1
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Farag N, Sacharen C, Avni L, Nachman I. Coordination between endoderm progression and mouse gastruloid elongation controls endodermal morphotype choice. Dev Cell 2024; 59:2364-2374.e4. [PMID: 38838673 DOI: 10.1016/j.devcel.2024.05.017] [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: 03/24/2023] [Revised: 09/11/2023] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Embryonic development is highly robust. Morphogenetic variability between embryos (under ideal conditions) is largely quantitative. This robustness stands in contrast to in vitro embryo-like models, which, like most organoids, can display a high degree of tissue morphogenetic variability. The source of this difference is not fully understood. We use the mouse gastruloid model to study the morphogenetic progression of definitive endoderm (DE) and its divergence. We first catalog the different morphologies and characterize their statistics. We then learn predictive models for DE morphotype based on earlier expression and morphology measurements. Finally, we analyze these models to identify key drivers of morphotype variability and devise gastruloid-specific and global interventions that can lower this variability and steer morphotype choice. In the process, we identify two types of coordination lacking in the in vitro model but required for robust gut-tube formation. This approach can help improve the quality and usability of 3D embryo-like models.
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Affiliation(s)
- Naama Farag
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Chen Sacharen
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Lara Avni
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel
| | - Iftach Nachman
- School of Neurobiology, Biochemistry and Biophysics, Tel Aviv University, Tel Aviv, Israel.
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2
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Rabeling A, van der Hoven A, Andersen N, Goolam M. Neural Tube Organoids: A Novel System to Study Developmental Timing. Stem Cell Rev Rep 2024:10.1007/s12015-024-10785-5. [PMID: 39230820 DOI: 10.1007/s12015-024-10785-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
The neural tube (NT) is a transient structure formed during embryogenesis which develops into the brain and spinal cord. While mouse models have been commonly used in place of human embryos to study NT development, species-specific differences limit their applicability. One major difference is developmental timing, with NT formation from the neural plate in 16 days in humans compared to 4 days in mice, as well as differences in the time taken to form neuronal subtypes and complete neurogenesis. Neural tube organoids (NTOs) represent a new way to study NT development in vitro. While mouse and human NTOs have been shown to recapitulate the major developmental events of NT formation; it is unknown whether species-specific developmental timing, also termed allochrony, is also recapitulated. This review summarises current research using both mouse and human NTOs and compares developmental timing events in order to assess if allochrony is maintained in organoids.
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Affiliation(s)
- Alexa Rabeling
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- UCT Neuroscience Institute, Cape Town, South Africa
| | - Amy van der Hoven
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- UCT Neuroscience Institute, Cape Town, South Africa
| | - Nathalie Andersen
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa
- UCT Neuroscience Institute, Cape Town, South Africa
| | - Mubeen Goolam
- Department of Human Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.
- UCT Neuroscience Institute, Cape Town, South Africa.
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3
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Yan C, Jin G, Li L. Spinal scoliosis: insights into developmental mechanisms and animal models. Spine Deform 2024:10.1007/s43390-024-00941-9. [PMID: 39164474 DOI: 10.1007/s43390-024-00941-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 07/29/2024] [Indexed: 08/22/2024]
Abstract
Spinal scoliosis, a prevalent spinal deformity impacting both physical and mental well-being, has a significant genetic component, though the exact pathogenic mechanisms remain elusive. This review offers a comprehensive exploration of current research on embryonic spinal development, focusing on the genetic and biological intricacies governing axial elongation and straightening. Zebrafish, a vital model in developmental biology, takes a prominent role in understanding spinal scoliosis. Insights from zebrafish studies illustrate genetic and physiological aspects, including notochord development and cerebrospinal fluid dynamics, revealing the anomalies contributing to scoliosis. In this review, we acknowledge existing challenges, such as deciphering the unique dynamics of human spinal development, variations in physiological curvature, and disparities in cerebrospinal fluid circulation. Further, we emphasize the need for caution when extrapolating findings to humans and for future research to bridge current knowledge gaps. We hope that this review will be a beneficial frame of reference for the guidance of future studies on animal models and genetic research for spinal scoliosis.
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Affiliation(s)
- Chongnan Yan
- Department of Spine Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Guoxin Jin
- Department of Spine Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Lei Li
- Department of Spine Surgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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4
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Newman SA. Form, function, mind: What doesn't compute (and what might). Biochem Biophys Res Commun 2024; 721:150141. [PMID: 38781663 DOI: 10.1016/j.bbrc.2024.150141] [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: 10/24/2023] [Revised: 03/07/2024] [Accepted: 05/17/2024] [Indexed: 05/25/2024]
Abstract
The applicability of computational and dynamical systems models to organisms is scrutinized, using examples from developmental biology and cognition. Developmental morphogenesis is dependent on the inherent material properties of developing animal (metazoan) tissues, a non-computational modality, but cell differentiation, which utilizes chromatin-based revisable memory banks and program-like function-calling, via the developmental gene co-expression system unique to the metazoans, has a quasi-computational basis. Multi-attractor dynamical models are argued to be misapplied to global properties of development, and it is suggested that along with computationalism, classic forms of dynamicism are similarly unsuitable to accounting for cognitive phenomena. Proposals are made for treating brains and other nervous tissues as novel forms of excitable matter with inherent properties which enable the intensification of cell-based basal cognition capabilities present throughout the tree of life. Finally, some connections are drawn between the viewpoint described here and active inference models of cognition, such as the Free Energy Principle.
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5
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Hamazaki N, Yang W, Kubo CA, Qiu C, Martin BK, Garge RK, Regalado SG, Nichols EK, Pendyala S, Bradley N, Fowler DM, Lee C, Daza RM, Srivatsan S, Shendure J. Retinoic acid induces human gastruloids with posterior embryo-like structures. Nat Cell Biol 2024:10.1038/s41556-024-01487-8. [PMID: 39164488 DOI: 10.1038/s41556-024-01487-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024]
Abstract
Gastruloids are a powerful in vitro model of early human development. However, although elongated and composed of all three germ layers, human gastruloids do not morphologically resemble post-implantation human embryos. Here we show that an early pulse of retinoic acid (RA), together with later Matrigel, robustly induces human gastruloids with posterior embryo-like morphological structures, including a neural tube flanked by segmented somites and diverse cell types, including neural crest, neural progenitors, renal progenitors and myocytes. Through in silico staging based on single-cell RNA sequencing, we find that human RA-gastruloids progress further than other human or mouse embryo models, aligning to E9.5 mouse and CS11 cynomolgus monkey embryos. We leverage chemical and genetic perturbations of RA-gastruloids to confirm that WNT and BMP signalling regulate somite formation and neural tube length in the human context, while transcription factors TBX6 and PAX3 underpin presomitic mesoderm and neural crest, respectively. Looking forward, RA-gastruloids are a robust, scalable model for decoding early human embryogenesis.
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Affiliation(s)
- Nobuhiko Hamazaki
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
| | - Wei Yang
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Connor A Kubo
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Riddhiman K Garge
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Samuel G Regalado
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Eva K Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sriram Pendyala
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nicholas Bradley
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Seattle Hub for Synthetic Biology, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Seattle Hub for Synthetic Biology, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
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6
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Peraldi R, Kmita M. 40 years of the homeobox: mechanisms of Hox spatial-temporal collinearity in vertebrates. Development 2024; 151:dev202508. [PMID: 39167089 DOI: 10.1242/dev.202508] [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: 08/23/2024]
Abstract
Animal body plans are established during embryonic development by the Hox genes. This patterning process relies on the differential expression of Hox genes along the head-to-tail axis. Hox spatial collinearity refers to the relationship between the organization of Hox genes in clusters and the differential Hox expression, whereby the relative order of the Hox genes within a cluster mirrors the spatial sequence of expression in the developing embryo. In vertebrates, the cluster organization is also associated with the timing of Hox activation, which harmonizes Hox expression with the progressive emergence of axial tissues. Thereby, in vertebrates, Hox temporal collinearity is intimately linked to Hox spatial collinearity. Understanding the mechanisms contributing to Hox temporal and spatial collinearity is thus key to the comprehension of vertebrate patterning. Here, we provide an overview of the main discoveries pertaining to the mechanisms of Hox spatial-temporal collinearity.
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Affiliation(s)
- Rodrigue Peraldi
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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7
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Liu Y, Kim YS, Xue X, Miao Y, Kobayashi N, Sun S, Yan RZ, Yang Q, Pourquié O, Fu J. A human pluripotent stem cell-based somitogenesis model using microfluidics. Cell Stem Cell 2024; 31:1113-1126.e6. [PMID: 38981471 DOI: 10.1016/j.stem.2024.06.004] [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: 09/10/2023] [Revised: 03/04/2024] [Accepted: 06/04/2024] [Indexed: 07/11/2024]
Abstract
Emerging human pluripotent stem cell (hPSC)-based embryo models are useful for studying human embryogenesis. Particularly, there are hPSC-based somitogenesis models using free-floating culture that recapitulate somite formation. Somitogenesis in vivo involves intricately orchestrated biochemical and biomechanical events. However, none of the current somitogenesis models controls biochemical gradients or biomechanical signals in the culture, limiting their applicability to untangle complex biochemical-biomechanical interactions that drive somitogenesis. Herein, we develop a human somitogenesis model by confining hPSC-derived presomitic mesoderm (PSM) tissues in microfabricated trenches. Exogenous microfluidic morphogen gradients imposed on the PSM tissues cause axial patterning and trigger spontaneous rostral-to-caudal somite formation. A mechanical theory is developed to explain the size dependency between somites and the PSM. The microfluidic somitogenesis model is further exploited to reveal regulatory roles of cellular and tissue biomechanics in somite formation. This study presents a useful microengineered, hPSC-based model for understanding the biochemical and biomechanical events that guide somite formation.
