBAS (Instituto de Ciências Biomédicas Abel Salazar), UMIB (Unidade Multidisciplinar de Investigação Biomédica), Universidade do Porto, Porto, Portugal
| | - Sandra Afonso
- CIBIO/InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
| | - Miguel Carneiro
- CIBIO/InBIO, Centro de Investigacão em Biodiversidade e Recursos Genéticos, Universidade do Porto, Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - James M A Turner
- Sex Chromosome Biology Laboratory, The Francis Crick Institute, London, UK
| | - John L VandeBerg
- South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, Harlingen and Edinburg, TX, USA
- The Department of Human Genetics, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, Harlingen and Edinburg, TX, USA
| | - Amir Fallahshahroudi
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Per Jensen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Linköping University, Linköping, Sweden
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research (DPZ), Göttingen, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Göttingen, Göttingen, Germany
| | - Steven Lisgo
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Susan Lindsay
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, Newcastle, UK
| | - Philipp Khaitovich
- Center for Neurobiology and Brain Restoration, Skolkovo Institute of Science and Technology, Moscow, Russia
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Wolfgang Huber
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julie Baker
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg, Germany.
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Doan RN, Lim ET, De Rubeis S, Betancur C, Cutler DJ, Chiocchetti AG, Overman LM, Soucy A, Goetze S, Freitag CM, Daly MJ, Walsh CA, Buxbaum JD, Yu TW. Recessive gene disruptions in autism spectrum disorder. Nat Genet 2019; 51:1092-1098. [PMID: 31209396 PMCID: PMC6629034 DOI: 10.1038/s41588-019-0433-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 05/02/2019] [Indexed: 01/27/2023]
Abstract
Autism spectrum disorder (ASD) affects up to 1 in 59 individuals1. Genome-wide association and large-scale sequencing studies strongly implicate both common variants2-4 and rare de novo variants5-10 in ASD. Recessive mutations have also been implicated11-14 but their contribution remains less well defined. Here we demonstrate an excess of biallelic loss-of-function and damaging missense mutations in a large ASD cohort, corresponding to approximately 5% of total cases, including 10% of females, consistent with a female protective effect. We document biallelic disruption of known or emerging recessive neurodevelopmental genes (CA2, DDHD1, NSUN2, PAH, RARB, ROGDI, SLC1A1, USH2A) as well as other genes not previously implicated in ASD including FEV (FEV transcription factor, ETS family member), which encodes a key regulator of the serotonergic circuitry. Our data refine estimates of the contribution of recessive mutation to ASD and suggest new paths for illuminating previously unknown biological pathways responsible for this condition.
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Affiliation(s)
- Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Elaine T Lim
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Neuroscience Paris Seine, Institut de Biologie Paris Seine, Sorbonne Université, INSERM, CNRS, Paris, France
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Lynne M Overman
- Human Developmental Biology Resource, Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle-upon-Tyne, UK
| | - Aubrie Soucy
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Susanne Goetze
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Mark J Daly
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Human Genetic Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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12
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Takakuwa T. 3D Analysis of Human Embryos and Fetuses Using Digitized Datasets From the Kyoto Collection. Anat Rec (Hoboken) 2018; 301:960-969. [DOI: 10.1002/ar.23784] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 11/16/2016] [Accepted: 12/12/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Tetsuya Takakuwa
- Human Health Science, Graduate School of Medicine; Kyoto University; Kyoto Japan
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13
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Hill MA. Developing the Digital Kyoto Collection in Education and Research. Anat Rec (Hoboken) 2018; 301:998-1003. [DOI: 10.1002/ar.23783] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 11/24/2016] [Accepted: 12/27/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Mark Anthony Hill
- Anatomy, School of Medical Sciences, Faculty of Medicine; UNSW; Australia
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14
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The logistics of afferent cortical specification in mice and men. Semin Cell Dev Biol 2018; 76:112-119. [DOI: 10.1016/j.semcdb.2017.08.047] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 08/25/2017] [Accepted: 08/28/2017] [Indexed: 11/17/2022]
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15
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Behjati S, Lindsay S, Teichmann SA, Haniffa M. Mapping human development at single-cell resolution. Development 2018; 145:145/3/dev152561. [PMID: 29439135 DOI: 10.1242/dev.152561] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human development is regulated by spatiotemporally restricted molecular programmes and is pertinent to many areas of basic biology and human medicine, such as stem cell biology, reproductive medicine and childhood cancer. Mapping human development has presented significant technological, logistical and ethical challenges. The availability of established human developmental biorepositories and the advent of cutting-edge single-cell technologies provide new opportunities to study human development. Here, we present a working framework for the establishment of a human developmental cell atlas exploiting single-cell genomics and spatial analysis. We discuss how the development atlas will benefit the scientific and clinical communities to advance our understanding of basic biology, health and disease.
