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Zhang W, Chen H, Liu W, Jia K, Yi M. Characterizing Marine Medaka ( Oryzias melastigma) Haploid Embryonic Stem Cells: A Valuable Tool for Marine Fish Genetic Research. Animals (Basel) 2024; 14:2739. [PMID: 39335329 PMCID: PMC11428384 DOI: 10.3390/ani14182739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 09/14/2024] [Accepted: 09/20/2024] [Indexed: 09/30/2024] Open
Abstract
Haploid embryonic stem cells (ESCs), which combine the properties of haploidy and pluripotency, hold significant potential for advancing developmental biology and reproductive technology. However, while previous research has largely focused on haploid ESCs in freshwater species like Japanese medaka (Oryzias latipes), little is known about their counterparts in marine species. This study hypothesizes that haploid ESCs from marine fish could offer unique insights and tools for genetic and virological research. To address this, we successfully established and characterized a novel haploid ESC line, hMMES1, derived from marine medaka (Oryzias melastigma). The hMMES1 cells contain 24 chromosomes, exhibit core stem cell characteristics, and express key pluripotency markers. In vitro, hMMES1 cells form embryonic bodies (EBs) capable of differentiating into the three germ layers. In vivo, hMMES1 cells were successfully transplanted into marine medaka and zebrafish, resulting in the generation of interspecies and interordinal chimeras. Additionally, hMMES1 cells demonstrate high efficiency in transfection and transduction, and show susceptibility to major aquaculture viruses, nodavirus (NNV) and iridovirus (SGIV). These findings suggest that hMMES1 cells represent a valuable model for genetic manipulation and virological studies in marine fish species.
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Affiliation(s)
- Wanwan Zhang
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou 519082, China
| | - Huiquan Chen
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou 519082, China
| | - Wei Liu
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou 519082, China
| | - Kuntong Jia
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou 519082, China
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 519082, China
| | - Meisheng Yi
- School of Marine Sciences, Sun Yat-sen University, Guangzhou 519082, China
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou 519082, China
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Afting C, Walther T, Drozdowski OM, Schlagheck C, Schwarz US, Wittbrodt J, Göpfrich K. DNA microbeads for spatio-temporally controlled morphogen release within organoids. NATURE NANOTECHNOLOGY 2024:10.1038/s41565-024-01779-y. [PMID: 39251862 DOI: 10.1038/s41565-024-01779-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 08/05/2024] [Indexed: 09/11/2024]
Abstract
Organoids are transformative in vitro model systems that mimic features of the corresponding tissue in vivo. However, across tissue types and species, organoids still often fail to reach full maturity and function because biochemical cues cannot be provided from within the organoid to guide their development. Here we introduce nanoengineered DNA microbeads with tissue mimetic tunable stiffness for implementing spatio-temporally controlled morphogen gradients inside of organoids at any point in their development. Using medaka retinal organoids and early embryos, we show that DNA microbeads can be integrated into embryos and organoids by microinjection and erased in a non-invasive manner with light. Coupling a recombinant surrogate Wnt to the DNA microbeads, we demonstrate the spatio-temporally controlled morphogen release from the microinjection site, which leads to morphogen gradients resulting in the formation of retinal pigmented epithelium while maintaining neuroretinal cell types. Thus, we bioengineered retinal organoids to more closely mirror the cell type diversity of in vivo retinae. Owing to the facile, one-pot fabrication process, the DNA microbead technology can be adapted to other organoid systems for improved tissue mimicry.
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Affiliation(s)
- Cassian Afting
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
- HeiKa Graduate School on "Functional Materials", Heidelberg, Germany
| | - Tobias Walther
- HeiKa Graduate School on "Functional Materials", Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Oliver M Drozdowski
- BioQuant Center, Heidelberg University, Heidelberg, Germany
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
- Max Planck School Matter to Life, Heidelberg, Germany
| | - Christina Schlagheck
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Heidelberg, Germany
- Heidelberg International Biosciences Graduate School HBIGS, Heidelberg, Germany
- HeiKa Graduate School on "Functional Materials", Heidelberg, Germany
| | - Ulrich S Schwarz
- BioQuant Center, Heidelberg University, Heidelberg, Germany
- Institute for Theoretical Physics, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Heidelberg, Germany.
| | - Kerstin Göpfrich
- Center for Molecular Biology of Heidelberg University (ZMBH), Heidelberg University, Heidelberg, Germany.
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Heidelberg, Germany.
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3
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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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4
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Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. Trends Genet 2023; 39:830-843. [PMID: 37714733 PMCID: PMC11147682 DOI: 10.1016/j.tig.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.
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Affiliation(s)
- Stacy Li
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA.