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Affiliation(s)
- Yue Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Yung Su Kim
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yuchuan Miao
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Norio Kobayashi
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shiyu Sun
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robin Zhexuan Yan
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qiong Yang
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Physics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Jianping Fu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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8
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Iwata R, Vanderhaeghen P. Metabolic mechanisms of species-specific developmental tempo. Dev Cell 2024; 59:1628-1639. [PMID: 38906137 PMCID: PMC11266843 DOI: 10.1016/j.devcel.2024.05.027] [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: 01/19/2024] [Revised: 04/27/2024] [Accepted: 05/23/2024] [Indexed: 06/23/2024]
Abstract
Development consists of a highly ordered suite of steps and transitions, like choreography. Although these sequences are often evolutionarily conserved, they can display species variations in duration and speed, thereby modifying final organ size or function. Despite their evolutionary significance, the mechanisms underlying species-specific scaling of developmental tempo have remained unclear. Here, we will review recent findings that implicate global cellular mechanisms, particularly intermediary and protein metabolism, as species-specific modifiers of developmental tempo. In various systems, from somitic cell oscillations to neuronal development, metabolic pathways display species differences. These have been linked to mitochondrial metabolism, which can influence the species-specific speed of developmental transitions. Thus, intermediary metabolic pathways regulate developmental tempo together with other global processes, including proteostasis and chromatin remodeling. By linking metabolism and the evolution of developmental trajectories, these findings provide opportunities to decipher how species-specific cellular timing can influence organism fitness.
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Affiliation(s)
- Ryohei Iwata
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium
| | - Pierre Vanderhaeghen
- VIB-KU Leuven Center for Brain & Disease Research, 3000 Leuven, Belgium; Department of Neurosciences, Leuven Brain Institute, KUL, 3000 Leuven, Belgium.
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9
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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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10
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Baheux Blin M, Loreau V, Schnorrer F, Mangeol P. PatternJ: an ImageJ toolset for the automated and quantitative analysis of regular spatial patterns found in sarcomeres, axons, somites, and more. Biol Open 2024; 13:bio060548. [PMID: 38887972 PMCID: PMC11212633 DOI: 10.1242/bio.060548] [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: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Regular spatial patterns are ubiquitous forms of organization in nature. In animals, regular patterns can be found from the cellular scale to the tissue scale, and from early stages of development to adulthood. To understand the formation of these patterns, how they assemble and mature, and how they are affected by perturbations, a precise quantitative description of the patterns is essential. However, accessible tools that offer in-depth analysis without the need for computational skills are lacking for biologists. Here, we present PatternJ, a novel toolset to analyze regular one-dimensional patterns precisely and automatically. This toolset, to be used with the popular imaging processing program ImageJ/Fiji, facilitates the extraction of key geometric features within and between pattern repeats in static images and time-lapse series. We validate PatternJ with simulated data and test it on images of sarcomeres from insect muscles and contracting cardiomyocytes, actin rings in neurons, and somites from zebrafish embryos obtained using confocal fluorescence microscopy, STORM, electron microscopy, and brightfield imaging. We show that the toolset delivers subpixel feature extraction reliably even with images of low signal-to-noise ratio. PatternJ's straightforward use and functionalities make it valuable for various scientific fields requiring quantitative one-dimensional pattern analysis, including the sarcomere biology of muscles or the patterning of mammalian axons, speeding up discoveries with the bonus of high reproducibility.
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Affiliation(s)
- Mélina Baheux Blin
- Aix Marseille Université, CNRS, Institut de Biologie du Développement de Marseille, IBDM-UMR7288, Marseille 13009, France
| | - Vincent Loreau
- Aix Marseille Université, CNRS, Institut de Biologie du Développement de Marseille, IBDM-UMR7288, Marseille 13009, France
| | - Frank Schnorrer
- Aix Marseille Université, CNRS, Institut de Biologie du Développement de Marseille, IBDM-UMR7288, Marseille 13009, France
| | - Pierre Mangeol
- Aix Marseille Université, CNRS, Institut de Biologie du Développement de Marseille, IBDM-UMR7288, Marseille 13009, France
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11
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Diaz-Cuadros M. Mitochondrial metabolism and the continuing search for ultimate regulators of developmental rate. Curr Opin Genet Dev 2024; 86:102178. [PMID: 38461774 DOI: 10.1016/j.gde.2024.102178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/12/2024]
Abstract
The rate of embryonic development is a species-specific trait that depends on the properties of the intracellular environment, namely, the rate at which gene products flow through the central dogma of molecular biology. Although any given step in the production and degradation of gene products could theoretically be co-opted by evolution to modulate developmental speed, species are observed to accelerate or slow down all steps simultaneously. This suggests the rate of these molecular processes is jointly regulated by an upstream, ultimate factor. Mitochondrial metabolism was recently proposed to act as an ultimate regulator by controlling the pace of protein synthesis upstream of developmental tempo. Alternative candidates for ultimate regulators include species-specific gene expression levels of factors involved in the central dogma, as well as species-specific cell size. Overall, much work remains to be done before we can confidently identify the ultimate causes of species-specific developmental rates.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA.
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12
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Lin P, Gan YB, He J, Lin SE, Xu JK, Chang L, Zhao LM, Zhu J, Zhang L, Huang S, Hu O, Wang YB, Jin HJ, Li YY, Yan PL, Chen L, Jiang JX, Liu P. Advancing skeletal health and disease research with single-cell RNA sequencing. Mil Med Res 2024; 11:33. [PMID: 38816888 PMCID: PMC11138034 DOI: 10.1186/s40779-024-00538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
Orthopedic conditions have emerged as global health concerns, impacting approximately 1.7 billion individuals worldwide. However, the limited understanding of the underlying pathological processes at the cellular and molecular level has hindered the development of comprehensive treatment options for these disorders. The advent of single-cell RNA sequencing (scRNA-seq) technology has revolutionized biomedical research by enabling detailed examination of cellular and molecular diversity. Nevertheless, investigating mechanisms at the single-cell level in highly mineralized skeletal tissue poses technical challenges. In this comprehensive review, we present a streamlined approach to obtaining high-quality single cells from skeletal tissue and provide an overview of existing scRNA-seq technologies employed in skeletal studies along with practical bioinformatic analysis pipelines. By utilizing these methodologies, crucial insights into the developmental dynamics, maintenance of homeostasis, and pathological processes involved in spine, joint, bone, muscle, and tendon disorders have been uncovered. Specifically focusing on the joint diseases of degenerative disc disease, osteoarthritis, and rheumatoid arthritis using scRNA-seq has provided novel insights and a more nuanced comprehension. These findings have paved the way for discovering novel therapeutic targets that offer potential benefits to patients suffering from diverse skeletal disorders.
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Grants
- 2022YFA1103202 National Key Research and Development Program of China
- 82272507 National Natural Science Foundation of China
- 32270887 National Natural Science Foundation of China
- 32200654 National Natural Science Foundation of China
- CSTB2023NSCQ-ZDJO008 Natural Science Foundation of Chongqing
- BX20220397 Postdoctoral Innovative Talent Support Program
- SFLKF202201 Independent Research Project of State Key Laboratory of Trauma and Chemical Poisoning
- 2021-XZYG-B10 General Hospital of Western Theater Command Research Project
- 14113723 University Grants Committee, Research Grants Council of Hong Kong, China
- N_CUHK472/22 University Grants Committee, Research Grants Council of Hong Kong, China
- C7030-18G University Grants Committee, Research Grants Council of Hong Kong, China
- T13-402/17-N University Grants Committee, Research Grants Council of Hong Kong, China
- AoE/M-402/20 University Grants Committee, Research Grants Council of Hong Kong, China
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Affiliation(s)
- Peng Lin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yi-Bo Gan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian He
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
- Pancreatic Injury and Repair Key Laboratory of Sichuan Province, the General Hospital of Western Theater Command, Chengdu, 610031, China
| | - Si-En Lin
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Jian-Kun Xu
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopaedics & Traumatology, Faculty of Medicine, the Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR, 999077, China
| | - Li-Ming Zhao
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Sacramento, CA, 94305, USA
| | - Jun Zhu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Liang Zhang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Sha Huang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ou Hu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Ying-Bo Wang
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Huai-Jian Jin
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Yang-Yang Li
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Pu-Lin Yan
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Lin Chen
- Center of Bone Metabolism and Repair, State Key Laboratory of Trauma and Chemical Poisoning, Trauma Center, Research Institute of Surgery, Laboratory for the Prevention and Rehabilitation of Military Training Related Injuries, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Jian-Xin Jiang
- Wound Trauma Medical Center, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
| | - Peng Liu
- Department of Spine Surgery, Center of Orthopedics, State Key Laboratory of Trauma and Chemical Poisoning, Daping Hospital, Army Medical University, Chongqing, 400042, China.
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13
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Del Olmo M, Legewie S, Brunner M, Höfer T, Kramer A, Blüthgen N, Herzel H. Network switches and their role in circadian clocks. J Biol Chem 2024; 300:107220. [PMID: 38522517 PMCID: PMC11044057 DOI: 10.1016/j.jbc.2024.107220] [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: 07/03/2023] [Revised: 03/07/2024] [Accepted: 03/18/2024] [Indexed: 03/26/2024] Open
Abstract
Circadian rhythms are generated by complex interactions among genes and proteins. Self-sustained ∼24 h oscillations require negative feedback loops and sufficiently strong nonlinearities that are the product of molecular and network switches. Here, we review common mechanisms to obtain switch-like behavior, including cooperativity, antagonistic enzymes, multisite phosphorylation, positive feedback, and sequestration. We discuss how network switches play a crucial role as essential components in cellular circadian clocks, serving as integral parts of transcription-translation feedback loops that form the basis of circadian rhythm generation. The design principles of network switches and circadian clocks are illustrated by representative mathematical models that include bistable systems and negative feedback loops combined with Hill functions. This work underscores the importance of negative feedback loops and network switches as essential design principles for biological oscillations, emphasizing how an understanding of theoretical concepts can provide insights into the mechanisms generating biological rhythms.
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Affiliation(s)
- Marta Del Olmo
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
| | - Stefan Legewie
- Department of Systems Biology, Institute for Biomedical Genetics (IBMG), University of Stuttgart, Stuttgart, Germany; Stuttgart Research Center for Systems Biology (SRCSB), University of Stuttgart, Stuttgart, Germany
| | - Michael Brunner
- Biochemistry Center, Universität Heidelberg, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Universität Heidelberg, Heidelberg, Germany
| | - Achim Kramer
- Laboratory of Chronobiology, Institute for Medical Immunology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Nils Blüthgen
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany; Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Humboldt Universität zu Berlin and Charité Universitätsmedizin Berlin, Berlin, Germany.