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Affiliation(s)
- Sam Behjati
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Department of Paediatrics, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Susan Lindsay
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Sarah A Teichmann
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK .,Theory of Condensed Matter, Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK
| | - Muzlifah Haniffa
- Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK .,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
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16
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Renner M, Lancaster MA, Bian S, Choi H, Ku T, Peer A, Chung K, Knoblich JA. Self-organized developmental patterning and differentiation in cerebral organoids. EMBO J 2017; 36:1316-1329. [PMID: 28283582 PMCID: PMC5430225 DOI: 10.15252/embj.201694700] [Citation(s) in RCA: 230] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 12/11/2022] Open
Abstract
Cerebral organoids recapitulate human brain development at a considerable level of detail, even in the absence of externally added signaling factors. The patterning events driving this self-organization are currently unknown. Here, we examine the developmental and differentiative capacity of cerebral organoids. Focusing on forebrain regions, we demonstrate the presence of a variety of discrete ventral and dorsal regions. Clearing and subsequent 3D reconstruction of entire organoids reveal that many of these regions are interconnected, suggesting that the entire range of dorso-ventral identities can be generated within continuous neuroepithelia. Consistent with this, we demonstrate the presence of forebrain organizing centers that express secreted growth factors, which may be involved in dorso-ventral patterning within organoids. Furthermore, we demonstrate the timed generation of neurons with mature morphologies, as well as the subsequent generation of astrocytes and oligodendrocytes. Our work provides the methodology and quality criteria for phenotypic analysis of brain organoids and shows that the spatial and temporal patterning events governing human brain development can be recapitulated in vitro.
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Affiliation(s)
- Magdalena Renner
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Madeline A Lancaster
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Shan Bian
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Heejin Choi
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Taeyun Ku
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Angela Peer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA
- Broad Institute of Harvard University and MIT, Cambridge, MA, USA
| | - Juergen A Knoblich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
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17
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Mason JO, Price DJ. Building brains in a dish: Prospects for growing cerebral organoids from stem cells. Neuroscience 2016; 334:105-118. [PMID: 27506142 DOI: 10.1016/j.neuroscience.2016.07.048] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/22/2016] [Accepted: 07/30/2016] [Indexed: 11/27/2022]
Abstract
The recent development of organoid techniques, in which embryonic brain-like tissue can be grown from human or mouse stem cells in vitro offers the potential to transform the way in which brain development is studied. In this review, we summarize key aspects of the embryonic development of mammalian forebrains, focussing in particular on the cerebral cortex and highlight significant differences between mouse and primates, including human. We discuss recent work using cerebral organoids that has revealed key similarities and differences between their development and that of the brain in vivo. Finally, we outline the ways in which cerebral organoids can be used in combination with CRISPR/Cas9 genome editing to unravel genetic mechanisms that control embryonic development of the cerebral cortex, how this can help us understand the causes of neurodevelopmental disorders and some of the key challenges which will have to be resolved before organoids can become a mainstream tool to study brain development.
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Affiliation(s)
- John O Mason
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK.
| | - David J Price
- Centre for Integrative Physiology, Edinburgh Medical School: Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh EH8 9XD, UK.
