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Spiess K, Taylor SE, Fulton T, Toh K, Saunders D, Hwang S, Wang Y, Paige B, Steventon B, Verd B. Approximated gene expression trajectories for gene regulatory network inference on cell tracks. iScience 2024; 27:110840. [PMID: 39290835 PMCID: PMC11407030 DOI: 10.1016/j.isci.2024.110840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/20/2024] [Accepted: 08/21/2024] [Indexed: 09/19/2024] Open
Abstract
The study of pattern formation has benefited from our ability to reverse-engineer gene regulatory network (GRN) structure from spatiotemporal quantitative gene expression data. Traditional approaches have focused on systems where the timescales of pattern formation and morphogenesis can be separated. Unfortunately, this is not the case in most animal patterning systems, where pattern formation and morphogenesis are co-occurring and tightly linked. To elucidate patterning mechanisms in such systems we need to adapt our GRN inference methodologies to include cell movements. In this work, we fill this gap by integrating quantitative data from live and fixed embryos to approximate gene expression trajectories (AGETs) in single cells and use these to reverse-engineer GRNs. This framework generates candidate GRNs that recapitulate pattern at the tissue level, gene expression dynamics at the single cell level, recover known genetic interactions and recapitulate experimental perturbations while incorporating cell movements explicitly for the first time.
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Affiliation(s)
- Kay Spiess
- Department of Genetics, University of Cambridge, Cambridge, UK
- The Alan Turing Institute, London, UK
| | | | - Timothy Fulton
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Kane Toh
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Dillan Saunders
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Seongwon Hwang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Yuxuan Wang
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Brooks Paige
- The Alan Turing Institute, London, UK
- Centre for Artificial Intelligence, University College London, London, UK
| | | | - Berta Verd
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Biology, University of Oxford, Oxford, UK
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Miao Y, Pourquié O. Cellular and molecular control of vertebrate somitogenesis. Nat Rev Mol Cell Biol 2024; 25:517-533. [PMID: 38418851 DOI: 10.1038/s41580-024-00709-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Segmentation is a fundamental feature of the vertebrate body plan. This metameric organization is first implemented by somitogenesis in the early embryo, when paired epithelial blocks called somites are rhythmically formed to flank the neural tube. Recent advances in in vitro models have offered new opportunities to elucidate the mechanisms that underlie somitogenesis. Notably, models derived from human pluripotent stem cells introduced an efficient proxy for studying this process during human development. In this Review, we summarize the current understanding of somitogenesis gained from both in vivo studies and in vitro studies. We deconstruct the spatiotemporal dynamics of somitogenesis into four distinct modules: dynamic events in the presomitic mesoderm, segmental determination, somite anteroposterior polarity patterning, and epithelial morphogenesis. We first focus on the segmentation clock, as well as signalling and metabolic gradients along the tissue, before discussing the clock and wavefront and other models that account for segmental determination. We then detail the molecular and cellular mechanisms of anteroposterior polarity patterning and somite epithelialization.
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Affiliation(s)
- Yuchuan Miao
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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Serra KM, Vyzas C, Shehreen S, Chipendo I, Clifford KM, Youngstrom DW, Devoto SH. Vertebral pattern and morphology is determined during embryonic segmentation. Dev Dyn 2024; 253:204-214. [PMID: 37688793 DOI: 10.1002/dvdy.649] [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: 01/03/2023] [Revised: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND The segmented nature of the adult vertebral column is based on segmentation of the paraxial mesoderm during early embryogenesis. Disruptions to embryonic segmentation, whether caused by genetic lesions or environmental stress, result in adult vertebral pathologies. However, the mechanisms linking embryonic segmentation and the details of adult vertebral morphology are poorly understood. RESULTS We induced border defects using two approaches in zebrafish: heat stress and misregulation of embryonic segmentation genes tbx6, mesp-ba, and ripply1. We assayed vertebral length, regularity, and polarity using microscopic and radiological imaging. In population studies, we find a correlation between specific embryonic border defects and specific vertebral defects, and within individual fish, we trace specific adult vertebral defects to specific embryonic border defects. CONCLUSIONS Our data reveal that transient disruptions of embryonic segment border formation led to significant vertebral anomalies that persist through adulthood. The spacing of embryonic borders controls the length of the vertebra. The positions of embryonic borders control the positions of ribs and arches. Embryonic borders underlie fusions and divisions between adjacent spines and ribs. These data suggest that segment borders have a dominant role in vertebral development.