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14
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Feng X, Ye Y, Zhang J, Zhang Y, Zhao S, Mak JCW, Otomo N, Zhao Z, Niu Y, Yonezawa Y, Li G, Lin M, Li X, Cheung PWH, Xu K, Takeda K, Wang S, Xie J, Kotani T, Choi VNT, Song YQ, Yang Y, Luk KDK, Lee KS, Li Z, Li PS, Leung CYH, Lin X, Wang X, Qiu G, Watanabe K, Wu Z, Posey JE, Ikegawa S, Lupski JR, Cheung JPY, Zhang TJ, Gao B, Wu N. Core planar cell polarity genes VANGL1 and VANGL2 in predisposition to congenital vertebral malformations. Proc Natl Acad Sci U S A 2024; 121:e2310283121. [PMID: 38669183 PMCID: PMC11067467 DOI: 10.1073/pnas.2310283121] [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: 06/20/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital scoliosis (CS), affecting approximately 0.5 to 1 in 1,000 live births, is commonly caused by congenital vertebral malformations (CVMs) arising from aberrant somitogenesis or somite differentiation. While Wnt/ß-catenin signaling has been implicated in somite development, the function of Wnt/planar cell polarity (Wnt/PCP) signaling in this process remains unclear. Here, we investigated the role of Vangl1 and Vangl2 in vertebral development and found that their deletion causes vertebral anomalies resembling human CVMs. Analysis of exome sequencing data from multiethnic CS patients revealed a number of rare and deleterious variants in VANGL1 and VANGL2, many of which exhibited loss-of-function and dominant-negative effects. Zebrafish models confirmed the pathogenicity of these variants. Furthermore, we found that Vangl1 knock-in (p.R258H) mice exhibited vertebral malformations in a Vangl gene dose- and environment-dependent manner. Our findings highlight critical roles for PCP signaling in vertebral development and predisposition to CVMs in CS patients, providing insights into the molecular mechanisms underlying this disorder.
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Affiliation(s)
- Xin Feng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing100730, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yongyu Ye
- Department of Orthopedic Surgery, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou510080, China
| | - Jianan Zhang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Yuanqiang Zhang
- Department of Orthopaedic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan250012, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Judith C. W. Mak
- Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nao Otomo
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - Zhengye Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Yoshiro Yonezawa
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Mao Lin
- Department of Orthopedic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou310003, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Prudence Wing Hang Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Kazuki Takeda
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Junjie Xie
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Toshiaki Kotani
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
| | - Vanessa N. T. Choi
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - You-Qiang Song
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Medicine, The University of Hong Kong-Shenzhen Hospital, Shenzhen518009, China
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Keith Dip Kei Luk
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kin Shing Lee
- Center for Comparative Medicine Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Ziquan Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Pik Shan Li
- Center for Comparative Medicine Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Connie Y. H. Leung
- Center for Comparative Medicine Research, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaochen Lin
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Xiaolu Wang
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | | | - Kota Watanabe
- Department of Orthopedic Surgery, Keio University School of Medicine, Tokyo160-8582, Japan
| | | | - Zhihong Wu
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston77030, TX
| | - Shiro Ikegawa
- Laboratory of Bone and Joint Diseases, RIKEN Center for Integrative Medical Sciences, Tokyo108-8639, Japan
| | - James R. Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston77030, TX
- Human Genome Sequencing Center, Baylor College of Medicine, Houston77030, TX
- Texas Children’s Hospital, Houston77030, TX
- Department of Pediatrics, Baylor College of Medicine, Houston77030, TX
| | - Jason Pui Yin Cheung
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen518009, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
| | - Bo Gao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
- Department of Orthopedics and Traumatology, The University of Hong Kong-Shenzhen Hospital, Shenzhen518009, China
- Centre for Translational Stem Cell Biology, Hong Kong Special Administrative Region, China
- Key Laboratory of Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, all at Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing100730, China
- Key laboratory of big data for spinal deformities, Chinese Academy of Medical Sciences, Beijing100730, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing100730, China
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15
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Pappas MP, Kawakami H, Corcoran D, Chen KQ, Scott EP, Wong J, Gearhart MD, Nishinakamura R, Nakagawa Y, Kawakami Y. Sall4 regulates posterior trunk mesoderm development by promoting mesodermal gene expression and repressing neural genes in the mesoderm. Development 2024; 151:dev202649. [PMID: 38345319 PMCID: PMC10946440 DOI: 10.1242/dev.202649] [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: 12/28/2023] [Accepted: 01/30/2024] [Indexed: 03/05/2024]
Abstract
The trunk axial skeleton develops from paraxial mesoderm cells. Our recent study demonstrated that conditional knockout of the stem cell factor Sall4 in mice by TCre caused tail truncation and a disorganized axial skeleton posterior to the lumbar level. Based on this phenotype, we hypothesized that, in addition to the previously reported role of Sall4 in neuromesodermal progenitors, Sall4 is involved in the development of the paraxial mesoderm tissue. Analysis of gene expression and SALL4 binding suggests that Sall4 directly or indirectly regulates genes involved in presomitic mesoderm differentiation, somite formation and somite differentiation. Furthermore, ATAC-seq in TCre; Sall4 mutant posterior trunk mesoderm shows that Sall4 knockout reduces chromatin accessibility. We found that Sall4-dependent open chromatin status drives activation and repression of WNT signaling activators and repressors, respectively, to promote WNT signaling. Moreover, footprinting analysis of ATAC-seq data suggests that Sall4-dependent chromatin accessibility facilitates CTCF binding, which contributes to the repression of neural genes within the mesoderm. This study unveils multiple mechanisms by which Sall4 regulates paraxial mesoderm development by directing activation of mesodermal genes and repression of neural genes.
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Affiliation(s)
- Matthew P. Pappas
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Hiroko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Katherine Q. Chen
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Earl Parker Scott
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Julia Wong
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Micah D. Gearhart
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ryuichi Nishinakamura
- Department of Kidney Development, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Yasushi Nakagawa
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
- Department of Neuroscience, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Developmental Biology Center, University of Minnesota, Minneapolis, MN 55455, USA
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16
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Hiroki S, Yoshitane H. Ror homolog nhr-23 is essential for both developmental clock and circadian clock in C. elegans. Commun Biol 2024; 7:243. [PMID: 38418700 PMCID: PMC10902330 DOI: 10.1038/s42003-024-05894-3] [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: 06/05/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Animals have internal clocks that generate biological rhythms. In mammals, clock genes such as Period form the circadian clock to generate approximately 24-h biological rhythms. In C. elegans, the clock gene homologs constitute the "developmental clock", which has an 8-h period during larval development to determine the timing of molting. Thus, the ancestral circadian clock has been believed to evolve into the oscillator with a shorter period in C. elegans. However, circadian rhythms have also been observed in adult C. elegans, albeit relatively weak. This prompts the question: if the clock gene homologs drive the developmental rhythm with 8-h period, which genes generate the circadian rhythms in C. elegans? In this study, we discovered that nhr-23, a homolog of the mammalian circadian clock gene Ror, is essential for circadian transcriptional rhythms in adult C. elegans. Interestingly, nhr-23 was also known to be essential for the molting clock. The bilaterian ancestral circadian clock genes might have evolved to function over multiple periods depending on developmental contexts rather than a single 8-h period in C. elegans.
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Affiliation(s)
- Shingo Hiroki
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
| | - Hikari Yoshitane
- Tokyo Metropolitan Institute of Medical Sciences, Tokyo, Japan.
- Department of Biological Sciences, School of Science, University of Tokyo, Tokyo, Japan.
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17
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Agriesti F, Cela O, Capitanio N. "Time Is out of Joint" in Pluripotent Stem Cells: How and Why. Int J Mol Sci 2024; 25:2063. [PMID: 38396740 PMCID: PMC10889767 DOI: 10.3390/ijms25042063] [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: 01/10/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
The circadian rhythm is necessary for the homeostasis and health of living organisms. Molecular clocks interconnected by transcription/translation feedback loops exist in most cells of the body. A puzzling exemption to this, otherwise, general biological hallmark is given by the cell physiology of pluripotent stem cells (PSCs) that lack circadian oscillations gradually acquired following their in vivo programmed differentiation. This process can be nicely phenocopied following in vitro commitment and reversed during the reprogramming of somatic cells to induce PSCs. The current understanding of how and why pluripotency is "time-uncoupled" is largely incomplete. A complex picture is emerging where the circadian core clockwork is negatively regulated in PSCs at the post-transcriptional/translational, epigenetic, and other-clock-interaction levels. Moreover, non-canonical functions of circadian core-work components in the balance between pluripotency identity and metabolic-driven cell reprogramming are emerging. This review selects and discusses results of relevant recent investigations providing major insights into this context.
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Affiliation(s)
- Francesca Agriesti
- Department of Clinical and Experimental Medicine, University of Foggia, 71122 Foggia, Italy; (O.C.); (N.C.)
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18
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Yagita K. Emergence of the circadian clock oscillation during the developmental process in mammals. Curr Opin Genet Dev 2024; 84:102152. [PMID: 38266394 DOI: 10.1016/j.gde.2024.102152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/26/2024]
Abstract
The circadian clocks are cell-autonomous intrinsic oscillators existing throughout the body to coordinate intracellular and intercellular functions of each organ or tissue. The circadian clock oscillation gradually emerges during mid-to-late gestation in the mammalian developmental process. Recently, it has been revealed that the in vitro differentiation of mouse ES cells recapitulates the circadian clock development. Moreover, reprogramming of the cells results in the redisappearance of the clock, indicating that circadian clocks are tightly coupled with cellular differentiation. Interestingly, before the circadian clock develops, the embryo is governed under ultradian rhythms driven by the segmentation clock. This short review explores these observations, discussing the significance of the emergence of circadian clock oscillation during the mammalian developmental process.
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Affiliation(s)
- Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kawaramachi-Hirokoji, Kamigyo-ku, Kyoto 602-8566, Japan.
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19
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Lázaro J, Sochacki J, Ebisuya M. The stem cell zoo for comparative studies of developmental tempo. Curr Opin Genet Dev 2024; 84:102149. [PMID: 38199063 PMCID: PMC10882223 DOI: 10.1016/j.gde.2023.102149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024]
Abstract
The rate of development is highly variable across animal species. However, the mechanisms regulating developmental tempo have remained elusive due to difficulties in performing direct interspecies comparisons. Here, we discuss how pluripotent stem cell-based models of development can be used to investigate cell- and tissue-autonomous temporal processes. These systems enable quantitative comparisons of different animal species under similar experimental conditions. Moreover, the constantly growing stem cell zoo collection allows the extension of developmental studies to a great number of unconventional species. We argue that the stem cell zoo constitutes a powerful platform to perform comparative studies of developmental tempo, as well as to study other forms of biological time control such as species-specific lifespan, heart rate, and circadian clocks.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany. https://twitter.com/@JorgeLazaroF
| | - Jaroslaw Sochacki
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Arnoldstraße 18, 01307 Dresden, Germany.