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18
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Puelles L, Medina L, Borello U, Legaz I, Teissier A, Pierani A, Rubenstein JLR. Radial derivatives of the mouse ventral pallium traced with Dbx1-LacZ reporters. J Chem Neuroanat 2015; 75:2-19. [PMID: 26748312 DOI: 10.1016/j.jchemneu.2015.10.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/29/2015] [Indexed: 11/17/2022]
Abstract
The progeny of Dbx1-expressing progenitors was studied in the developing mouse pallium, using two transgenic mouse lines: (1) Dbx1(nlslacZ) mice, in which the gene of the β-galactosidase reporter (LacZ) is inserted directly under the control of the Dbx1 promoter, allowing short-term lineage tracing of Dbx1-derived cells; and (2) Dbx1(CRE) mice crossed with a Cre-dependent reporter strain (ROSA26(loxP-stop-loxP-LacZ)), in which the Dbx1-derived cells result permanently labeled (Bielle et al., 2005). We thus examined in detail the derivatives of the postulated longitudinal ventral pallium (VPall) sector, which has been defined among other features by its selective ventricular zone expression of Dbx1 (the recent ascription by Puelles, 2014 of the whole olfactory cortex primordium to the VPall was tested). Earlier notions about a gradiental caudorostral reduction of Dbx1 signal were corroborated, so that virtually no signal was found at the olfactory bulb and the anterior olfactory area. The piriform cortex was increasingly labeled caudalwards. The only endopiriform grisea labeled were the ventral endopiriform nucleus and the bed nucleus of the external capsule. Anterior and basolateral parts of the whole pallial amygdala also were densely marked, in contrast to the negative posterior parts of these pallial amygdalar nuclei (leaving apart medial amygdalar parts ascribed to subpallial or extratelencephalic sources of Dbx1-derived GABAergic and non-GABAergic neurons). Alternative tentative interpretations are discussed to explain the partial labeling obtained of both olfactory and amygdaloid structures. This includes the hypothesis of an as yet undefined part of the pallium, potentially responsible for the posterior amygdala, or the hypothesis that the VPall may not be wholly characterized by Dbx1 expression (this gene not being necessary for VPall molecular distinctness and histogenetic potency), which would leave a dorsal Dbx1-negative VPall subdomain of variable size that might contribute partially to olfactory and posterior amygdalar structures.
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Affiliation(s)
- Luis Puelles
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, IMIB (Instituto Murciano de Investigación Biosanitaria), Murcia 30071, Spain.
| | - Loreta Medina
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, IMIB (Instituto Murciano de Investigación Biosanitaria), Murcia 30071, Spain
| | - Ugo Borello
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - Isabel Legaz
- Department of Human Anatomy and Psychobiology, Faculty of Medicine, University of Murcia, IMIB (Instituto Murciano de Investigación Biosanitaria), Murcia 30071, Spain
| | - Anne Teissier
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France.
| | - Alessandra Pierani
- Institut Jacques Monod, CNRS UMR 7592, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex, France
| | - John L R Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, Department of Psychiatry, University of California at San Francisco, San Francisco, CA 94158, USA
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19
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Rabattu PY, Massé B, Ulliana F, Rousset MC, Rohmer D, Léon JC, Palombi O. My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development. J Biomed Semantics 2015; 6:36. [PMID: 26413258 PMCID: PMC4582726 DOI: 10.1186/s13326-015-0034-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 09/02/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. RESULTS In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. CONCLUSIONS Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge. AVAILABILITY http://www.mycorporisfabrica.org/.
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Affiliation(s)
| | - Benoit Massé
- LJK (CNRS-UJF-INPG-UPMF), INRIA, Université de Grenoble, Grenoble, France
| | - Federico Ulliana
- LIG (CNRS-UJF-INPG-UPMF), Université de Grenoble, Grenoble, France
| | | | - Damien Rohmer
- LJK (CNRS-UJF-INPG-UPMF), INRIA, Université de Grenoble, Grenoble, France ; CPE Lyon, Université de Lyon, Lyon, France
| | - Jean-Claude Léon
- LJK (CNRS-UJF-INPG-UPMF), INRIA, Université de Grenoble, Grenoble, France
| | - Olivier Palombi
- Department of Anatomy, LADAF, Université Joseph Fourier, Grenoble, France ; LJK (CNRS-UJF-INPG-UPMF), INRIA, Université de Grenoble, Grenoble, France
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20
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Shiraishi N, Katayama A, Nakashima T, Yamada S, Uwabe C, Kose K, Takakuwa T. Morphology and morphometry of the human embryonic brain: A three-dimensional analysis. Neuroimage 2015; 115:96-103. [DOI: 10.1016/j.neuroimage.2015.04.044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 04/14/2015] [Accepted: 04/21/2015] [Indexed: 01/26/2023] Open
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21
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Manuel MN, Mi D, Mason JO, Price DJ. Regulation of cerebral cortical neurogenesis by the Pax6 transcription factor. Front Cell Neurosci 2015; 9:70. [PMID: 25805971 PMCID: PMC4354436 DOI: 10.3389/fncel.2015.00070] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/18/2015] [Indexed: 12/19/2022] Open
Abstract