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Affiliation(s)
- Kevin M Serra
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Christina Vyzas
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Sarah Shehreen
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Iris Chipendo
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
| | - Katherine M Clifford
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
- Department of Neurology, Stanford University, Stanford, California, USA
| | - Daniel W Youngstrom
- Department of Orthopaedic Surgery, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Stephen H Devoto
- Department of Biology, Wesleyan University, Middletown, Connecticut, USA
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Janssen R, Budd GE. New insights into mesoderm and endoderm development, and the nature of the onychophoran blastopore. Front Zool 2024; 21:2. [PMID: 38267986 PMCID: PMC10809584 DOI: 10.1186/s12983-024-00521-7] [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: 11/29/2023] [Accepted: 01/09/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Early during onychophoran development and prior to the formation of the germ band, a posterior tissue thickening forms the posterior pit. Anterior to this thickening forms a groove, the embryonic slit, that marks the anterior-posterior orientation of the developing embryo. This slit is by some authors considered the blastopore, and thus the origin of the endoderm, while others argue that the posterior pit represents the blastopore. This controversy is of evolutionary significance because if the slit represents the blastopore, then this would support the amphistomy hypothesis that suggests that a slit-like blastopore in the bilaterian ancestor evolved into protostomy and deuterostomy. RESULTS In this paper, we summarize our current knowledge about endoderm and mesoderm development in onychophorans and provide additional data on early endoderm- and mesoderm-determining marker genes such as Blimp, Mox, and the T-box genes. CONCLUSION We come to the conclusion that the endoderm of onychophorans forms prior to the development of the embryonic slit, and thus that the slit is not the primary origin of the endoderm. It is thus unlikely that the embryonic slit represents the blastopore. We suggest instead that the posterior pit indeed represents the lips of the blastopore, and that the embryonic slit (and surrounding tissue) represents a morphologically superficial archenteron-like structure. We conclude further that both endoderm and mesoderm development are under control of conserved gene regulatory networks, and that many of the features found in arthropods including the model Drosophila melanogaster are likely derived.
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Affiliation(s)
- Ralf Janssen
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden.
| | - Graham E Budd
- Department of Earth Sciences, Palaeobiology, Uppsala University, Villavägen 16, 75236, Uppsala, Sweden
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Wynsberghe JV, Vanakker OM. Significance of Premature Vertebral Mineralization in Zebrafish Models in Mechanistic and Pharmaceutical Research on Hereditary Multisystem Diseases. Biomolecules 2023; 13:1621. [PMID: 38002303 PMCID: PMC10669475 DOI: 10.3390/biom13111621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Zebrafish are increasingly becoming an important model organism for studying the pathophysiological mechanisms of human diseases and investigating how these mechanisms can be effectively targeted using compounds that may open avenues to novel treatments for patients. The zebrafish skeleton has been particularly instrumental in modeling bone diseases as-contrary to other model organisms-the lower load on the skeleton of an aquatic animal enables mutants to survive to early adulthood. In this respect, the axial skeletons of zebrafish have been a good read-out for congenital spinal deformities such as scoliosis and degenerative disorders such as osteoporosis and osteoarthritis, in which aberrant mineralization in humans is reflected in the respective zebrafish models. Interestingly, there have been several reports of hereditary multisystemic diseases that do not affect the vertebral column in human patients, while the corresponding zebrafish models systematically show anomalies in mineralization and morphology of the spine as their leading or, in some cases, only phenotype. In this review, we describe such examples, highlighting the underlying mechanisms, the already-used or potential power of these models to help us understand and amend the mineralization process, and the outstanding questions on how and why this specific axial type of aberrant mineralization occurs in these disease models.