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20
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Ramesh PS, Chu LF. Species-specific roles of the Notch ligands, receptors, and targets orchestrating the signaling landscape of the segmentation clock. Front Cell Dev Biol 2024; 11:1327227. [PMID: 38348091 PMCID: PMC10859470 DOI: 10.3389/fcell.2023.1327227] [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: 10/24/2023] [Accepted: 12/20/2023] [Indexed: 02/15/2024] Open
Abstract
Somitogenesis is a hallmark feature of all vertebrates and some invertebrate species that involves the periodic formation of block-like structures called somites. Somites are transient embryonic segments that eventually establish the entire vertebral column. A highly conserved molecular oscillator called the segmentation clock underlies this periodic event and the pace of this clock regulates the pace of somite formation. Although conserved signaling pathways govern the clock in most vertebrates, the mechanisms underlying the species-specific divergence in various clock characteristics remain elusive. For example, the segmentation clock in classical model species such as zebrafish, chick, and mouse embryos tick with a periodicity of ∼30, ∼90, and ∼120 min respectively. This enables them to form the species-specific number of vertebrae during their overall timespan of somitogenesis. Here, we perform a systematic review of the species-specific features of the segmentation clock with a keen focus on mouse embryos. We perform this review using three different perspectives: Notch-responsive clock genes, ligand-receptor dynamics, and synchronization between neighboring oscillators. We further review reports that use non-classical model organisms and in vitro model systems that complement our current understanding of the segmentation clock. Our review highlights the importance of comparative developmental biology to further our understanding of this essential developmental process.
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Affiliation(s)
- Pranav S. Ramesh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Calgary, AB, Canada
| | - Li-Fang Chu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB, Canada
- Alberta Children’s Hospital Research Institute, Calgary, AB, Canada
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21
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McDaniel C, Simsek MF, Chandel AS, Özbudak EM. Spatiotemporal control of pattern formation during somitogenesis. SCIENCE ADVANCES 2024; 10:eadk8937. [PMID: 38277458 PMCID: PMC10816718 DOI: 10.1126/sciadv.adk8937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/27/2023] [Indexed: 01/28/2024]
Abstract
Spatiotemporal patterns widely occur in biological, chemical, and physical systems. Particularly, embryonic development displays a diverse gamut of repetitive patterns established in many tissues and organs. Branching treelike structures in lungs, kidneys, livers, pancreases, and mammary glands as well as digits and bones in appendages, teeth, and palates are just a few examples. A fascinating instance of repetitive patterning is the sequential segmentation of the primary body axis, which is conserved in all vertebrates and many arthropods and annelids. In these species, the body axis elongates at the posterior end of the embryo containing an unsegmented tissue. Meanwhile, segments sequentially bud off from the anterior end of the unsegmented tissue, laying down an exquisite repetitive pattern and creating a segmented body plan. In vertebrates, the paraxial mesoderm is sequentially divided into somites. In this review, we will discuss the most prominent models, the most puzzling experimental data, and outstanding questions in vertebrate somite segmentation.
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Affiliation(s)
- Cassandra McDaniel
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - M. Fethullah Simsek
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Angad Singh Chandel
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Systems Biology and Physiology Graduate Program, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
| | - Ertuğrul M. Özbudak
- Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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22
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Davis SN, Grindel SH, Viola JM, Liu GY, Liu J, Qian G, Porter CM, Hughes AJ. Nephron progenitors rhythmically alternate between renewal and differentiation phases that synchronize with kidney branching morphogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568157. [PMID: 38045273 PMCID: PMC10690271 DOI: 10.1101/2023.11.21.568157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The mammalian kidney achieves massive parallelization of function by exponentially duplicating nephron-forming niches during development. Each niche caps a tip of the ureteric bud epithelium (the future urinary collecting duct tree) as it undergoes branching morphogenesis, while nephron progenitors within niches balance self-renewal and differentiation to early nephron cells. Nephron formation rate approximately matches branching rate over a large fraction of mouse gestation, yet the nature of this apparent pace-maker is unknown. Here we correlate spatial transcriptomics data with branching 'life-cycle' to discover rhythmically alternating signatures of nephron progenitor differentiation and renewal across Wnt, Hippo-Yap, retinoic acid (RA), and other pathways. We then find in human stem-cell derived nephron progenitor organoids that Wnt/β-catenin-induced differentiation is converted to a renewal signal when it temporally overlaps with YAP activation. Similar experiments using RA activation indicate a role in setting nephron progenitor exit from the naive state, the spatial extent of differentiation, and nephron segment bias. Together the data suggest that nephron progenitor interpretation of consistent Wnt/β-catenin differentiation signaling in the niche may be modified by rhythmic activity in ancillary pathways to set the pace of nephron formation. This would synchronize nephron formation with ureteric bud branching, which creates new sites for nephron condensation. Our data bring temporal resolution to the renewal vs. differentiation balance in the nephrogenic niche and inform new strategies to achieve self-sustaining nephron formation in synthetic human kidney tissues.
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Affiliation(s)
- Sachin N Davis
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Samuel H Grindel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - John M Viola
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace Y Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jiageng Liu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Grace Qian
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Catherine M Porter
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, 19104, PA, USA
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23
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Miao Y, Diaz-Cuadros M, Pourquié O. Modeling Human Paraxial Mesoderm Development with Pluripotent Stem Cells. Methods Mol Biol 2024; 2767:115-122. [PMID: 37843773 DOI: 10.1007/7651_2023_507] [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: 10/17/2023]
Abstract
Paraxial mesoderm in the early embryo is segmented into epithelial blocks called somites that establish the metameric organization of the vertebrate body plan. Somites are sequentially formed from head to tail in a rhythmic manner controlled by an oscillating gene regulatory network known as the segmentation clock. We know very little about this important process during human development due to limited access to human embryos and ethical concerns. To bypass these difficulties, model systems derived from human pluripotent stem cells have been established. Here, we detail three protocols modeling different aspects of human paraxial mesoderm development in vitro: a 2D cell monolayer system recapitulating dynamics of the human segmentation clock, a 3D organoid system called "somitoid" supporting the simultaneous formation of somite-like structures, and another organoid system called "segmentoid" reconstituting in vivo-like hallmarks of somitogenesis. Together, these complementary model systems provide an excellent platform to decode somitogenesis and advance human developmental biology.
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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
| | - Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Molecular Biology, Massachusetts General 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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24
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Simpson L, Alberio R. Interspecies control of development during mammalian gastrulation. Emerg Top Life Sci 2023; 7:397-408. [PMID: 37933589 PMCID: PMC10754326 DOI: 10.1042/etls20230083] [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: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
Gastrulation represents a pivotal phase of development and aberrations during this period can have major consequences, from minor anatomical deviations to severe congenital defects. Animal models are used to study gastrulation, however, there is considerable morphological and molecular diversity of gastrula across mammalian species. Here, we provide an overview of the latest research on interspecies developmental control across mammals. This includes single-cell atlases of several mammalian gastrula which have enabled comparisons of the temporal and molecular dynamics of differentiation. These studies highlight conserved cell differentiation regulators and both absolute and relative differences in differentiation dynamics between species. Recent advances in in vitro culture techniques have facilitated the derivation, maintenance and differentiation of cell lines from a range of species and the creation of multi-species models of gastrulation. Gastruloids are three-dimensional aggregates capable of self-organising and recapitulating aspects of gastrulation. Such models enable species comparisons outside the confines of the embryo. We highlight recent in vitro evidence that differentiation processes such as somitogenesis and neuronal maturation scale with known in vivo differences in developmental tempo across species. This scaling is likely due to intrinsic differences in cell biochemistry. We also highlight several studies which provide examples of cell differentiation dynamics being influenced by extrinsic factors, including culture conditions, chimeric co-culture, and xenotransplantation. These collective studies underscore the complexity of gastrulation across species, highlighting the necessity of additional datasets and studies to decipher the intricate balance between intrinsic cellular programs and extrinsic signals in shaping embryogenesis.
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Affiliation(s)
- Luke Simpson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, U.K
| | - Ramiro Alberio
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, U.K
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25
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Conrad JV, Meyer S, Ramesh PS, Neira JA, Rusteika M, Mamott D, Duffin B, Bautista M, Zhang J, Hiles E, Higgins EM, Steill J, Freeman J, Ni Z, Liu S, Ungrin M, Rancourt D, Clegg DO, Stewart R, Thomson JA, Chu LF. Efficient derivation of transgene-free porcine induced pluripotent stem cells enables in vitro modeling of species-specific developmental timing. Stem Cell Reports 2023; 18:2328-2343. [PMID: 37949072 PMCID: PMC10724057 DOI: 10.1016/j.stemcr.2023.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 11/12/2023] Open
Abstract
Sus scrofa domesticus (pig) has served as a superb large mammalian model for biomedical studies because of its comparable physiology and organ size to humans. The derivation of transgene-free porcine induced pluripotent stem cells (PiPSCs) will, therefore, benefit the development of porcine-specific models for regenerative biology and its medical applications. In the past, this effort has been hampered by a lack of understanding of the signaling milieu that stabilizes the porcine pluripotent state in vitro. Here, we report that transgene-free PiPSCs can be efficiently derived from porcine fibroblasts by episomal vectors along with microRNA-302/367 using optimized protocols tailored for this species. PiPSCs can be differentiated into derivatives representing the primary germ layers in vitro and can form teratomas in immunocompromised mice. Furthermore, the transgene-free PiPSCs preserve intrinsic species-specific developmental timing in culture, known as developmental allochrony. This is demonstrated by establishing a porcine in vitro segmentation clock model that, for the first time, displays a specific periodicity at ∼3.7 h, a timescale recapitulating in vivo porcine somitogenesis. We conclude that the transgene-free PiPSCs can serve as a powerful tool for modeling development and disease and developing transplantation strategies. We also anticipate that they will provide insights into conserved and unique features on the regulations of mammalian pluripotency and developmental timing mechanisms.
