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Kairišs K, Sokolova N, Zilova L, Schlagheck C, Reinhardt R, Baumbach T, Faragó T, van de Kamp T, Wittbrodt J, Weinhardt V. Visualisation of gene expression within the context of tissues using an X-ray computed tomography-based multimodal approach. Sci Rep 2024; 14:8543. [PMID: 38609416 PMCID: PMC11015006 DOI: 10.1038/s41598-024-58766-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
The development of an organism is orchestrated by the spatial and temporal expression of genes. Accurate visualisation of gene expression patterns in the context of the surrounding tissues offers a glimpse into the mechanisms that drive morphogenesis. We developed correlative light-sheet fluorescence microscopy and X-ray computed tomography approach to map gene expression patterns to the whole organism`s 3D anatomy. We show that this multimodal approach is applicable to gene expression visualized by protein-specific antibodies and fluorescence RNA in situ hybridisation offering a detailed understanding of individual phenotypic variations in model organisms. Furthermore, the approach offers a unique possibility to identify tissues together with their 3D cellular and molecular composition in anatomically less-defined in vitro models, such as organoids. We anticipate that the visual and quantitative insights into the 3D distribution of gene expression within tissue architecture, by multimodal approach developed here, will be equally valuable for reference atlases of model organisms development, as well as for comprehensive screens, and morphogenesis studies of in vitro models.
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Affiliation(s)
- Kristaps Kairišs
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
| | - Natalia Sokolova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Lucie Zilova
- Centre for Organismal Studies, 69120, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- HeiKa Graduate School On "Functional Materials", Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
| | - Robert Reinhardt
- Centre for Organismal Studies, 69120, Heidelberg, Germany
- European Molecular Biology Laboratory, Heidelberg, Germany
| | - Tilo Baumbach
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tomáš Faragó
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Thomas van de Kamp
- Institute for Photon Science and Synchrotron Radiation (IPS), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
- Laboratory for Applications of Synchrotron Radiation (LAS), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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Kaucka M, Joven Araus A, Tesarova M, Currie JD, Boström J, Kavkova M, Petersen J, Yao Z, Bouchnita A, Hellander A, Zikmund T, Elewa A, Newton PT, Fei JF, Chagin AS, Fried K, Tanaka EM, Kaiser J, Simon A, Adameyko I. Altered developmental programs and oriented cell divisions lead to bulky bones during salamander limb regeneration. Nat Commun 2022; 13:6949. [PMID: 36376278 PMCID: PMC9663504 DOI: 10.1038/s41467-022-34266-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 10/14/2022] [Indexed: 11/16/2022] Open
Abstract
There are major differences in duration and scale at which limb development and regeneration proceed, raising the question to what extent regeneration is a recapitulation of development. We address this by analyzing skeletal elements using a combination of micro-CT imaging, molecular profiling and clonal cell tracing. We find that, in contrast to development, regenerative skeletal growth is accomplished based entirely on cartilage expansion prior to ossification, not limiting the transversal cartilage expansion and resulting in bulkier skeletal parts. The oriented extension of salamander cartilage and bone appear similar to the development of basicranial synchondroses in mammals, as we found no evidence for cartilage stem cell niches or growth plate-like structures during neither development nor regeneration. Both regenerative and developmental ossification in salamanders start from the cortical bone and proceeds inwards, showing the diversity of schemes for the synchrony of cortical and endochondral ossification among vertebrates.
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Affiliation(s)
- Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Alberto Joven Araus
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - Joshua D Currie
- Department of Biology, Wake Forest University, Winston-Salem, NC, USA
| | - Johan Boström
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, 1090, Austria
| | - Michaela Kavkova
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - Julian Petersen
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, 1090, Austria
- Department of Orthodontics, University of Leipzig Medical Center, Leipzig, 04103, Germany
| | - Zeyu Yao
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
| | - Anass Bouchnita
- Department of Information Technology, Uppsala University, Uppsala, Sweden
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, TX, 79902, USA
| | - Andreas Hellander
- Department of Information Technology, Uppsala University, Uppsala, Sweden
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - Ahmed Elewa
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Phillip T Newton
- Department of Women's and Children's Health, Karolinska Institute, Solna, Sweden
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Solna, Sweden
| | - Ji-Feng Fei
- The Research Institute of Molecular Pathology (IMP), Vienna, 1030, Austria
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Andrei S Chagin
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Göteborg, 41346, Sweden
| | - Kaj Fried
- Department of Neuroscience, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden
| | - Elly M Tanaka
- The Research Institute of Molecular Pathology (IMP), Vienna, 1030, Austria
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, 61200, Czech Republic
| | - András Simon
- Department of Cell and Molecular Biology, Biomedicum, Karolinska Institute, Stockholm, 17165, Sweden.
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, 1090, Austria.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, 17165, Sweden.