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Cheng T, Xing YY, Liu C, Li YF, Huang Y, Liu X, Zhang YJ, Zhao GQ, Dong Y, Fu XX, Tian YM, Shu LP, Megason SG, Xu PF. Nodal coordinates the anterior-posterior patterning of germ layers and induces head formation in zebrafish explants. Cell Rep 2023; 42:112351. [PMID: 37018074 DOI: 10.1016/j.celrep.2023.112351] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 01/16/2023] [Accepted: 03/21/2023] [Indexed: 04/06/2023] Open
Abstract
Much progress has been made toward generating analogs of early embryos, such as gastruloids and embryoids, in vitro. However, methods for how to fully mimic the cell movements of gastrulation and coordinate germ-layer patterning to induce head formation are still lacking. Here, we show that a regional Nodal gradient applied to zebrafish animal pole explant can generate a structure that recapitulates the key cell movements of gastrulation. Using single-cell transcriptome and in situ hybridization analysis, we assess the dynamics of the cell fates and patterning of this structure. The mesendoderm differentiates into the anterior endoderm, prechordal plate, notochord, and tailbud-like cells along an anterior-posterior axis, and an anterior-posterior-patterned head-like structure (HLS) progressively forms during late gastrulation. Among 105 immediate Nodal targets, 14 genes contain axis-induction ability, and 5 of them induce a complete or partial head structure when overexpressed in the ventral side of zebrafish embryos.
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Affiliation(s)
- Tao Cheng
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan-Yi Xing
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorders, Hangzhou, Zhejiang, China
| | - Cong Liu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yun-Fei Li
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Huang
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiang Liu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying-Jie Zhang
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Guo-Qin Zhao
- Department of Immunology, Guizhou Medical University, Guiyang 550004, China
| | - Yang Dong
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xin-Xin Fu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yi-Meng Tian
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Li-Ping Shu
- Department of Immunology, Guizhou Medical University, Guiyang 550004, China
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
| | - Peng-Fei Xu
- Women's Hospital, Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
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Cardozo MJ, Sánchez-Bustamante E, Bovolenta P. Optic cup morphogenesis across species and related inborn human eye defects. Development 2023; 150:dev200399. [PMID: 36714981 PMCID: PMC10110496 DOI: 10.1242/dev.200399] [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] [Indexed: 01/31/2023]
Abstract
The vertebrate eye is shaped as a cup, a conformation that optimizes vision and is acquired early in development through a process known as optic cup morphogenesis. Imaging living, transparent teleost embryos and mammalian stem cell-derived organoids has provided insights into the rearrangements that eye progenitors undergo to adopt such a shape. Molecular and pharmacological interference with these rearrangements has further identified the underlying molecular machineries and the physical forces involved in this morphogenetic process. In this Review, we summarize the resulting scenarios and proposed models that include common and species-specific events. We further discuss how these studies and those in environmentally adapted blind species may shed light on human inborn eye malformations that result from failures in optic cup morphogenesis, including microphthalmia, anophthalmia and coloboma.
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Affiliation(s)
- Marcos J. Cardozo
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| | - Elena Sánchez-Bustamante
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), c/ Nicolás Cabrera 1, Cantoblanco, Madrid 28049, Spain
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7
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Pakari K, Wittbrodt J, Thumberger T. De novo PAM generation to reach initially inaccessible target sites for base editing. Development 2023; 150:286701. [PMID: 36683434 PMCID: PMC10110497 DOI: 10.1242/dev.201115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/16/2022] [Indexed: 01/24/2023]
Abstract
Base editing by CRISPR crucially depends on the presence of a protospacer adjacent motif (PAM) at the correct distance from the editing site. Here, we present and validate an efficient one-shot approach termed 'inception' that expands the editing range. This is achieved by sequential, combinatorial base editing: de novo generated synonymous, non-synonymous or intronic PAM sites facilitate subsequent base editing at nucleotide positions that were initially inaccessible, further opening the targeting range of highly precise editing approaches. We demonstrate the applicability of the inception concept in medaka (Oryzias latipes) in three settings: loss of function, by introducing a pre-termination STOP codon in the open reading frame of oca2; locally confined multi-codon changes to generate allelic variants with different phenotypic severity in kcnh6a; and the removal of a splice acceptor site by targeting intronic sequences of rx3. Using sequentially acting base editors in the described combinatorial approach expands the number of accessible target sites by 65% on average. This allows the use of well-established tools with NGG PAM recognition for the establishment of thus far unreachable disease models, for hypomorphic allele studies and for efficient targeted mechanistic investigations in a precise and predictable manner.