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Affiliation(s)
- J Vanessa Conrad
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Susanne Meyer
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Pranav S Ramesh
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jaime A Neira
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Margaret Rusteika
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Daniel Mamott
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Bret Duffin
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Monica Bautista
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Jue Zhang
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Emily Hiles
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - Eve M Higgins
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada
| | - John Steill
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Jack Freeman
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Zijian Ni
- Department of Statistics, University of Wisconsin, Madison, WI 53706, USA
| | - Shiying Liu
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Mark Ungrin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biomedical Engineering, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Derrick Rancourt
- Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Dennis O Clegg
- Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Thomson
- Morgridge Institute for Research, Madison, WI 53715, USA; Department of Molecular, Cellular, & Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Li-Fang Chu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Reproductive Biology and Regenerative Medicine Research Group, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, Calgary, AB T2N 4N1, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
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26
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Masak G, Davidson LA. Constructing the pharyngula: Connecting the primary axial tissues of the head with the posterior axial tissues of the tail. Cells Dev 2023; 176:203866. [PMID: 37394035 PMCID: PMC10756936 DOI: 10.1016/j.cdev.2023.203866] [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: 03/23/2023] [Revised: 06/04/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
The pharyngula stage of vertebrate development is characterized by stereotypical arrangement of ectoderm, mesoderm, and neural tissues from the anterior spinal cord to the posterior, yet unformed tail. While early embryologists over-emphasized the similarity between vertebrate embryos at the pharyngula stage, there is clearly a common architecture upon which subsequent developmental programs generate diverse cranial structures and epithelial appendages such as fins, limbs, gills, and tails. The pharyngula stage is preceded by two morphogenetic events: gastrulation and neurulation, which establish common shared structures despite the occurrence of cellular processes that are distinct to each of the species. Even along the body axis of a singular organism, structures with seemingly uniform phenotypic characteristics at the pharyngula stage have been established by different processes. We focus our review on the processes underlying integration of posterior axial tissue formation with the primary axial tissues that creates the structures laid out in the pharyngula. Single cell sequencing and novel gene targeting technologies have provided us with new insights into the differences between the processes that form the anterior and posterior axis, but it is still unclear how these processes are integrated to create a seamless body. We suggest that the primary and posterior axial tissues in vertebrates form through distinct mechanisms and that the transition between these mechanisms occur at different locations along the anterior-posterior axis. Filling gaps that remain in our understanding of this transition could resolve ongoing problems in organoid culture and regeneration.
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Affiliation(s)
- Geneva Masak
- Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Lance A Davidson
- Integrative Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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27
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Hisler V, Bardot P, Detilleux D, Stierle M, Sanchez EG, Richard C, Arab LH, Ehrhard C, Morlet B, Hadzhiev Y, Jung M, Gras SL, Négroni L, Müller F, Tora L, Vincent SD. RNA polymerase II transcription with partially assembled TFIID complexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.567046. [PMID: 38076793 PMCID: PMC10705246 DOI: 10.1101/2023.11.27.567046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
The recognition of core promoter sequences by the general transcription factor TFIID is the first step in the process of RNA polymerase II (Pol II) transcription initiation. Metazoan holo-TFIID is composed of the TATA binding protein (TBP) and of 13 TBP associated factors (TAFs). Inducible Taf7 knock out (KO) results in the formation of a Taf7-less TFIID complex, while Taf10 KO leads to serious defects within the TFIID assembly pathway. Either TAF7 or TAF10 depletions correlate with the detected TAF occupancy changes at promoters, and with the distinct phenotype severities observed in mouse embryonic stem cells or mouse embryos. Surprisingly however, under either Taf7 or Taf10 deletion conditions, TBP is still associated to the chromatin, and no major changes are observed in nascent Pol II transcription. Thus, partially assembled TFIID complexes can sustain Pol II transcription initiation, but cannot replace holo-TFIID over several cell divisions and/or development.
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Affiliation(s)
- Vincent Hisler
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Paul Bardot
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Dylane Detilleux
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Matthieu Stierle
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Emmanuel Garcia Sanchez
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Claire Richard
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Lynda Hadj Arab
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Cynthia Ehrhard
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Bastien Morlet
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- Proteomics platform
| | - Yavor Hadzhiev
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - Matthieu Jung
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- GenomEast
| | - Stéphanie Le Gras
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- GenomEast
| | - Luc Négroni
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
- Proteomics platform
| | - Ferenc Müller
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, B152TT, Birmingham, UK
| | - László Tora
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
| | - Stéphane D. Vincent
- Université de Strasbourg, IGBMC UMR 7104- UMR-S 1258, F-67400 Illkirch, France
- CNRS, UMR 7104, F-67400 Illkirch, France
- Inserm, UMR-S 1258, F-67400 Illkirch, France
- IGBMC, Institut de Génétique et de Biologie Moléculaire et Cellulaire, F-67400 Illkirch, France
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28
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Abstract
Organismal development requires the reproducible unfolding of an ordered sequence of discrete steps (cell fate determination, migration, tissue folding, etc.) in both time and space. Here, we review the mechanisms that grant temporal specificity to developmental steps, including molecular clocks and timers. Individual timing mechanisms must be coordinated with each other to maintain the overall developmental sequence. However, phenotypic novelties can also arise through the modification of temporal patterns over the course of evolution. Two main types of variation in temporal patterning characterize interspecies differences in developmental time: allochrony, where the overall developmental sequence is either accelerated or slowed down while maintaining the relative duration of individual steps, and heterochrony, where the duration of specific developmental steps is altered relative to the rest. New advances in in vitro modeling of mammalian development using stem cells have recently enabled the revival of mechanistic studies of allochrony and heterochrony. In both cases, differences in the rate of basic cellular functions such as splicing, translation, protein degradation, and metabolism seem to underlie differences in developmental time. In the coming years, these studies should identify the genetic differences that drive divergence in developmental time between species.
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Affiliation(s)
- Margarete Diaz-Cuadros
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
| | - Olivier Pourquié
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA;
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts, USA
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29
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Ye Y, Zhang J, Feng X, Chen C, Chang Y, Qiu G, Wu Z, Zhang TJ, Gao B, Wu N. Exploring the association between congenital vertebral malformations and neural tube defects. J Med Genet 2023; 60:1146-1152. [PMID: 37775263 DOI: 10.1136/jmg-2023-109501] [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: 07/08/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
Congenital vertebral malformations (CVMs) and neural tube defects (NTDs) are common birth defects affecting the spine and nervous system, respectively, due to defects in somitogenesis and neurulation. Somitogenesis and neurulation rely on factors secreted from neighbouring tissues and the integrity of the axial structure. Crucial signalling pathways like Wnt, Notch and planar cell polarity regulate somitogenesis and neurulation with significant crosstalk. While previous studies suggest an association between CVMs and NTDs, the exact mechanism underlying this relationship remains unclear. In this review, we explore embryonic development, signalling pathways and clinical phenotypes involved in the association between CVMs and NTDs. Moreover, we provide a summary of syndromes that exhibit occurrences of both CVMs and NTDs. We aim to provide insights into the potential mechanisms underlying the association between CVMs and NTDs, thereby facilitating clinical diagnosis and management of these anomalies.
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Affiliation(s)
- Yongyu Ye
- Department of Orthopedic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Jianan Zhang
- Department of Orthopaedics and Traumatology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
| | - Xin Feng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Chong Chen
- Department of Orthopedic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Yunbing Chang
- Department of Orthopedic Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Zhihong Wu
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
| | - Bo Gao
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Translational Stem Cell Biology, Hong Kong, China
| | - Nan Wu
- Department of Orthopedic Surgery, Key Laboratory of Big Data for Spinal Deformities, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
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30
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Liu Y, Kim YS, Xue X, Kobayashi N, Sun S, Yang Q, Pourquié O, Fu J. A human pluripotent stem cell-based somitogenesis model using microfluidics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.29.564399. [PMID: 37961125 PMCID: PMC10634932 DOI: 10.1101/2023.10.29.564399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Emerging human pluripotent stem cell (hPSC)-based embryo models are useful for studying human embryogenesis. Particularly, there are hPSC-based somitogenesis models using free-floating culture that recapitulate somite formation. Somitogenesis in vivo involves intricately orchestrated bio-chemical and -mechanical events. However, none of the current somitogenesis models controls biochemical gradients or biomechanical signals in the culture, limiting their applicability to untangle complex biochemical-biomechanical interactions that drive somitogenesis. Here we report a new human somitogenesis model by confining hPSC-derived presomitic mesoderm (PSM) tissues in microfabricated trenches. Exogenous microfluidic morphogen gradients imposed on PSM cause axial patterning and trigger spontaneous rostral-to-caudal somite formation. A mechanical theory is developed to explain the size dependency between somites and PSM. The microfluidic somitogenesis model is further exploited to reveal regulatory roles of cellular and tissue biomechanics in somite formation. This study presents a useful microengineered, hPSC-based model for understanding the bio-chemical and -mechanical events that guide somite formation.
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31
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Meyer K, Lammers NC, Bugaj LJ, Garcia HG, Weiner OD. Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation. Nat Commun 2023; 14:6929. [PMID: 37903793 PMCID: PMC10616176 DOI: 10.1038/s41467-023-42643-2] [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: 02/17/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
YAP is a transcriptional regulator that controls pluripotency, cell fate, and proliferation. How cells ensure the selective activation of YAP effector genes is unknown. This knowledge is essential to rationally control cellular decision-making. Here we leverage optogenetics, live-imaging of transcription, and cell fate analysis to understand and control gene activation and cell behavior. We reveal that cells decode the steady-state concentrations and timing of YAP activation to control proliferation, cell fate, and expression of the pluripotency regulators Oct4 and Nanog. While oscillatory YAP inputs induce Oct4 expression and proliferation optimally at frequencies that mimic native dynamics, cellular differentiation requires persistently low YAP levels. We identify the molecular logic of the Oct4 dynamic decoder, which acts through an adaptive change sensor. Our work reveals how YAP levels and dynamics enable multiplexing of information transmission for the regulation of developmental decision-making and establishes a platform for the rational control of these behaviors.
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Affiliation(s)
- Kirstin Meyer
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas C Lammers
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Hernan G Garcia
- Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA, USA
- Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA.
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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32
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Roberson EC, Tran NK, Godambe AN, Mark H, Nguimtsop M, Rust T, Ung E, Barker LJ, Fitch RD, Wallingford JB. Hedgehog signaling is required for endometrial remodeling and myometrial homeostasis in the cycling mouse uterus. iScience 2023; 26:107993. [PMID: 37810243 PMCID: PMC10551904 DOI: 10.1016/j.isci.2023.107993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/24/2023] [Accepted: 09/16/2023] [Indexed: 10/10/2023] Open
Abstract
Decades of work demonstrate that the mammalian estrous cycle is controlled by cycling steroid hormones. However, the signaling mechanisms that act downstream, linking hormonal action to the physical remodeling of the cycling uterus, remain unclear. To address this issue, we analyzed gene expression at all stages of the mouse estrous cycle. Strikingly, we found that several genetic programs well-known to control tissue morphogenesis in developing embryos displayed cyclical patterns of expression. We find that most of the genetic architectures of Hedgehog signaling (ligands, receptors, effectors, and transcription factors) are transcribed cyclically in the uterus, and that conditional disruption of the Hedgehog receptor smoothened not only elicits a failure of normal cyclical thickening of the endometrial lining but also induces aberrant deformation of the uterine smooth muscle. Together, our data shed light on the mechanisms underlying normal uterine remodeling specifically and cyclical gene expression generally.