Understanding brain development remains a major challenge at the heart of understanding what makes us human. The neocortex, in evolutionary terms the newest part of the cerebral cortex, is the seat of higher cognitive functions. Its normal development requires the production, positioning, and appropriate interconnection of very large numbers of both excitatory and inhibitory neurons. Pax6 is one of a relatively small group of transcription factors that exert high-level control of cortical development, and whose mutation or deletion from developing embryos causes major brain defects and a wide range of neurodevelopmental disorders. Pax6 is very highly conserved between primate and non-primate species, is expressed in a gradient throughout the developing cortex and is essential for normal corticogenesis. Our understanding of Pax6’s functions and the cellular processes that it regulates during mammalian cortical development has significantly advanced in the last decade, owing to the combined application of genetic and biochemical analyses. Here, we review the functional importance of Pax6 in regulating cortical progenitor proliferation, neurogenesis, and formation of cortical layers and highlight important differences between rodents and primates. We also review the pathological effects of PAX6 mutations in human neurodevelopmental disorders. We discuss some aspects of Pax6’s molecular actions including its own complex transcriptional regulation, the distinct molecular functions of its splice variants and some of Pax6’s known direct targets which mediate its actions during cortical development.
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Affiliation(s)
- Martine N Manuel
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - Da Mi
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - John O Mason
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - David J Price
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
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22
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Directed differentiation and functional maturation of cortical interneurons from human embryonic stem cells. Cell Stem Cell 2014; 12:559-72. [PMID: 23642365 DOI: 10.1016/j.stem.2013.04.008] [Citation(s) in RCA: 431] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 03/02/2013] [Accepted: 04/12/2013] [Indexed: 12/16/2022]
Abstract
Human pluripotent stem cells are a powerful tool for modeling brain development and disease. The human cortex is composed of two major neuronal populations: projection neurons and local interneurons. Cortical interneurons comprise a diverse class of cell types expressing the neurotransmitter GABA. Dysfunction of cortical interneurons has been implicated in neuropsychiatric diseases, including schizophrenia, autism, and epilepsy. Here, we demonstrate the highly efficient derivation of human cortical interneurons in an NKX2.1::GFP human embryonic stem cell reporter line. Manipulating the timing of SHH activation yields three distinct GFP+ populations with specific transcriptional profiles, neurotransmitter phenotypes, and migratory behaviors. Further differentiation in a murine cortical environment yields parvalbumin- and somatostatin-expressing neurons that exhibit synaptic inputs and electrophysiological properties of cortical interneurons. Our study defines the signals sufficient for modeling human ventral forebrain development in vitro and lays the foundation for studying cortical interneuron involvement in human disease pathology.
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23
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Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KWY, Nie Q. Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC SYSTEMS BIOLOGY 2014; 8:3. [PMID: 24397936 PMCID: PMC3896677 DOI: 10.1186/1752-0509-8-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 12/19/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND During embryogenesis, signaling molecules produced by one cell population direct gene regulatory changes in neighboring cells and influence their developmental fates and spatial organization. One of the earliest events in the development of the vertebrate embryo is the establishment of three germ layers, consisting of the ectoderm, mesoderm and endoderm. Attempts to measure gene expression in vivo in different germ layers and cell types are typically complicated by the heterogeneity of cell types within biological samples (i.e., embryos), as the responses of individual cell types are intermingled into an aggregate observation of heterogeneous cell types. Here, we propose a novel method to elucidate gene regulatory circuits from these aggregate measurements in embryos of the frog Xenopus tropicalis using gene network inference algorithms and then test the ability of the inferred networks to predict spatial gene expression patterns. RESULTS We use two inference models with different underlying assumptions that incorporate existing network information, an ODE model for steady-state data and a Markov model for time series data, and contrast the performance of the two models. We apply our method to both control and knockdown embryos at multiple time points to reconstruct the core mesoderm and endoderm regulatory circuits. Those inferred networks are then used in combination with known dorsal-ventral spatial expression patterns of a subset of genes to predict spatial expression patterns for other genes. Both models are able to predict spatial expression patterns for some of the core mesoderm and endoderm genes, but interestingly of different gene subsets, suggesting that neither model is sufficient to recapitulate all of the spatial patterns, yet they are complementary for the patterns that they do capture. CONCLUSION The presented methodology of gene network inference combined with spatial pattern prediction provides an additional layer of validation to elucidate the regulatory circuits controlling the spatial-temporal dynamics in embryonic development.