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Affiliation(s)
- Judith Van Wynsberghe
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Ectopic Mineralization Research Group, 9000 Ghent, Belgium
| | - Olivier M Vanakker
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Ectopic Mineralization Research Group, 9000 Ghent, Belgium
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Yabe T, Uriu K, Takada S. Ripply suppresses Tbx6 to induce dynamic-to-static conversion in somite segmentation. Nat Commun 2023; 14:2115. [PMID: 37055428 PMCID: PMC10102234 DOI: 10.1038/s41467-023-37745-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/29/2023] [Indexed: 04/15/2023] Open
Abstract
The metameric pattern of somites is created based on oscillatory expression of clock genes in presomitic mesoderm. However, the mechanism for converting the dynamic oscillation to a static pattern of somites is still unclear. Here, we provide evidence that Ripply/Tbx6 machinery is a key regulator of this conversion. Ripply1/Ripply2-mediated removal of Tbx6 protein defines somite boundary and also leads to cessation of clock gene expression in zebrafish embryos. On the other hand, activation of ripply1/ripply2 mRNA and protein expression is periodically regulated by clock oscillation in conjunction with an Erk signaling gradient. Whereas Ripply protein decreases rapidly in embryos, Ripply-triggered Tbx6 suppression persists long enough to complete somite boundary formation. Mathematical modeling shows that a molecular network based on results of this study can reproduce dynamic-to-static conversion in somitogenesis. Furthermore, simulations with this model suggest that sustained suppression of Tbx6 caused by Ripply is crucial in this conversion.
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Affiliation(s)
- Taijiro Yabe
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
| | - Koichiro Uriu
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
| | - Shinji Takada
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
- The Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji-cho, Okazaki, Aichi, 444-8787, Japan.
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Akama K, Ebata K, Maeno A, Taminato T, Otosaka S, Gengyo-Ando K, Nakai J, Yamasu K, Kawamura A. Role of somite patterning in the formation of Weberian apparatus and pleural rib in zebrafish. J Anat 2019; 236:622-629. [PMID: 31840255 DOI: 10.1111/joa.13135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2019] [Indexed: 01/12/2023] Open
Abstract
In the vertebrate body, a metameric structure is present along the anterior-posterior axis. Zebrafish tbx6-/- larvae, in which somite boundaries do not form during embryogenesis, were shown to exhibit abnormal skeletal morphology such as rib, neural arch and hemal arch. In this study, we investigated the role of somite patterning in the formation of anterior vertebrae and ribs in more detail. Using three-dimensional computed tomography scans, we found that anterior vertebrae including the Weberian apparatus were severely affected in tbx6-/- larvae. In addition, pleural ribs of tbx6 mutants exhibited severe defects in the initial ossification, extension of ossification, and formation of parapophyses. Two-colour staining revealed that bifurcation of ribs was caused by fusion or branching of ribs in tbx6-/- . The parapophyses in tbx6-/- juvenile fish showed irregular positioning to centra and abnormal attachment to ribs. Furthermore, we found that the ossification of the distal portion of ribs proceeded along myotome boundaries even in irregularly positioned myotome boundaries. These results provide evidence of the contribution of somite patterning to the formation of the Weberian apparatus and rib in zebrafish.
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Affiliation(s)
- Kagari Akama
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Kanami Ebata
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Akiteru Maeno
- Plant Cytogenetics Laboratory, National Institute of Genetics, Mishima, Japan
| | - Tomohito Taminato
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Shiori Otosaka
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Keiko Gengyo-Ando
- Brain and Body System Science Institute, Saitama University, Saitama, Japan
| | - Junichi Nakai
- Brain and Body System Science Institute, Saitama University, Saitama, Japan
| | - Kyo Yamasu
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
| | - Akinori Kawamura
- Division of Life Science, Graduate School of Science and Engineering, Saitama University, Saitama, Japan
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