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Affiliation(s)
- Elle C. Roberson
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Ngan Kim Tran
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Anushka N. Godambe
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Harrison Mark
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michelle Nguimtsop
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Trinity Rust
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elizabeth Ung
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - LeCaine J. Barker
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Rebecca D. Fitch
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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33
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Keseroglu K, Zinani OQH, Keskin S, Seawall H, Alpay EE, Özbudak EM. Stochastic gene expression and environmental stressors trigger variable somite segmentation phenotypes. Nat Commun 2023; 14:6497. [PMID: 37838784 PMCID: PMC10576776 DOI: 10.1038/s41467-023-42220-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 10/04/2023] [Indexed: 10/16/2023] Open
Abstract
Mutations of several genes cause incomplete penetrance and variable expressivity of phenotypes, which are usually attributed to modifier genes or gene-environment interactions. Here, we show stochastic gene expression underlies the variability of somite segmentation defects in embryos mutant for segmentation clock genes her1 or her7. Phenotypic strength is further augmented by low temperature and hypoxia. By performing live imaging of the segmentation clock reporters, we further show that groups of cells with higher oscillation amplitudes successfully form somites while those with lower amplitudes fail to do so. In unfavorable environments, the number of cycles with high amplitude oscillations and the number of successful segmentations proportionally decrease. These results suggest that individual oscillation cycles stochastically fail to pass a threshold amplitude, resulting in segmentation defects in mutants. Our quantitative methodology is adaptable to investigate variable phenotypes of mutant genes in different tissues.
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Affiliation(s)
- Kemal Keseroglu
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Oriana Q H Zinani
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Molecular and Developmental Biology Graduate Program, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - Sevdenur Keskin
- Allergy and Immunology, University of Arkansas for Medical Science and Arkansas Children's Hospital, Little Rock, AR, 72202, USA
| | - Hannah Seawall
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Eslim E Alpay
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ertuğrul M Özbudak
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45229, USA.
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34
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Liu L, Oura S, Markham Z, Hamilton JN, Skory RM, Li L, Sakurai M, Wang L, Pinzon-Arteaga CA, Plachta N, Hon GC, Wu J. Modeling post-implantation stages of human development into early organogenesis with stem-cell-derived peri-gastruloids. Cell 2023; 186:3776-3792.e16. [PMID: 37478861 DOI: 10.1016/j.cell.2023.07.018] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
In vitro stem cell models that replicate human gastrulation have been generated, but they lack the essential extraembryonic cells needed for embryonic development, morphogenesis, and patterning. Here, we describe a robust and efficient method that prompts human extended pluripotent stem cells to self-organize into embryo-like structures, termed peri-gastruloids, which encompass both embryonic (epiblast) and extraembryonic (hypoblast) tissues. Although peri-gastruloids are not viable due to the exclusion of trophoblasts, they recapitulate critical stages of human peri-gastrulation development, such as forming amniotic and yolk sac cavities, developing bilaminar and trilaminar embryonic discs, specifying primordial germ cells, initiating gastrulation, and undergoing early neurulation and organogenesis. Single-cell RNA-sequencing unveiled transcriptomic similarities between advanced human peri-gastruloids and primary peri-gastrulation cell types found in humans and non-human primates. This peri-gastruloid platform allows for further exploration beyond gastrulation and may potentially aid in the development of human fetal tissues for use in regenerative medicine.
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Affiliation(s)
- Lizhong Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Seiya Oura
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zachary Markham
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - James N Hamilton
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Robin M Skory
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leijie Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Wang
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carlos A Pinzon-Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicolas Plachta
- Department of Cell and Developmental Biology, Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gary C Hon
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA; Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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35
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Lázaro J, Costanzo M, Sanaki-Matsumiya M, Girardot C, Hayashi M, Hayashi K, Diecke S, Hildebrandt TB, Lazzari G, Wu J, Petkov S, Behr R, Trivedi V, Matsuda M, Ebisuya M. A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell 2023; 30:938-949.e7. [PMID: 37343565 PMCID: PMC10321541 DOI: 10.1016/j.stem.2023.05.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 04/03/2023] [Accepted: 05/25/2023] [Indexed: 06/23/2023]
Abstract
Differential speeds in biochemical reactions have been proposed to be responsible for the differences in developmental tempo between mice and humans. However, the underlying mechanism controlling the species-specific kinetics remains to be determined. Using in vitro differentiation of pluripotent stem cells, we recapitulated the segmentation clocks of diverse mammalian species varying in body weight and taxa: marmoset, rabbit, cattle, and rhinoceros. Together with mouse and human, the segmentation clock periods of the six species did not scale with the animal body weight, but with the embryogenesis length. The biochemical kinetics of the core clock gene HES7 displayed clear scaling with the species-specific segmentation clock period. However, the cellular metabolic rates did not show an evident correlation. Instead, genes involving biochemical reactions showed an expression pattern that scales with the segmentation clock period. Altogether, our stem cell zoo uncovered general scaling laws governing species-specific developmental tempo.
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Affiliation(s)
- Jorge Lázaro
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Maria Costanzo
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marina Sanaki-Matsumiya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Charles Girardot
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Masafumi Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Katsuhiko Hayashi
- Department of Genome Biology, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | | | | | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Stoyan Petkov
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center - Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Partner site Göttingen, Göttingen, Germany
| | - Vikas Trivedi
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Mitsuhiro Matsuda
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Miki Ebisuya
- European Molecular Biology Laboratory (EMBL) Barcelona, Dr. Aiguader 88, 08003 Barcelona, Spain; Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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36
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Zhang H, Xiang G, Li J, He S, Wang Y, Deng A, Wang Y, Guo C. Promotion effect of FGF23 on osteopenia in congenital scoliosis through FGFr3/TNAP/OPN pathway. Chin Med J (Engl) 2023; 136:1468-1477. [PMID: 37192015 PMCID: PMC10278695 DOI: 10.1097/cm9.0000000000002690] [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: 11/09/2022] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Congenital scoliosis (CS) is a complex spinal malformation of unknown etiology with abnormal bone metabolism. Fibroblast growth factor 23 (FGF23), secreted by osteoblasts and osteocytes, can inhibit bone formation and mineralization. This research aims to investigate the relationship between CS and FGF23. METHODS We collected peripheral blood from two pairs of identical twins for methylation sequencing of the target region. FGF23 mRNA levels in the peripheral blood of CS patients and age-matched controls were measured. Receiver operator characteristic (ROC) curve analyses were conducted to evaluate the specificity and sensitivity of FGF23. The expression levels of FGF23 and its downstream factors fibroblast growth factor receptor 3 (FGFr3)/tissue non-specific alkaline phosphatase (TNAP)/osteopontin (OPN) in primary osteoblasts from CS patients (CS-Ob) and controls (CT-Ob) were detected. In addition, the osteogenic abilities of FGF23-knockdown or FGF23-overexpressing Ob were examined. RESULTS DNA methylation of the FGF23 gene in CS patients was decreased compared to that of their identical twins, accompanied by increased mRNA levels. CS patients had increased peripheral blood FGF23 mRNA levels and decreased computed tomography (CT) values compared with controls. The FGF23 mRNA levels were negatively correlated with the CT value of the spine, and ROCs of FGF23 mRNA levels showed high sensitivity and specificity for CS. Additionally, significantly increased levels of FGF23, FGFr3, OPN, impaired osteogenic mineralization and lower TNAP levels were observed in CS-Ob. Moreover, FGF23 overexpression in CT-Ob increased FGFr3 and OPN levels and decreased TNAP levels, while FGF23 knockdown induced downregulation of FGFr3 and OPN but upregulation of TNAP in CS-Ob. Mineralization of CS-Ob was rescued after FGF23 knockdown. CONCLUSIONS Our results suggested increased peripheral blood FGF23 levels, decreased bone mineral density in CS patients, and a good predictive ability of CS by peripheral blood FGF23 levels. FGF23 may contribute to osteopenia in CS patients through FGFr3/TNAP / OPN pathway.
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Affiliation(s)
- Hongqi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Gang Xiang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Jiong Li
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Sihan He
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yunjia Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Ang Deng
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Yuxiang Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
| | - Chaofeng Guo
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
- National Clinical Research Center for Geriatric Disorder, Xiangya Hospital, Central South University, Changsha, Hunan 410000, China
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37
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Emig AA, Williams MLK. Gastrulation morphogenesis in synthetic systems. Semin Cell Dev Biol 2023; 141:3-13. [PMID: 35817656 PMCID: PMC9825685 DOI: 10.1016/j.semcdb.2022.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 04/19/2022] [Accepted: 07/04/2022] [Indexed: 01/11/2023]
Abstract
Recent advances in pluripotent stem cell culture allow researchers to generate not only most embryonic cell types, but also morphologies of many embryonic structures, entirely in vitro. This recreation of embryonic form from naïve cells, known as synthetic morphogenesis, has important implications for both developmental biology and regenerative medicine. However, the capacity of stem cell-based models to recapitulate the morphogenetic cell behaviors that shape natural embryos remains unclear. In this review, we explore several examples of synthetic morphogenesis, with a focus on models of gastrulation and surrounding stages. By varying cell types, source species, and culture conditions, researchers have recreated aspects of primitive streak formation, emergence and elongation of the primary embryonic axis, neural tube closure, and more. Here, we describe cell behaviors within in vitro/ex vivo systems that mimic in vivo morphogenesis and highlight opportunities for more complete models of early development.
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Affiliation(s)
- Alyssa A Emig
- Center for Precision Environmental Health & Department of Molecular and Cellular Biology, Baylor College of Medicine, USA
| | - Margot L K Williams
- Center for Precision Environmental Health & Department of Molecular and Cellular Biology, Baylor College of Medicine, USA.