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Handschuh S, Glösmann M. Mouse embryo phenotyping using X-ray microCT. Front Cell Dev Biol 2022; 10:949184. [PMID: 36187491 PMCID: PMC9523164 DOI: 10.3389/fcell.2022.949184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022] Open
Abstract
Microscopic X-ray computed tomography (microCT) is a structural ex vivo imaging technique providing genuine isotropic 3D images from biological samples at micron resolution. MicroCT imaging is non-destructive and combines well with other modalities such as light and electron microscopy in correlative imaging workflows. Protocols for staining embryos with X-ray dense contrast agents enable the acquisition of high-contrast and high-resolution datasets of whole embryos and specific organ systems. High sample throughput is achieved with dedicated setups. Consequently, microCT has gained enormous importance for both qualitative and quantitative phenotyping of mouse development. We here summarize state-of-the-art protocols of sample preparation and imaging procedures, showcase contemporary applications, and discuss possible pitfalls and sources for artefacts. In addition, we give an outlook on phenotyping workflows using microscopic dual energy CT (microDECT) and tissue-specific contrast agents.
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Matula J, Polakova V, Salplachta J, Tesarova M, Zikmund T, Kaucka M, Adameyko I, Kaiser J. Resolving complex cartilage structures in developmental biology via deep learning-based automatic segmentation of X-ray computed microtomography images. Sci Rep 2022; 12:8728. [PMID: 35610276 PMCID: PMC9130254 DOI: 10.1038/s41598-022-12329-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/03/2022] [Indexed: 11/18/2022] Open
Abstract
The complex shape of embryonic cartilage represents a true challenge for phenotyping and basic understanding of skeletal development. X-ray computed microtomography (μCT) enables inspecting relevant tissues in all three dimensions; however, most 3D models are still created by manual segmentation, which is a time-consuming and tedious task. In this work, we utilised a convolutional neural network (CNN) to automatically segment the most complex cartilaginous system represented by the developing nasal capsule. The main challenges of this task stem from the large size of the image data (over a thousand pixels in each dimension) and a relatively small training database, including genetically modified mouse embryos, where the phenotype of the analysed structures differs from the norm. We propose a CNN-based segmentation model optimised for the large image size that we trained using a unique manually annotated database. The segmentation model was able to segment the cartilaginous nasal capsule with a median accuracy of 84.44% (Dice coefficient). The time necessary for segmentation of new samples shortened from approximately 8 h needed for manual segmentation to mere 130 s per sample. This will greatly accelerate the throughput of μCT analysis of cartilaginous skeletal elements in animal models of developmental diseases.
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Affiliation(s)
- Jan Matula
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic
| | - Veronika Polakova
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic
| | - Jakub Salplachta
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic
| | - Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str.2, 24306, Ploen, Germany
| | - Igor Adameyko
- Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.,Department of Physiology and Pharmacology, Karolinska Institutet, 17165, Stockholm, Sweden
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Purkynova 123, Brno, 61200, Czech Republic.
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Matula J, Tesarova M, Zikmund T, Kaucka M, Adameyko I, Kaiser J. X-ray microtomography-based atlas of mouse cranial development. Gigascience 2021; 10:giab012. [PMID: 33677535 PMCID: PMC7936920 DOI: 10.1093/gigascience/giab012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/21/2020] [Accepted: 02/02/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND X-ray microtomography (μCT) has become an invaluable tool for non-destructive analysis of biological samples in the field of developmental biology. Mouse embryos are a typical model for investigation of human developmental diseases. By obtaining 3D high-resolution scans of the mouse embryo heads, we gain valuable morphological information about the structures prominent in the development of future face, brain, and sensory organs. The development of facial skeleton tracked in these μCT data provides a valuable background for further studies of congenital craniofacial diseases and normal development. FINDINGS In this work, reusable tomographic data from 7 full 3D scans of mouse embryo heads are presented and made publicly available. The ages of these embryos range from E12.5 to E18.5. The samples were stained by phosphotungstic acid prior to scanning, which greatly enhanced the contrast of various tissues in the reconstructed images and enabled precise segmentation. The images were obtained on a laboratory-based μCT system. Furthermore, we provide manually segmented masks of mesenchymal condensations (for E12.5 and E13.5) and cartilage present in the nasal capsule of the scanned embryos. CONCLUSION We present a comprehensive dataset of X-ray 3D computed tomography images of the developing mouse head with high-quality manual segmentation masks of cartilaginous nasal capsules. The provided μCT images can be used for studying any other major structure within the developing mouse heads. The high quality of the manually segmented models of nasal capsules may be instrumental to understanding the complex process of the development of the face in a mouse model.
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Affiliation(s)
- Jan Matula
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno, 61200, Czech Republic
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno, 61200, Czech Republic
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno, 61200, Czech Republic
| | - Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, 24306, Germany
- Medical University of Vienna, Spitalgasse 23, Vienna, 1090, Austria
| | - Igor Adameyko
- Medical University of Vienna, Spitalgasse 23, Vienna, 1090, Austria
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Purkyňova 123, Brno, 61200, Czech Republic
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