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Affiliation(s)
| | | | | | | | | | | | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA 92697, USA.
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24
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Wong MD, Dazai J, Walls JR, Gale NW, Henkelman RM. Design and implementation of a custom built optical projection tomography system. PLoS One 2013; 8:e73491. [PMID: 24023880 PMCID: PMC3762719 DOI: 10.1371/journal.pone.0073491] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/23/2013] [Indexed: 11/18/2022] Open
Abstract
Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm3. This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop.
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Affiliation(s)
- Michael D. Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail:
| | - Jun Dazai
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario, Canada
| | - Johnathon R. Walls
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Nicholas W. Gale
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - R. Mark Henkelman
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario, Canada
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25
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Castro-González C, Ledesma-Carbayo MJ, Peyriéras N, Santos A. Assembling models of embryo development: Image analysis and the construction of digital atlases. ACTA ACUST UNITED AC 2012; 96:109-20. [DOI: 10.1002/bdrc.21012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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26
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Husz ZL, Burton N, Hill B, Milyaev N, Baldock RA. Web tools for large-scale 3D biological images and atlases. BMC Bioinformatics 2012; 13:122. [PMID: 22676296 PMCID: PMC3412715 DOI: 10.1186/1471-2105-13-122] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 06/07/2012] [Indexed: 12/18/2022] Open
Abstract
Background Large-scale volumetric biomedical image data of three or more dimensions are a significant challenge for distributed browsing and visualisation. Many images now exceed 10GB which for most users is too large to handle in terms of computer RAM and network bandwidth. This is aggravated when users need to access tens or hundreds of such images from an archive. Here we solve the problem for 2D section views through archive data delivering compressed tiled images enabling users to browse through very-large volume data in the context of a standard web-browser. The system provides an interactive visualisation for grey-level and colour 3D images including multiple image layers and spatial-data overlay. Results The standard Internet Imaging Protocol (IIP) has been extended to enable arbitrary 2D sectioning of 3D data as well a multi-layered images and indexed overlays. The extended protocol is termed IIP3D and we have implemented a matching server to deliver the protocol and a series of Ajax/Javascript client codes that will run in an Internet browser. We have tested the server software on a low-cost linux-based server for image volumes up to 135GB and 64 simultaneous users. The section views are delivered with response times independent of scale and orientation. The exemplar client provided multi-layer image views with user-controlled colour-filtering and overlays. Conclusions Interactive browsing of arbitrary sections through large biomedical-image volumes is made possible by use of an extended internet protocol and efficient server-based image tiling. The tools open the possibility of enabling fast access to large image archives without the requirement of whole image download and client computers with very large memory configurations. The system was demonstrated using a range of medical and biomedical image data extending up to 135GB for a single image volume.
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Affiliation(s)
- Zsolt L Husz
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, UK
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27
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Mitchell AW, McConnell JR. A historical review of Contemporary Educational Psychology from 1995 to 2010. CONTEMPORARY EDUCATIONAL PSYCHOLOGY 2012. [DOI: 10.1016/j.cedpsych.2011.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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28
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Baldock RA, Burger A. Biomedical atlases: systematics, informatics and analysis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 736:655-77. [PMID: 22161358 DOI: 10.1007/978-1-4419-7210-1_39] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biomedical imaging is ubiquitous in the Life Sciences. Technology advances, and the resulting multitude of imaging modalities, have led to a sharp rise in the quantity and quality of such images. In addition, computational models are increasingly used to study biological processes involving spatio-temporal changes from the cell to the organism level, e.g., the development of an embryo or the growth of a tumour, and models and images are extensively described in natural language, for example, in research publications and patient records. Together this leads to a major spatio-temporal data and model integration challenge. Biomedical atlases have emerged as a key technology in solving this integration problem. Such atlases typically include an image-based (2D and/or 3D) component as well as a conceptual representation (ontologies) of the organisms involved. In this chapter, we review the notion of atlases in the biomedical domain, how they can be created, how they provide an index to spatio-temporal experimental data, issues of atlas data integration and their use for the analysis of large volumes of biomedical data.