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38
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Stepien BK, Pawolski V, Wagner MC, Kurth T, Schmidt MHH, Epperlein HH. The Role of Posterior Neural Plate-Derived Presomitic Mesoderm (PSM) in Trunk and Tail Muscle Formation and Axis Elongation. Cells 2023; 12:cells12091313. [PMID: 37174713 PMCID: PMC10177618 DOI: 10.3390/cells12091313] [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: 03/22/2023] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
Elongation of the posterior body axis is distinct from that of the anterior trunk and head. Early drivers of posterior elongation are the neural plate/tube and notochord, later followed by the presomitic mesoderm (PSM), together with the neural tube and notochord. In axolotl, posterior neural plate-derived PSM is pushed posteriorly by convergence and extension of the neural plate. The PSM does not go through the blastopore but turns anteriorly to join the gastrulated paraxial mesoderm. To gain a deeper understanding of the process of axial elongation, a detailed characterization of PSM morphogenesis, which precedes somite formation, and of other tissues (such as the epidermis, lateral plate mesoderm and endoderm) is needed. We investigated these issues with specific tissue labelling techniques (DiI injections and GFP+ tissue grafting) in combination with optical tissue clearing and 3D reconstructions. We defined a spatiotemporal order of PSM morphogenesis that is characterized by changes in collective cell behaviour. The PSM forms a cohesive tissue strand and largely retains this cohesiveness even after epidermis removal. We show that during embryogenesis, the PSM, as well as the lateral plate and endoderm move anteriorly, while the net movement of the axis is posterior.
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Affiliation(s)
- Barbara K Stepien
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, 01062 Dresden, Germany
| | - Verena Pawolski
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, 01062 Dresden, Germany
| | - Marc-Christoph Wagner
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, 01062 Dresden, Germany
| | - Thomas Kurth
- Center for Molecular and Cellular Bioengineering (CMCB), Technology Platform, Electron Microscopy and Histology Facility, Technische Universität Dresden, 01062 Dresden, Germany
| | - Mirko H H Schmidt
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, 01062 Dresden, Germany
| | - Hans-Henning Epperlein
- Institute of Anatomy, Medical Faculty Carl Gustav Carus, Technische Universität Dresden School of Medicine, 01062 Dresden, Germany
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39
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Xu Q, Luo Y, Chao Z, Zhang J, Liu X, Tang Q, Wang K, Tan S, Fang M. Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326-NKX3.2-Regulated Porcine Chondrocyte Differentiation. Int J Mol Sci 2023; 24:ijms24087257. [PMID: 37108419 PMCID: PMC10138716 DOI: 10.3390/ijms24087257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (NKX3.2), Wnt ligand secretion mediator (WLS), gremlin 1 (GREM1), fibroblast growth factor receptor 3 (FGFR3), hematopoietically expressed homeobox (HHEX), (collagen type XI alpha 1 chain (COL11A1), and Wnt Family Member 16 (WNT16)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA-gene, miRNA-gene, and lncRNA-miRNA-gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. NKX3.2 was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting NKX3.2. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA-miRNA-gene interaction networks, and confirms the function of NKX3.2 in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies.
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Affiliation(s)
- Qiao Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yabiao Luo
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Zhe Chao
- Institute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Jibin Zhang
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA 91006, USA
| | - Ximing Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qiguo Tang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kejun Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuyi Tan
- Institute of Animal Sciences and Veterinary, Hainan Academy of Agricultural Sciences, Haikou 571100, China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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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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41
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Warren J, Kumar JP. Patterning of the Drosophila retina by the morphogenetic furrow. Front Cell Dev Biol 2023; 11:1151348. [PMID: 37091979 PMCID: PMC10117938 DOI: 10.3389/fcell.2023.1151348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 03/23/2023] [Indexed: 04/25/2023] Open
Abstract
Pattern formation is the process by which cells within a homogeneous epithelial sheet acquire distinctive fates depending upon their relative spatial position to each other. Several proposals, starting with Alan Turing's diffusion-reaction model, have been put forth over the last 70 years to describe how periodic patterns like those of vertebrate somites and skin hairs, mammalian molars, fish scales, and avian feather buds emerge during development. One of the best experimental systems for testing said models and identifying the gene regulatory networks that control pattern formation is the compound eye of the fruit fly, Drosophila melanogaster. Its cellular morphogenesis has been extensively studied for more than a century and hundreds of mutants that affect its development have been isolated. In this review we will focus on the morphogenetic furrow, a wave of differentiation that takes an initially homogeneous sheet of cells and converts it into an ordered array of unit eyes or ommatidia. Since the discovery of the furrow in 1976, positive and negative acting morphogens have been thought to be solely responsible for propagating the movement of the furrow across a motionless field of cells. However, a recent study has challenged this model and instead proposed that mechanical driven cell flow also contributes to retinal pattern formation. We will discuss both models and their impact on patterning.
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Affiliation(s)
| | - Justin P. Kumar
- Department of Biology, Indiana University, Bloomington, IN, United States
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Wu N, Liu L, Zhang Y, Wang L, Wang S, Zhao S, Li G, Yang Y, Lin G, Shen J, Wu Z, Qiu G, Zhang TJ. Retrospective Analysis of Associated Anomalies in 636 Patients with Operatively Treated Congenital Scoliosis. J Bone Joint Surg Am 2023; 105:537-548. [PMID: 37017616 DOI: 10.2106/jbjs.22.00277] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/06/2023]
Abstract
BACKGROUND Congenital scoliosis is frequently associated with anomalies in multiple organ systems. However, the prevalence and distribution of associated anomalies remain unclear, and there is a large amount of variation in data among different studies. METHODS Six hundred and thirty-six Chinese patients who had undergone scoliosis correction surgery at Peking Union Medical College Hospital from January 2012 to July 2019 were recruited, as a part of the Deciphering disorders Involving Scoliosis and COmorbidities (DISCO) study. The medical data for each subject were collected and analyzed. RESULTS The mean age (and standard deviation) at the time of presentation for scoliosis was 6.4 ± 6.3 years, and the mean Cobb angle of the major curve was 60.8° ± 26.5°. Intraspinal abnormalities were found in 186 (30.3%) of 614 patients, with diastematomyelia being the most common anomaly (59.1%; 110 of 186). The prevalence of intraspinal abnormalities was remarkably higher in patients with failure of segmentation and mixed deformities than in patients with failure of formation (p < 0.001). Patients with intraspinal anomalies showed more severe deformities, including larger Cobb angles of the major curve (p < 0.001). We also demonstrated that cardiac anomalies were associated with remarkably worse pulmonary function, i.e., lower forced expiratory volume in the first second (FEV1), forced vital capacity (FVC), and peak expiratory flow (PEF). Additionally, we identified associations among different concomitant malformations. We found that patients with musculoskeletal anomalies of types other than intraspinal and maxillofacial were 9.2 times more likely to have additional maxillofacial anomalies. CONCLUSIONS In our cohort, comorbidities associated with congenital scoliosis occurred at a rate of 55%. To our knowledge, our study is the first to show that patients with congenital scoliosis and cardiac anomalies have reduced pulmonary function, as demonstrated by lower FEV1, FVC, and PEF. Moreover, the potential associations among concomitant anomalies revealed the importance of a comprehensive preoperative evaluation scheme. LEVEL OF EVIDENCE Diagnostic Level III. See Instructions for Authors for a complete description of levels of evidence.
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Affiliation(s)
- Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Lian Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Department of Emergency Surgery, Qilu Hospital of Shandong University, Jinan, Shandong Province, People's Republic of China
| | - Yuanqiang Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong Province, People's Republic of China
| | - Lianlei Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Department of Orthopedic Surgery, Qilu Hospital of Shandong University, Jinan, Shandong Province, People's Republic of China
| | - Shengru Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Yang Yang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Guanfeng Lin
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Jianxiong Shen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, People's Republic of China
- Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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Liu K, Hou L, Yin Y, Wang B, Liu C, Zhou W, Niu P, Li Q, Huang R, Li P. Genome-wide association study reveals new QTL and functional candidate genes for the number of ribs and carcass length in pigs. Anim Genet 2023. [PMID: 36911996 DOI: 10.1111/age.13315] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 02/11/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023]
Abstract
The number of ribs (NR) and carcass length (CL) are important economic traits in pig breeding programs. Pigs with a higher NR and longer CL produce greater pork yields. In the present study, Suhuai pigs with NR and CL phenotypes were genotyped using the Neogen® GGP Porcine 80 K SNP array to identify the QTL affecting NR and CL and dissect the candidate genes for the two traits. The SNP-chip data was imputed to the whole-genome sequence (iWGS) to increase the probability of identifying causal variants. Through genome-wide association studies (GWAS) based on both chip and iWGS data, significant SNPs were detected on Sus scrofa chromosome (SSC) 1, SSC4 and SSC7 for NR and on SSC5, SSC16 and SSC17 for CL. Moreover, two SNPs (H3GA0022644 and WU_10.2_7_103460706) on SSC7 detected in chip-based GWAS were significantly associated with both NR and CL. Through Bayes fine mapping, one reported QTL for NR on SSC7 and two reported QTL for CL on SSC17 were verified, and two new QTL (SSC1: 14.05-15.84 Mb and SSC4: 64.83-66.59 Mb) affecting NR and two new QTL (SSC5: 58.31-59.84 Mb and SSC16: 22.98-23.43 Mb) affecting CL were detected. According to the biological functions of genes, MTHFD1L on SSC1 and SULF1 on SSC4 are novel functional candidate genes for NR, and EMP1 on SSC5 and EGFLAM on SSC16 are novel functional candidate genes for CL. Overall, our findings provide a basis for identifying new causal genes and mutations affecting NR and CL.