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Affiliation(s)
- Kaisa Pakari
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.,Heidelberg Biosciences International Graduate School (HBIGS), Heidelberg University, Im Neuenheimer Feld 501, 69120 Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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8
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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9
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Huch M, Gouti M. Once upon a dish: the next frontier in engineering multicellular systems. Development 2022; 149:277955. [DOI: 10.1242/dev.200744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
ABSTRACT
In June 2022, the second meeting on ‘Engineering Multicellular Systems’, organized by the European Molecular Biology Laboratory and the Institute of Bioengineering of Catalonia, took place in Barcelona. Stem cell and systems biologists, physicists and engineers from all over the world gathered to discuss how recent breakthroughs in organoid technologies, engineering and mechanobiology are boosting our understanding of early morphogenesis, organogenesis and organ function with applications in tissue engineering, disease modeling and drug screening. The meeting was organized with sustainability in mind, and included an ethics session and an outreach public activity.
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Affiliation(s)
- Meritxell Huch
- The Max Planck Institute of Molecular Cell Biology and Genetics 1 , 01307, Dresden , Germany
| | - Mina Gouti
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association 2 , 13125, Berlin , Germany
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Fasano G, Compagnucci C, Dallapiccola B, Tartaglia M, Lauri A. Teleost Fish and Organoids: Alternative Windows Into the Development of Healthy and Diseased Brains. Front Mol Neurosci 2022; 15:855786. [PMID: 36034498 PMCID: PMC9403253 DOI: 10.3389/fnmol.2022.855786] [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: 01/19/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
The variety in the display of animals’ cognition, emotions, and behaviors, typical of humans, has its roots within the anterior-most part of the brain: the forebrain, giving rise to the neocortex in mammals. Our understanding of cellular and molecular events instructing the development of this domain and its multiple adaptations within the vertebrate lineage has progressed in the last decade. Expanding and detailing the available knowledge on regionalization, progenitors’ behavior and functional sophistication of the forebrain derivatives is also key to generating informative models to improve our characterization of heterogeneous and mechanistically unexplored cortical malformations. Classical and emerging mammalian models are irreplaceable to accurately elucidate mechanisms of stem cells expansion and impairments of cortex development. Nevertheless, alternative systems, allowing a considerable reduction of the burden associated with animal experimentation, are gaining popularity to dissect basic strategies of neural stem cells biology and morphogenesis in health and disease and to speed up preclinical drug testing. Teleost vertebrates such as zebrafish, showing conserved core programs of forebrain development, together with patients-derived in vitro 2D and 3D models, recapitulating more accurately human neurogenesis, are now accepted within translational workflows spanning from genetic analysis to functional investigation. Here, we review the current knowledge of common and divergent mechanisms shaping the forebrain in vertebrates, and causing cortical malformations in humans. We next address the utility, benefits and limitations of whole-brain/organism-based fish models or neuronal ensembles in vitro for translational research to unravel key genes and pathological mechanisms involved in neurodevelopmental diseases.
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Thumberger T, Tavhelidse-Suck T, Gutierrez-Triana JA, Cornean A, Medert R, Welz B, Freichel M, Wittbrodt J. Boosting targeted genome editing using the hei-tag. eLife 2022; 11:70558. [PMID: 35333175 PMCID: PMC9068219 DOI: 10.7554/elife.70558] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 03/15/2022] [Indexed: 11/25/2022] Open
Abstract
Precise, targeted genome editing by CRISPR/Cas9 is key for basic research and translational approaches in model and non-model systems. While active in all species tested so far, editing efficiencies still leave room for improvement. The bacterial Cas9 needs to be efficiently shuttled into the nucleus as attempted by fusion with nuclear localization signals (NLSs). Additional peptide tags such as FLAG- or myc-tags are usually added for immediate detection or straightforward purification. Immediate activity is usually granted by administration of preassembled protein/RNA complexes. We present the ‘hei-tag (high efficiency-tag)’ which boosts the activity of CRISPR/Cas genome editing tools already when supplied as mRNA. The addition of the hei-tag, a myc-tag coupled to an optimized NLS via a flexible linker, to Cas9 or a C-to-T (cytosine-to-thymine) base editor dramatically enhances the respective targeting efficiency. This results in an increase in bi-allelic editing, yet reduction of allele variance, indicating an immediate activity even at early developmental stages. The hei-tag boost is active in model systems ranging from fish to mammals, including tissue culture applications. The simple addition of the hei-tag allows to instantly upgrade existing and potentially highly adapted systems as well as to establish novel highly efficient tools immediately applicable at the mRNA level. The genetic code stored within DNA provides cells with the instructions they need to carry out their role in the body. Any changes to these genes, or the DNA sequence around them, has the potential to completely alter how a cell behaves. Scientists have developed various tools that allow them to experimentally modify the genome of cells or even entire living organisms. This includes the popular Cas9 enzyme