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Affiliation(s)
- Richard A Baldock
- MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, UK.
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Jiménez-Lozano N, Segura J, Macías JR, Vega J, Carazo JM. Integrating human and murine anatomical gene expression data for improved comparisons. ACTA ACUST UNITED AC 2011; 28:397-402. [PMID: 22106336 DOI: 10.1093/bioinformatics/btr639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
MOTIVATION Information concerning the gene expression pattern in four dimensions (species, genes, anatomy and developmental stage) is crucial for unraveling the roles of genes through time. There are a variety of anatomical gene expression databases, but extracting information from them can be hampered by their diversity and heterogeneity. RESULTS aGEM 3.1 (anatomic Gene Expression Mapping) addresses the issues of diversity and heterogeneity of anatomical gene expression databases by integrating six mouse gene expression resources (EMAGE, GXD, GENSAT, Allen Brain Atlas data base, EUREXPRESS and BioGPS) and three human gene expression databases (HUDSEN, Human Protein Atlas and BioGPS). Furthermore, aGEM 3.1 provides new cross analysis tools to bridge these resources. AVAILABILITY AND IMPLEMENTATION aGEM 3.1 can be queried using gene and anatomical structure. Output information is presented in a friendly format, allowing the user to display expression maps and correlation matrices for a gene or structure during development. An in-depth study of a specific developmental stage is also possible using heatmaps that relate gene expression with anatomical components. http://agem.cnb.csic.es CONTACT natalia@cnb.csic.es SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Hawrylycz M, Ng L, Page D, Morris J, Lau C, Faber S, Faber V, Sunkin S, Menon V, Lein E, Jones A. Multi-scale correlation structure of gene expression in the brain. Neural Netw 2011; 24:933-42. [PMID: 21764550 DOI: 10.1016/j.neunet.2011.06.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 06/16/2011] [Accepted: 06/16/2011] [Indexed: 01/25/2023]
Abstract
The mammalian brain is best understood as a multi-scale hierarchical neural system, in the sense that connection and function occur on multiple scales from micro to macro. Modern genomic-scale expression profiling can provide insight into methodologies that elucidate this architecture. We present a methodology for understanding the relationship of gene expression and neuroanatomy based on correlation between gene expression profiles across tissue samples. A resulting tool, NeuroBlast, can identify networks of genes co-expressed within or across neuroanatomic structures. The method applies to any data modality that can be mapped with sufficient spatial resolution, and provides a computation technique to elucidate neuroanatomy via patterns of gene expression on spatial and temporal scales. In addition, from the perspective of spatial location, we discuss a complementary technique that identifies gene classes that contribute to defining anatomic patterns.
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Affiliation(s)
- Mike Hawrylycz
- Allen Institute for Brain Science, 551 N. 34th Street, Seattle, WA 98103, USA.
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Abstract
Many specifically human psychiatric and neurological conditions have developmental origins. Rodent models are extremely valuable for the investigation of brain development, but cannot provide insight into aspects that are specifically human. The human brain, and particularly the cerebral cortex, has some unique genetic, molecular, cellular and anatomical features, and these need to be further explored. Cortical expansion in human is not just quantitative; there are some novel types of neurons and cytoarchitectonic areas identified by their gene expression, connectivity and functions that do not exist in rodents. Recent research into human brain development has revealed more elaborated neurogenetic compartments, radial and tangential migration, transient cell layers in the subplate, and a greater diversity of early-generated neurons, including predecessor neurons. Recently there has been a renaissance of the study of human brain development because of these unique differences, made possible by the availability of new techniques. This review gives a flavour of the recent studies stemming from this renewed focus on the developing human brain.
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Affiliation(s)
- Gavin Clowry
- Institute of Neuroscience, Newcastle UniversityNewcastle upon Tyne, UK
| | - Zoltán Molnár
- Department of Physiology, Anatomy and Genetics, University of OxfordOxford, UK
| | - Pasko Rakic
- Department of Neurobiology, Kavli Institute of Neuroscience, Yale University School of MedicineNew Haven, CT, USA
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