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Affiliation(s)
- Kaiyue Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Liming Hou
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Yanzhen Yin
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Binbin Wang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Chenxi Liu
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Wuduo Zhou
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Peipei Niu
- Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Qiang Li
- Huaiyin Xinhuai Pig Breeding Farm of Huaian City, Huaian, China
| | - Ruihua Huang
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
| | - Pinghua Li
- Key Laboratory in Nanjing for Evaluation and Utilization of Pigs Resources, Ministry of Agriculture and Rural Areas of China, Institute of Swine Science, Nanjing Agricultural University, Nanjing, China.,Huaian Academy, Nanjing Agricultural University, Huaian, China
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Marconi A, Yang CZ, McKay S, Santos ME. Morphological and temporal variation in early embryogenesis contributes to species divergence in Malawi cichlid fishes. Evol Dev 2023; 25:170-193. [PMID: 36748313 PMCID: PMC10909517 DOI: 10.1111/ede.12429] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 12/18/2022] [Accepted: 01/20/2023] [Indexed: 02/08/2023]
Abstract
The cichlid fishes comprise the largest extant vertebrate family and are the quintessential example of rapid "explosive" adaptive radiations and phenotypic diversification. Despite low genetic divergence, East African cichlids harbor a spectacular intra- and interspecific morphological diversity, including the hyper-variable, neural crest (NC)-derived traits such as coloration and craniofacial skeleton. Although the genetic and developmental basis of these phenotypes has been investigated, understanding of when, and specifically how early, in ontogeny species-specific differences emerge, remains limited. Since adult traits often originate during embryonic development, the processes of embryogenesis could serve as a potential source of species-specific variation. Consequently, we designed a staging system by which we compare the features of embryogenesis between three Malawi cichlid species-Astatotilapia calliptera, Tropheops sp. 'mauve' and Rhamphochromis sp. "chilingali"-representing a wide spectrum of variation in pigmentation and craniofacial morphologies. Our results showed fundamental differences in multiple aspects of embryogenesis that could underlie interspecific divergence in adult adaptive traits. First, we identified variation in the somite number and signatures of temporal variation, or heterochrony, in the rates of somite formation. The heterochrony was also evident within and between species throughout ontogeny, up to the juvenile stages. Finally, the identified interspecific differences in the development of pigmentation and craniofacial cartilages, present at the earliest stages of their overt formation, provide compelling evidence that the species-specific trajectories begin divergence during early embryogenesis, potentially during somitogenesis and NC development. Altogether, our results expand our understanding of fundamental cichlid biology and provide new insights into the developmental origins of vertebrate morphological diversity.
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Affiliation(s)
| | | | - Samuel McKay
- Department of ZoologyUniversity of CambridgeCambridgeUK
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Espina JA, Cordeiro MH, Barriga EH. Tissue interplay during morphogenesis. Semin Cell Dev Biol 2023; 147:12-23. [PMID: 37002130 DOI: 10.1016/j.semcdb.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/25/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023]
Abstract
The process by which biological systems such as cells, tissues and organisms acquire shape has been named as morphogenesis and it is central to a plethora of biological contexts including embryo development, wound healing, or even cancer. Morphogenesis relies in both self-organising properties of the system and in environmental inputs (biochemical and biophysical). The classical view of morphogenesis is based on the study of external biochemical molecules, such as morphogens. However, recent studies are establishing that the mechanical environment is also used by cells to communicate within tissues, suggesting that this mechanical crosstalk is essential to synchronise morphogenetic transitions and self-organisation. In this article we discuss how tissue interaction drive robust morphogenesis, starting from a classical biochemical view, to finalise with more recent advances on how the biophysical properties of a tissue feedback with their surroundings to allow form acquisition. We also comment on how in silico models aid to integrate and predict changes in cell and tissue behaviour. Finally, considering recent advances from the developmental biomechanics field showing that mechanical inputs work as cues that promote morphogenesis, we invite to revisit the concept of morphogen.
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Affiliation(s)
- Jaime A Espina
- Mechanisms of Morphogenesis Lab, Gulbenkian Institute of Science (IGC), Oeiras, Portugal
| | - Marilia H Cordeiro
- Mechanisms of Morphogenesis Lab, Gulbenkian Institute of Science (IGC), Oeiras, Portugal
| | - Elias H Barriga
- Mechanisms of Morphogenesis Lab, Gulbenkian Institute of Science (IGC), Oeiras, Portugal.
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Yaman YI, Ramanathan S. Controlling human organoid symmetry breaking reveals signaling gradients drive segmentation clock waves. Cell 2023; 186:513-527.e19. [PMID: 36657441 PMCID: PMC10025047 DOI: 10.1016/j.cell.2022.12.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/29/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023]
Abstract
Axial development of mammals involves coordinated morphogenetic events, including axial elongation, somitogenesis, and neural tube formation. To gain insight into the signals controlling the dynamics of human axial morphogenesis, we generated axially elongating organoids by inducing anteroposterior symmetry breaking of spatially coupled epithelial cysts derived from human pluripotent stem cells. Each organoid was composed of a neural tube flanked by presomitic mesoderm sequentially segmented into somites. Periodic activation of the somite differentiation gene MESP2 coincided in space and time with anteriorly traveling segmentation clock waves in the presomitic mesoderm of the organoids, recapitulating critical aspects of somitogenesis. Timed perturbations demonstrated that FGF and WNT signaling play distinct roles in axial elongation and somitogenesis, and that FGF signaling gradients drive segmentation clock waves. By generating and perturbing organoids that robustly recapitulate the architecture of multiple axial tissues in human embryos, this work offers a means to dissect mechanisms underlying human embryogenesis.
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Affiliation(s)
- Yusuf Ilker Yaman
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Sharad Ramanathan
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.
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47
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Miao Y, Djeffal Y, De Simone A, Zhu K, Lee JG, Lu Z, Silberfeld A, Rao J, Tarazona OA, Mongera A, Rigoni P, Diaz-Cuadros M, Song LMS, Di Talia S, Pourquié O. Reconstruction and deconstruction of human somitogenesis in vitro. Nature 2023; 614:500-508. [PMID: 36543321 PMCID: PMC10018515 DOI: 10.1038/s41586-022-05655-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
The vertebrate body displays a segmental organization that is most conspicuous in the periodic organization of the vertebral column and peripheral nerves. This metameric organization is first implemented when somites, which contain the precursors of skeletal muscles and vertebrae, are rhythmically generated from the presomitic mesoderm. Somites then become subdivided into anterior and posterior compartments that are essential for vertebral formation and segmental patterning of the peripheral nervous system1-4. How this key somitic subdivision is established remains poorly understood. Here we introduce three-dimensional culture systems of human pluripotent stem cells called somitoids and segmentoids, which recapitulate the formation of somite-like structures with anteroposterior identity. We identify a key function of the segmentation clock in converting temporal rhythmicity into the spatial regularity of anterior and posterior somitic compartments. We show that an initial 'salt and pepper' expression of the segmentation gene MESP2 in the newly formed segment is transformed into compartments of anterior and posterior identity through an active cell-sorting mechanism. Our research demonstrates that the major patterning modules that are involved in somitogenesis, including the clock and wavefront, anteroposterior polarity patterning and somite epithelialization, can be dissociated and operate independently in our in vitro systems. Together, we define a framework for the symmetry-breaking process that initiates somite polarity patterning. Our work provides a platform for decoding general principles of somitogenesis and advancing knowledge of human development.
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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
| | - Yannis Djeffal
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Kongju Zhu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jong Gwan Lee
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ziqi Lu
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Andrew Silberfeld
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jyoti Rao
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Oscar A Tarazona
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Alessandro Mongera
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Pietro Rigoni
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Margarete Diaz-Cuadros
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Laura Min Sook Song
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Stefano Di Talia
- Department of Cell Biology, Duke University Medical Center, Durham, NC, 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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48
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Gómez de la Torre Canny S, Nordgård CT, Mathisen AJH, Degré Lorentsen E, Vadstein O, Bakke I. A novel gnotobiotic experimental system for Atlantic salmon ( Salmo salar L.) reveals a microbial influence on mucosal barrier function and adipose tissue accumulation during the yolk sac stage. Front Cell Infect Microbiol 2023; 12:1068302. [PMID: 36817693 PMCID: PMC9929952 DOI: 10.3389/fcimb.2022.1068302] [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: 10/12/2022] [Accepted: 12/05/2022] [Indexed: 02/04/2023] Open
Abstract
Gnotobiotic models have had a crucial role in studying the effect that commensal microbiota has on the health of their animal hosts. Despite their physiological and ecological diversity, teleost fishes are still underrepresented in gnotobiotic research. Moreover, a better understanding of host-microbe interactions in farmed fish has the potential to contribute to sustainable global food supply. We have developed a novel gnotobiotic experimental system that includes the derivation of fertilized eggs of farmed and wild Atlantic salmon, and gnotobiotic husbandry of fry during the yolk sac stage. We used a microscopy-based approach to estimate the barrier function of the skin mucus layer and used this measurement to select the derivation procedure that minimized adverse effects on the skin mucosa. We also used this method to demonstrate that the mucus barrier was reduced in germ-free fry when compared to fry colonized with two different bacterial communities. This alteration in the mucus barrier was preceded by an increase in the number of cells containing neutral mucosubstances in the anterior segment of the body, but without changes in the number of cells containing acidic substances in any of the other segments studied along the body axis. In addition, we showed how the microbial status of the fry temporarily affected body size and the utilization of internal yolk stores during the yolk sac stage. Finally, we showed that the presence of bacterial communities associated with the fry, as well as their composition, affected the size of adipose tissue. Fry colonized with water from a lake had a larger visceral adipose tissue depot than both conventionally raised and germ-free fry. Together, our results show that this novel gnotobiotic experimental system is a useful tool for the study of host-microbe interactions in this species of aquacultural importance.
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Affiliation(s)
| | | | | | | | | | - Ingrid Bakke
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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49
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Uriu K, Morelli LG. Orchestration of tissue shape changes and gene expression patterns in development. Semin Cell Dev Biol 2023; 147:24-33. [PMID: 36631335 DOI: 10.1016/j.semcdb.2022.12.009] [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: 10/28/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023]
Abstract
In development, tissue shape changes and gene expression patterns give rise to morphogenesis. Understanding tissue shape changes requires the analysis of mechanical properties of the tissue such as tissue rigidity, cell influx from neighboring tissues, cell shape changes and cell proliferation. Local and global gene expression patterns can be influenced by neighbor exchange and tissue shape changes. Here we review recent studies on the mechanisms for tissue elongation and its influences on dynamic gene expression patterns by focusing on vertebrate somitogenesis. We first introduce mechanical and biochemical properties of the segmenting tissue that drive tissue elongation. Then, we discuss patterning in the presence of cell mixing, scaling of signaling gradients, and dynamic phase waves of rhythmic gene expression under tissue shape changes. We also highlight the importance of theoretical approaches to address the relation between tissue shape changes and patterning.
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Affiliation(s)
- Koichiro Uriu
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192 Japan.
| | - Luis G Morelli
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Polo Científico Tecnológico, Godoy Cruz 2390, C1425FQD, Buenos Aires, Argentina; Departamento de Física, FCEyN UBA, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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50
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Blatnik MC, Gallagher TL, Amacher SL. Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1751. [PMID: 35851751 PMCID: PMC9840655 DOI: 10.1002/wrna.1751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.
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Affiliation(s)
- Monica C. Blatnik
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Thomas L. Gallagher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Sharon L. Amacher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
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