which cuts DNA at specific sites, and base editors which can precisely change bits of genetic code without cutting DNA. While there are lots of Cas9 enzymes and base editors currently available, these often differ greatly in their activity depending on which cell type or organism they are applied to. Finding a tool that can effectively modify the genome of an organism at the right time during development also poses a challenge. All the cells in an organism arise from a single fertilized cell. If this cell is genetically edited, all its subsequent daughter cells (which make up the entire organism) will contain the genetic modification. However, most genome editing tools only work efficiently later in development, resulting in an undesirable mosaic organism composed of both edited and non-edited cells. Here, Thumberger et al. have developed a new ‘high efficiency-tag’ (also known as hei-tag for short) that can enhance the activity of gene editing tools and overcome this barrier. The tag improves the efficiency of gene editing by immediately shuttling a Cas9 enzyme to the nucleus, the cellular compartment that stores DNA. In all cases, gene editing tools with hei-tag worked better than those without in fish embryos and mouse cells grown in the laboratory. When Cas9 enzymes connected to a hei-tag were injected into the first fertilized cell of a fish embryo, this resulted in an even distribution of edited genes spread throughout the whole organism. To understand how a gene affects an organism, researchers need to be able to edit it as early in development as possible. Attaching the ‘hei-tag’ to already available tools could help boost their activity and make them more efficient. It could also allow advances in medical research aimed at replacing faulty genes with fully functioning ones.
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Affiliation(s)
- Thomas Thumberger
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | | | - Alex Cornean
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Rebekka Medert
- Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - Bettina Welz
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Marc Freichel
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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Anlas K, Trivedi V. Studying evolution of the primary body axis in vivo and in vitro. eLife 2021; 10:e69066. [PMID: 34463611 PMCID: PMC8456739 DOI: 10.7554/elife.69066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023] Open
Abstract
The metazoan body plan is established during early embryogenesis via collective cell rearrangements and evolutionarily conserved gene networks, as part of a process commonly referred to as gastrulation. While substantial progress has been achieved in terms of characterizing the embryonic development of several model organisms, underlying principles of many early patterning processes nevertheless remain enigmatic. Despite the diversity of (pre-)gastrulating embryo and adult body shapes across the animal kingdom, the body axes, which are arguably the most fundamental features, generally remain identical between phyla. Recently there has been a renewed appreciation of ex vivo and in vitro embryo-like systems to model early embryonic patterning events. Here, we briefly review key examples and propose that similarities in morphogenesis and associated gene expression dynamics may reveal an evolutionarily conserved developmental mode as well as provide further insights into the role of external or extraembryonic cues in shaping the early embryo. In summary, we argue that embryo-like systems can be employed to inform previously uncharted aspects of animal body plan evolution as well as associated patterning rules.
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Affiliation(s)
| | - Vikas Trivedi
- EMBL BarcelonaBarcelonaSpain
- EMBL Heidelberg, Developmental BiologyHeidelbergGermany
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Zilova L, Weinhardt V, Tavhelidse T, Schlagheck C, Thumberger T, Wittbrodt J. Fish primary embryonic pluripotent cells assemble into retinal tissue mirroring in vivo early eye development. eLife 2021; 10:e66998. [PMID: 34252023 PMCID: PMC8275126 DOI: 10.7554/elife.66998] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Organoids derived from pluripotent stem cells promise the solution to current challenges in basic and biomedical research. Mammalian organoids are however limited by long developmental time, variable success, and lack of direct comparison to an in vivo reference. To overcome these limitations and address species-specific cellular organization, we derived organoids from rapidly developing teleosts. We demonstrate how primary embryonic pluripotent cells from medaka and zebrafish efficiently assemble into anterior neural structures, particularly retina. Within 4 days, blastula-stage cell aggregates reproducibly execute key steps of eye development: retinal specification, morphogenesis, and differentiation. The number of aggregated cells and genetic factors crucially impacted upon the concomitant morphological changes that were intriguingly reflecting the in vivo situation. High efficiency and rapid development of fish-derived organoids in combination with advanced genome editing techniques immediately allow addressing aspects of development and disease, and systematic probing of impact of the physical environment on morphogenesis and differentiation.
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Affiliation(s)
- Lucie Zilova
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Venera Weinhardt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Tinatini Tavhelidse
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Christina Schlagheck
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
- Heidelberg International Biosciences Graduate School HBIGS and HeiKa Graduate School on “Functional Materials”HeidelbergGermany
| | - Thomas Thumberger
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
| | - Joachim Wittbrodt
- Centre for Organismal Studies Heidelberg, Heidelberg UniversityHeidelbergGermany
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